@article {396, title = {The structure and physical properties of a packaged bacteriophage particle}, journal = {Nature}, year = {2024}, month = {03/2024}, abstract = {

A string of nucleotides confined within a protein capsid contains all the instructions necessary to make a functional virus particle, a virion. Although the structure of the protein capsid is known for many virus species, the three-dimensional organization of viral genomes has mostly eluded experimental probes. Here we report all-atom structural models of an HK97 virion, including its entire 39,732 base pair genome, obtained through multiresolution simulations. Mimicking the action of a packaging motor, the genome was gradually loaded into the capsid. The structure of the packaged capsid was then refined through simulations of increasing resolution, which produced a 26 million atom model of the complete virion, including water and ions confined within the capsid. DNA packaging occurs through a loop extrusion mechanism that produces globally different configurations of the packaged genome and gives each viral particle individual traits. Multiple microsecond-long all-atom simulations characterized the effect of the packaged genome on capsid structure, internal pressure, electrostatics and diffusion of water, ions and DNA, and revealed the structural imprints of the capsid onto the genome. Our approach can be generalized to obtain complete all-atom structural models of other virus species, thereby potentially revealing new drug targets at the genome{\textendash}capsid interface.

}, keywords = {DNA packaging, Multiresolution simulation, virology}, doi = {https://doi.org/10.1038/s41586-024-07150-4}, url = {https://www.nature.com/articles/s41586-024-07150-4$\#$Abs1}, author = {Kush Coshic and Christopher Maffeo and David Winogradoff and Aleksei Aksimentiev} } @article {397, title = {Dehydrated Biomimetic Membranes with Skinlike Structure and Function}, journal = {ACS Applied Materials \& Interfaces}, year = {2024}, pages = {null}, abstract = {

Novel vapor-permeable materials are sought after for applications in protective wear, energy generation, and water treatment. Current impermeable protective materials effectively block harmful agents but trap heat due to poor water vapor transfer. Here we present a new class of materials, vapor permeable dehydrated nanoporous biomimetic membranes (DBMs), based on channel proteins. This application for biomimetic membranes is unexpected as channel proteins and biomimetic membranes were assumed to be unstable under dry conditions. DBMs mimic human skin{\textquoteright}s structure to offer both high vapor transport and small molecule exclusion under dry conditions. DBMs feature highly organized pores resembling sweat pores in human skin, but at super high densities (\>1012\ pores/cm2). These DBMs achieved exceptional water vapor transport rates, surpassing commercial breathable fabrics by up to 6.2 times, despite containing \>2 orders of magnitude smaller pores (1 nm vs \>700 nm). These DBMs effectively excluded model biological agents and harmful chemicals both in liquid and vapor phases, again in contrast with the commercial breathable fabrics. Remarkably, while hydrated biomimetic membranes were highly permeable to liquid water, they exhibited higher water resistances after dehydration at values \>38 times that of commercial breathable fabrics. Molecular dynamics simulations support our hypothesis that dehydration induced protein hydrophobicity increases which enhanced DBM performance. DBMs hold promise for various applications, including membrane distillation, dehumidification, and protective barriers for atmospheric water harvesting materials.

}, doi = {10.1021/acsami.3c19572}, url = {https://doi.org/10.1021/acsami.3c19572}, author = {Oh, Hyeonji and Tu, Yu-Ming and Samineni, Laximicharan and De Respino, Sophie and Mehrafrooz, Behzad and Joshi, Himanshu and Massenburg, Lynnicia and Lopez-Marques, Horacio and Elessawy, Nada and Song, Woochul and Behera, Harekrushna and Dhiman, Raman and Boorla, Veda Sheersh and Kher, Kartik and Lin, Yi-Chih and Maranas, Costas and Aksimentiev, Aleksei and D. Freeman, Benny and Kumar, Manish} } @article {387, title = {DNA double helix, a tiny electromotor}, journal = {Nature Nanotechnology}, volume = {18}, year = {2023}, month = {12/2022}, pages = {238{\textendash}242}, chapter = {238}, abstract = {

Flowing fluid past chiral objects has been used for centuries to power rotary motion in man-made machines. By contrast, rotary motion in nanoscale biological or chemical systems is produced by biasing Brownian motion through cyclic chemical reactions. Here we show that a chiral biological molecule, a DNA or RNA duplex rotates unidirectionally at billions of revolutions per minute when an electric field is applied along the duplex, with the rotation direction being determined by the chirality of the duplex. The rotation is found to be powered by the drag force of the electro-osmotic flow, realizing the operating principle of a macroscopic turbine at the nanoscale. The resulting torques are sufficient to power rotation of nanoscale beads and rods, offering an engineering principle for constructing nanoscale systems powered by electric field.

}, issn = {1748-3387}, doi = {10.1038/s41565-022-01285-z}, url = {https://www.nature.com/articles/s41565-022-01285-z}, author = {Maffeo, Christopher and Quednau, Lauren and Wilson, James and Aksimentiev, Aleksei} } @article {395, title = {A Marcus-Type Inverted Region in the Translocation Kinetics of a Knotted Protein}, journal = {The Journal of Physical Chemistry Letters}, year = {2023}, month = {11/2023}, pages = {10719-10726}, abstract = {

Knotted proteins are rare but important species, yet how their complex topologies affect their physical properties is not fully understood. Here we combine single molecule nanopore experiments and all-atom MD simulations to study the electric-field-driven unfolding during the translocation through a model pore of individual protein knots important for methylating tRNA. One of these knots shows an unusual behavior that resembles the behavior of electrons hopping between two potential surfaces: as the electric potential driving the translocation reaction is increased, the rate eventually plateaus or slows back down in the {\textquotedblleft}Marcus inverted regime{\textquotedblright}. Our results shed light on the influence of topology in knotted proteins on their forced translocation through a pore connecting two electrostatic potential wells.

}, doi = {10.1021/acs.jpclett.3c02183}, url = {https://doi.org/10.1021/acs.jpclett.3c02183}, author = {Tripathi, Prabhat and Mehrafrooz, Behzad and Aksimentiev, Aleksei and Jackson, Sophie E. and Gruebele, Martin and Wanunu, Meni} } @article {394, title = {Molecular Determinants of Current Blockade Produced by Peptide Transport Through a Nanopore}, journal = {ACS Nanosci. Au}, year = {2023}, month = {11/2023}, abstract = {

The nanopore sensing method holds the promise of delivering a single molecule technology for identification of biological proteins, direct detection of post-translational modifications, and perhaps de novo determination of a protein{\textquoteright}s amino acid sequence. The key quantity measured in such nanopore sensing experiments is the magnitude of the ionic current passing through a nanopore blocked by a polypeptide chain. Establishing a relationship between the amino acid sequence of a peptide fragment confined within a nanopore and the blockade current flowing through the nanopore remains a major challenge for realizing the nanopore protein sequencing. Using the results of all-atom molecular dynamics simulations, here we compare nanopore sequencing of DNA with nanopore sequencing of proteins. We then delineate the factors affecting the blockade current modulation by the peptide sequence, showing that the current can be determined by (i) the steric footprint of an amino acid, (ii) its interactions with the pore wall, (iii) the local stretching of a polypeptide chain, and (iv) the local enhancement of the ion concentration at the nanopore constriction. We conclude with a brief discussion of the prospects for purely computational prediction of the blockade currents.

}, doi = {10.1021/acsnanoscienceau.3c00046}, author = {Jingqian Liu and Aleksei Aksimentiev} } @article {389, title = {A DNA turbine powered by a transmembrane potential across a nanopore}, journal = {Nature Nanotechnology}, year = {2023}, month = {11/2023}, abstract = {

Rotary motors play key roles in energy transduction, from macroscale windmills to nanoscale turbines such as ATP synthase in cells. Despite our abilities to construct engines at many scales, developing functional synthetic turbines at the nanoscale has remained challenging. Here, we experimentally demonstrate rationally designed nanoscale DNA origami turbines with three chiral blades. These DNA nanoturbines are 24{\textendash}27 nm in height and diameter and can utilize transmembrane electrochemical potentials across nanopores to drive DNA bundles into sustained unidirectional rotations of up to 10 revolutions s-1. The rotation direction is set by the designed chirality of the turbine. All-atom molecular dynamics simulations show how hydrodynamic flows drive this turbine. At high salt concentrations, the rotation direction of turbines with the same chirality is reversed, which is explained by a change in the anisotropy of the electrophoretic mobility. Our artificial turbines operate autonomously in physiological conditions, converting energy from naturally abundant electrochemical potentials into mechanical work. The results open new possibilities for engineering active robotics at the nanoscale.

}, issn = {1748-3395}, doi = {10.1038/s41565-023-01527-8}, url = {https://doi.org/10.1038/s41565-023-01527-8}, author = {Shi, Xin and Pumm, Anna-Katharina and Maffeo, Christopher and Kohler, Fabian and Feigl, Elija and Zhao, Wenxuan and Verschueren, Daniel and Golestanian, Ramin and Aksimentiev, Aleksei and Dietz, Hendrik and Dekker, Cees} } @article {390, title = {Engineering Biological Nanopore Approaches toward Protein Sequencing}, journal = {ACS Nano}, volume = {17}, year = {2023}, month = {09}, pages = {16369{\textendash}16395}, abstract = {

Biotechnological innovations have vastly improved the capacity to perform large-scale protein studies, while the methods we have for identifying and quantifying individual proteins are still inadequate to perform protein sequencing at the single-molecule level. Nanopore-inspired systems devoted to understanding how single molecules behave have been extensively developed for applications in genome sequencing. These nanopore systems are emerging as prominent tools for protein identification, detection, and analysis, suggesting realistic prospects for novel protein sequencing. This review summarizes recent advances in biological nanopore sensors toward protein sequencing, from the identification of individual amino acids to the controlled translocation of peptides and proteins, with attention focused on device and algorithm development and the delineation of molecular mechanisms with the aid of simulations. Specifically, the review aims to offer recommendations for the advancement of nanopore-based protein sequencing from an engineering perspective, highlighting the need for collaborative efforts across multiple disciplines. These efforts should include chemical conjugation, protein engineering, molecular simulation, machine-learning-assisted identification, and electronic device fabrication to enable practical implementation in real-world scenarios.

}, isbn = {1936-0851}, doi = {10.1021/acsnano.3c05628}, url = {https://doi.org/10.1021/acsnano.3c05628}, author = {Wei, Xiaojun and Penkauskas, Tadas and Reiner, Joseph E. and Kennard, Celeste and Uline, Mark J. and Wang, Qian and Li, Sheng and Aksimentiev, Aleksei and Robertson, Joseph W. F. and Liu, Chang} } @article {393, title = {Long-Range Conductivity in Proteins Mediated by Aromatic Residues}, journal = {ACS Physical Chemistry Au}, volume = {3}, year = {2023}, month = {09}, pages = {444{\textendash}455}, abstract = {

Single-molecule measurements show that many proteins, lacking any redox cofactors, nonetheless exhibit electrical conductance on the order of a nanosiemen over 10 nm distances, implying that electrons can transit an entire protein in less than a nanosecond when subject to a potential difference of less than 1 V. This is puzzling because, for fast transport (i.e., a free energy barrier of zero), the hopping rate is determined by the reorganization energy of approximately 0.8 eV, and this sets the time scale of a single hop to at least 1 μs. Furthermore, the Fermi energies of typical metal electrodes are far removed from the energies required for sequential oxidation and reduction of the aromatic residues of the protein, which should further reduce the hopping current. Here, we combine all-atom molecular dynamics (MD) simulations of non-redox-active proteins (consensus tetratricopeptide repeats) with an electron transfer theory to demonstrate a molecular mechanism that can account for the unexpectedly fast electron transport. According to our MD simulations, the reorganization energy produced by the energy shift on charging (the Stokes shift) is close to the conventional value of 0.8 eV. However, the non-ergodic sampling of molecular configurations by the protein results in reaction-reorganization energies, extracted directly from the distribution of the electrostatic energy fluctuations, that are only \~{}0.2 eV, which is small enough to enable long-range conductivity, without invoking quantum coherent transport. Using the MD values of the reorganization energies, we calculate a current decay with distance that is in agreement with experiment.

}, doi = {10.1021/acsphyschemau.3c00017}, url = {https://doi.org/10.1021/acsphyschemau.3c00017}, author = {Krishnan, Siddharth and Aksimentiev, Aleksei and Lindsay, Stuart and Matyushov, Dmitry} } @article {388, title = {Benchmarking Molecular Dynamics Force Fields for All-Atom Simulations of Biological Condensates}, journal = {Journal of Chemical Theory and Computation}, year = {2023}, month = {05/2023}, abstract = {

Proteins containing intrinsically disordered regions are integral parts of the cellular signaling pathways and common components of biological condensates. Point mutations in the protein sequence, genetic at birth or acquired through aging, can alter the properties of the condensates, marking the onset of neurodegenerative diseases such as ALS and dementia. While the all-atom molecular dynamics method can, in principle, elucidate the conformational changes that arise from point mutations, the applications of this method to protein condensate systems is conditioned upon the availability of molecular force fields that can accurately describe both structured and disordered regions of such proteins. Using the special-purpose Anton 2 supercomputer, we benchmarked the efficacy of nine presently available molecular force fields in describing the structure and dynamics of a Fused in sarcoma (FUS) protein. Five-microsecond simulations of the full-length FUS protein characterized the effect of the force field on the global conformation of the protein, self-interactions among its side chains, solvent accessible surface area, and the diffusion constant. Using the results of dynamic light scattering as a benchmark for the FUS radius of gyration, we identified several force fields that produced FUS conformations within the experimental range. Next, we used these force fields to perform ten-microsecond simulations of two structured RNA binding domains of FUS bound to their respective RNA targets, finding the choice of the force field to affect stability of the RNA{\textendash}FUS complex. Taken together, our data suggest that a combination of protein and RNA force fields sharing a common four-point water model provides an optimal description of proteins containing both disordered and structured regions and RNA{\textendash}protein interactions. To make simulations of such systems available beyond the Anton 2 machines, we describe and validate implementation of the best performing force fields in a publicly available molecular dynamics program NAMD. Our NAMD implementation enables simulations of large (tens of millions of atoms) biological condensate systems and makes such simulations accessible to a broader scientific community.

}, doi = {10.1021/acs.jctc.3c00148}, url = {https://pubs.acs.org/doi/10.1021/acs.jctc.3c00148}, author = {Kumar Sarthak and David Winogradoff and Yingda Ge and Sua Myong and Aleksei Aksimentiev} } @article {386, title = {Super-Resolution Detection of DNA Nanostructures Using a Nanopore}, journal = {Advanced Materials}, year = {2023}, month = {01/2023}, pages = {2207434}, abstract = {

Abstract High-resolution analysis of biomolecules has brought unprecedented insights into fundamental biological processes and dramatically advanced biosensing. Notwithstanding the ongoing resolution revolution in electron microscopy and optical imaging, only a few methods are presently available for high-resolution analysis of unlabelled single molecules in their native states. Here, we demonstrate label-free electrical sensing of structured single molecules with a spatial resolution down to single-digit nanometres. Using a narrow solid-state nanopore, we detect the passage of a series of nanostructures attached to a freely translocating DNA molecule, resolving individual nanostructures placed as close as 6\ nm apart and with a surface-to-surface gap distance of only 2\ nm. We attribute such super-resolution ability to the nanostructure-induced enhancement of the electric field at the tip of the nanopore. Our work demonstrates a general approach to improving the resolution of single-molecule nanopore sensing and presents a critical advance towards label-free, high-resolution DNA sequence mapping and digital information storage independent of molecular motors.

}, keywords = {biosensing, DNA nanostructures, Nanopores, single molecule, super resolution}, doi = {https://doi.org/10.1002/adma.202207434}, author = {Chen, Kaikai and Choudhary, Adnan and Sandler, Sarah E. and Maffeo, Christopher and Ducati, Caterina and Aksimentiev, Aleksei and Keyser, Ulrich F.} } @article {384, title = {Unidirectional single-file transport of full-length proteins through a nanopore}, journal = {Nature Biotechnology}, year = {2023}, month = {01/2023}, abstract = {

The electrical current blockade of a peptide or protein threading through a nanopore can be used as a fingerprint of the molecule in biosensor applications. However, threading of full-length proteins has only been achieved using enzymatic unfolding and translocation. Here we describe an enzyme-free approach for unidirectional, slow transport of full-length proteins through nanopores. We show that the combination of a chemically resistant biological nanopore, α-hemolysin (narrowest part is \textasciitilde1.4\thinspacenm in diameter), and a high concentration guanidinium chloride buffer enables unidirectional, single-file protein transport propelled by an electroosmotic effect. We show that the mean protein translocation velocity depends linearly on the applied voltage and translocation times depend linearly on length, resembling the translocation dynamics of ssDNA. Using a supervised machine-learning classifier, we demonstrate that single-translocation events contain sufficient information to distinguish their threading orientation and identity with accuracies larger than 90\%. Capture rates of protein are increased substantially when either a genetically encoded charged peptide tail or a DNA tag is added to a protein.

}, issn = {1546-1696}, doi = {10.1038/s41587-022-01598-3}, url = {https://doi.org/10.1038/s41587-022-01598-3}, author = {Yu, Luning and Kang, Xinqi and Li, Fanjun and Mehrafrooz, Behzad and Makhamreh, Amr and Fallahi, Ali and Foster, Joshua C. and Aksimentiev, Aleksei and Chen, Min and Wanunu, Meni} } @article {392, title = {Sulfur-Containing Foldamer-Based Artificial Lithium Channels}, journal = {Angewandte Chemie International Edition}, volume = {62}, year = {2023}, pages = {e202305623}, abstract = {

Abstract Unlike many other biologically relevant ions (Na+, K+, Ca2+, Cl-, etc) and protons, whose cellular concentrations are closely regulated by highly selective channel proteins, Li+ ion is unusual in that its concentration is well tolerated over many orders of magnitude and that no lithium-specific channel proteins have so far been identified. While one naturally evolved primary pathway for Li+ ions to traverse across the cell membrane is through sodium channels by competing with Na+ ions, highly sought-after artificial lithium-transporting channels remain a major challenge to develop. Here we show that sulfur-containing organic nanotubes derived from intramolecularly H-bonded helically folded aromatic foldamers of 3.6\ {\r A}\ in hollow cavity diameter could facilitate highly selective and efficient transmembrane transport of Li+ ions, with high transport selectivity factors of 15.3 and 19.9 over Na+ and K+ ions, respectively.

}, keywords = {Foldamers, H-Bonds, Lithium Channels, Organic Nanotubes, Supramolecular Chemistry}, doi = {https://doi.org/10.1002/anie.202305623}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/anie.202305623}, author = {Shen, Jie and R, Deepa and Li, Zhongyan and Oh, Hyeonji and Behera, Harekrushna and Joshi, Himanshu and Kumar, Manish and Aksimentiev, Aleksei and Zeng, Huaqiang} } @article {377, title = {Multi-resolution simulation of DNA transport through large synthetic nanostructures.}, journal = {Phys Chem Chem Phys}, volume = {24}, year = {2022}, month = {2022 Feb 02}, pages = {2706-2716}, abstract = {

Modeling and simulation has become an invaluable partner in development of nanopore sensing systems. The key advantage of the nanopore sensing method - the ability to rapidly detect individual biomolecules as a transient reduction of the ionic current flowing through the nanopore - is also its key deficiency, as the current signal itself rarely provides direct information about the chemical structure of the biomolecule. Complementing experimental calibration of the nanopore sensor readout, coarse-grained and all-atom molecular dynamics simulations have been used extensively to characterize the nanopore translocation process and to connect the microscopic events taking place inside the nanopore to the experimentally measured ionic current blockades. Traditional coarse-grained simulations, however, lack the precision needed to predict ionic current blockades with atomic resolution whereas traditional all-atom simulations are limited by the length and time scales amenable to the method. Here, we describe a multi-resolution framework for modeling electric field-driven passage of DNA molecules and nanostructures through to-scale models of synthetic nanopore systems. We illustrate the method by simulating translocation of double-stranded DNA through a solid-state nanopore and a micron-scale slit, capture and translocation of single-stranded DNA in a double nanopore system, and modeling ionic current readout from a DNA origami nanostructure passage through a nanocapillary. We expect our multi-resolution simulation framework to aid development of the nanopore field by providing accurate, to-scale modeling capability to research laboratories that do not have access to leadership supercomputer facilities.

}, keywords = {Biological Transport, DNA, Electricity, Molecular Dynamics Simulation, Nanopores}, issn = {1463-9084}, doi = {10.1039/d1cp04589j}, author = {Choudhary, Adnan and Maffeo, Christopher and Aleksei Aksimentiev} } @article {370, title = {Fluorofoldamer-Based Salt- and Proton-Rejecting Artificial Water Channels for Ultrafast Water Transport.}, journal = {Nano Lett}, volume = {22}, year = {2022}, month = {2022 06 22}, pages = {4831-4838}, abstract = {

Here, we report on a novel class of fluorofoldamer-based artificial water channels (AWCs) that combines excellent water transport rate and selectivity with structural simplicity and robustness. Produced by a facile one-pot copolymerization reaction under mild conditions, the best-performing channel (AWC ) is an n-CH-decorated foldamer nanotube with an average channel length of 2.8 nm and a pore diameter of 5.2 {\r A}. AWC demonstrates an ultrafast water conduction rate of 1.4 {\texttimes} 10 HO/s per channel, outperforming the archetypal biological water channel, aquaporin 1, while excluding salts (i.e., NaCl and KCl) and protons. Unique to this class of channels, the inwardly facing C(sp2)-F atoms being the most electronegative in the periodic table are proposed as being critical to enabling the ultrafast and superselective water transport properties by decreasing the channel{\textquoteright}s cavity and enhancing the channel wall smoothness via reducing intermolecular forces with water molecules or hydrated ions.

}, keywords = {Aquaporins, Biological Transport, Protons, Sodium Chloride, Water}, issn = {1530-6992}, doi = {10.1021/acs.nanolett.2c01137}, author = {Shen, Jie and Roy, Arundhati and Joshi, Himanshu and Samineni, Laxmicharan and Ye, Ruijuan and Tu, Yu-Ming and Song, Woochul and Skiles, Matthew and Kumar, Manish and Aleksei Aksimentiev and Zeng, Huaqiang} } @article {385, title = {Trapping of protein cargo molecules inside DNA origami nanocages}, journal = {Nanoscale}, volume = {14}, year = {2022}, month = {11/2022}, pages = {18041{\textendash}18050}, abstract = {

The development of the DNA origami technique has directly inspired the idea of using three-dimensional DNA cages for the encapsulation and targeted delivery of drug or cargo molecules. The cages would be filled with molecules that would be released at a site of interest upon cage opening triggered by an external stimulus. Though different cage variants have been developed, efficient loading of DNA cages with freely-diffusing cargo molecules that are not attached to the DNA nanostructure and their efficient retention within the cages has not been presented. Here we address these challenges using DNA origami nanotubes formed by a double-layer of DNA helices that can be sealed with tight DNA lids at their ends. In a first step we attach DNA-conjugated cargo proteins to complementary target strands inside the DNA tubes. After tube sealing, the cargo molecules are released inside the cavity using toehold-mediated strand displacement by externally added invader strands. We show that DNA invaders are rapidly entering the cages through their DNA walls. Retention of \~{}70 kDa protein cargo molecules inside the cages was, however, poor. Guided by coarse-grained simulations of the DNA cage dynamics, a tighter sealing of the DNA tubes was developed which greatly reduced the undesired escape of cargo proteins. These improved DNA nanocages allow for efficient encapsulation of medium-sized cargo molecules while remaining accessible to small molecules that can be used to trigger reactions, including a controlled release of the cargo via nanocage opening.

}, doi = {10.1039/d2nr05356j}, author = {Merle Scherf and Florian Scheffler and Christopher Maffeo and Ulrich Kemper and Jingjing Ye and Aleksei Aksimentiev and Ralf Seidel and Uta Reibetanz} } @article {372, title = {Percolation transition prescribes protein size-specific barrier to passive transport through the nuclear pore complex.}, journal = {Nature Communications}, volume = {13}, year = {2022}, month = {09/2022}, pages = {5138}, chapter = {5138}, abstract = {

Nuclear pore complexes (NPCs) control biomolecular transport in and out of the nucleus. Disordered nucleoporins in the complex{\textquoteright}s pore form a permeation barrier, preventing unassisted transport of large biomolecules. Here, we combine coarse-grained simulations of experimentally derived NPC structures with a theoretical model to determine the microscopic mechanism of passive transport. Brute-force simulations of protein transport reveal telegraph-like behavior, where prolonged diffusion on one side of the NPC is interrupted by rapid crossings to the other. We rationalize this behavior using a theoretical model that reproduces the energetics and kinetics of permeation solely from statistics of transient voids within the disordered mesh. As the protein size increases, the mesh transforms from a soft to a hard barrier, enabling orders-of-magnitude reduction in permeation rate for proteins beyond the percolation size threshold. Our model enables exploration of alternative NPC architectures and sets the stage for uncovering molecular mechanisms of facilitated nuclear transport.

}, keywords = {NPC, nuclear pore, passive transport}, issn = {2041-1723}, doi = {10.1038/s41467-022-32857-1}, author = {Winogradoff, David and Chou, Han-Yi and Maffeo, Christopher and Aleksei Aksimentiev} } @article {380, title = {Leakless end-to-end transport of small molecules through micron-length DNA nanochannels}, journal = {Science Advances}, volume = {8}, year = {2022}, month = {09/09/2022}, abstract = {
Designed and engineered protein and DNA nanopores can be used to sense and characterize single molecules and control transmembrane transport of molecular species. However, designed biomolecular pores are less than 100 nm in length and are used primarily for transport across lipid membranes. Nanochannels that span longer distances could be used as conduits for molecules between nonadjacent compartments or cells. Here, we design micrometer-long, 7-nm-diameter DNA nanochannels that small molecules can traverse according to the laws of continuum diffusion. Binding DNA origami caps to channel ends eliminates transport and demonstrates that molecules diffuse from one channel end to the other rather than permeating through channel walls. These micrometer-length nanochannels can also grow, form interconnects, and interface with living cells. This work thus shows how to construct multifunctional, dynamic agents that control molecular transport, opening ways of studying intercellular signaling and modulating molecular transport between synthetic and living cells.
}, doi = {10.1126/sciadv.abq4834}, url = {https://www.science.org/doi/10.1126/sciadv.abq4834}, author = {Li, Yi and Maffeo, Christopher and Joshi, Himanshu and Aleksei Aksimentiev and M{\'e}nard, Brice and Schulman, Rebecca} } @article {371, title = {Resolving Isomeric Posttranslational Modifications Using a Biological Nanopore as a Sensor of Molecular Shape}, journal = {Journal of the American Chemical Society}, volume = {144}, year = {2022}, month = {08/2022}, pages = {16060--16068}, abstract = {

The chemical nature and precise position of posttranslational modifications (PTMs) in proteins or peptides are crucial for various severe diseases, such as cancer. State-of-the-art PTM diagnosis is based on elaborate and costly mass-spectrometry or immunoassay-based approaches, which are limited in selectivity and specificity. Here, we demonstrate the use of a protein nanopore to differentiate peptides-derived from human histone H4 protein-of identical mass according to the positions of acetylated and methylated lysine residues. Unlike sequencing by stepwise threading, our method detects PTMs and their positions by sensing the shape of a fully entrapped peptide, thus eliminating the need for controlled translocation. Molecular dynamics simulations show that the sensitivity to molecular shape derives from a highly nonuniform electric field along the pore. This molecular shape-sensing principle offers a path to versatile, label-free, and high-throughput characterizations of protein isoforms.

}, doi = {10.1021/jacs.2c06211}, url = {https://pubs.acs.org/doi/full/10.1021/jacs.2c06211}, author = {Tobias Ennslen and Kumar Sarthak and Aleksei Aksimentiev and Jan C. Behrends} } @article {374, title = {Discrimination of RNA fiber structures using solid-state nanopores}, journal = {Nanoscale}, volume = {14}, year = {2022}, month = {05/2023}, pages = {6866-6875}, abstract = {

RNA fibers are a class of biomaterials that can be assembled using HIV-like kissing loop interactions. Because of the programmability of molecular design and low immunorecognition, these structures present an interesting opportunity to solve problems in nanobiotechnology and synthetic biology. However, the experimental tools to fully characterize and discriminate among different fiber structures in solution are limited. Herein, we utilize solid-state nanopore experiments and Brownian dynamics simulations to characterize and distinguish several RNA fiber structures that differ in their degrees of branching. We found that, regardless of the electrolyte type and concentration, fiber structures that have more branches produce longer and deeper ionic current blockades in comparison to the unbranched fibers. Experiments carried out at temperatures ranging from 20{\textendash}60 {\textdegree}C revealed almost identical distributions of current blockade amplitudes, suggesting that the kissing loop interactions in fibers are resistant to heating within this range.

}, issn = {2040-3364}, doi = {10.1039/D1NR08002D}, url = {http://pubs.rsc.org/en/content/articlepdf/2022/NR/D1NR08002D}, author = {Tripathi, Prabhat and Chandler, Morgan and Maffeo, Christopher Michael and Fallahi, Ali and Makhamreh, Amr and Halman, Justin and Aleksei Aksimentiev and Afonin, Kirill A. and Wanunu, Meni} } @article {373, title = {Single-molecule biophysics experiments in silico: Toward a physical model of a replisome}, journal = {iScience}, volume = {25}, year = {2022}, month = {05/2022}, pages = {104264}, abstract = {

The interpretation of single-molecule experiments is frequently aided by computational modeling of biomolecular dynamics. The growth of computing power and ongoing validation of computational models suggest that it soon may be possible to replace some experiments outright with computational mimics. Here, we offer a blueprint for performing single-molecule studies in silico using a DNA-binding protein as a test bed. We demonstrate how atomistic simulations, typically limited to sub-millisecond durations and zeptoliter volumes, can guide development of a coarse-grained model for use in simulations that mimic single-molecule experiments. We apply the model to recapitulate, in silico, force-extension characterization of protein binding to single-stranded DNA and protein and DNA replacement assays, providing a detailed portrait of the underlying mechanics. Finally, we use the model to simulate the trombone loop of a replication fork, a large complex of proteins and DNA.

}, doi = {10.1016/j.isci.2022.104264}, url = {https://api.elsevier.com/content/article/PII:S258900422200534}, author = {Maffeo, Christopher and Chou, Han-Yi and Aleksei Aksimentiev} } @article {366, title = {Expanding the Molecular Alphabet of DNA-Based Data Storage Systems with Neural Network Nanopore Readout Processing}, journal = {Nano Letters}, year = {2022}, month = {02/2022}, abstract = {

DNA is a promising next-generation data storage medium, but challenges remain with synthesis costs and recording latency. Here, we describe a prototype of a DNA data storage system that uses an extended molecular alphabet combining natural and chemically modified nucleotides. Our results show that MspA nanopores can discriminate different combinations and ordered sequences of natural and chemically modified nucleotides in custom-designed oligomers. We further demonstrate singlemolecule sequencing of the extended alphabet using a neural network architecture that classifies raw current signals generated by Oxford Nanopore sequencers with an average accuracy exceeding 60\% (39{\texttimes} larger than random guessing). Molecular dynamics simulations show that the majority of modified nucleotides lead to only minor perturbations of the DNA double helix. Overall, the extended molecular alphabet may potentially offer a nearly 2-fold increase in storage density and potentially the same order of reduction in the recording latency, thereby enabling new implementations of molecular recorders.

}, doi = {10.1021/acs.nanolett.1c04203}, author = {Tabatabaei, S Kasra and Pham, Bach and Pan, Chao and Liu, Jingqian and Chandak, Shubham and Shorkey, Spencer A and Hernandez, Alvaro G and Aleksei Aksimentiev and Chen, Min and Schroeder, Charles M and Milenkovic, Olgica} } @article {364, title = {A nanoscale reciprocating rotary mechanism with coordinated mobility control.}, journal = {Nature Communications}, volume = {12}, year = {2021}, month = {12/2021}, pages = {7138}, chapter = {7138}, abstract = {

Biological molecular motors transform chemical energy into mechanical work by coupling cyclic catalytic reactions to large-scale structural transitions. Mechanical deformation can be surprisingly efficient in realizing such coupling, as demonstrated by the FoF1 ATP synthase. Here, we describe a synthetic molecular mechanism that transforms a rotary motion of an asymmetric camshaft into reciprocating large-scale transitions in a surrounding stator orchestrated by mechanical deformation. We design the mechanism using DNA origami, characterize its structure via cryo-electron microscopy, and examine its dynamic behavior using single-particle fluorescence microscopy and molecular dynamics simulations. While the camshaft can rotate inside the stator by diffusion, the stator{\textquoteright}s mechanics makes the camshaft pause at preferred orientations. By changing the stator{\textquoteright}s mechanical stiffness, we accelerate or suppress the Brownian rotation, demonstrating an allosteric coupling between the camshaft and the stator. Our mechanism provides a framework for manufacturing artificial nanomachines that function because of coordinated movements of their components.

}, keywords = {Cryoelectron Microscopy, DNA, Molecular Conformation, Molecular Dynamics Simulation, Nanostructures, Nanotechnology, Rotation}, issn = {2041-1723}, doi = {10.1038/s41467-021-27230-7}, author = {Bertosin, Eva and Maffeo, Christopher M and Drexler, Thomas and Honemann, Maximilian N and Aleksei Aksimentiev and Dietz, Hendrik} } @article {363, title = {Membrane Activity of a DNA-Based Ion Channel Depends on the Stability of Its Double-Stranded Structure}, journal = {Nano Letters}, volume = {21}, year = {2021}, month = {11/2021}, pages = {9789{\textendash}9796}, chapter = {9789}, abstract = {

DNA nanotechnology has emerged as a promising method for designing spontaneously inserting and fully controllable synthetic ion channels. However, both insertion efficiency and stability of existing DNA-based membrane channels leave much room for improvement. Here, we demonstrate an approach to overcoming the unfavorable DNA{\textendash}lipid interactions that hinder the formation of a stable transmembrane pore. Our all-atom MD simulations and experiments show that the insertion-driving cholesterol modifications can cause fraying of terminal base pairs of nicked DNA constructs, distorting them when embedded in a lipid bilayer. Importantly, we show that DNA nanostructures with no backbone discontinuities form more stable conductive pores and insert into membranes with higher efficiency than the equivalent nicked constructs. Moreover, lack of nicks allows the design and maintenance of membrane-spanning helices in a tilted orientation within the lipid bilayer. Thus, reducing the conformational degrees of freedom of the DNA nanostructures enables better control over their function as synthetic ion channels.

}, keywords = {DNA structures, lipid membranes, nicks, protein-mimicking, synthetic ion channel, tilt}, doi = {10.1021/acs.nanolett.1c03791}, url = {https://pubs.acs.org/doi/10.1021/acs.nanolett.1c03791}, author = {Morzy, Diana and Joshi, Himanshu and Sandler, Sarah E. and Aleksei Aksimentiev and Keyser, Ulrich F.} } @article {365, title = {Multiple rereads of single proteins at single{\textendash}amino acid resolution using nanopores}, journal = {Science}, volume = {374}, year = {2021}, month = {11/2021}, pages = {1509{\textendash}1513}, abstract = {

A proteomics tool capable of identifying single proteins would be important for cell biology research and applications. Here, we demonstrate a nanopore-based single-molecule peptide reader sensitive to single{\textendash}amino acid substitutions within individual peptides. A DNA-peptide conjugate was pulled through the biological nanopore MspA by the DNA helicase Hel308. Reading the ion current signal through the nanopore enabled discrimination of single{\textendash}amino acid substitutions in single reads. Molecular dynamics simulations showed these signals to result from size exclusion and pore binding. We also demonstrate the capability to {\textquotedblleft}rewind{\textquotedblright} peptide reads, obtaining numerous independent reads of the same molecule, yielding an error rate of \<10-6\ in single amino acid variant identification. These proof-of-concept experiments constitute a promising basis for the development of a single-molecule protein fingerprinting and analysis technology.

}, doi = {10.1021/acs.nanolett.1c04203}, author = {Brinkerhoff, Henry and Kang, Albert SW and Liu, Jingqian and Aleksei Aksimentiev and Dekker, Cees} } @article {369, title = {DNA sequence and methylation prescribe the inside-out conformational dynamics and bending energetics of DNA minicircles.}, journal = {Nucleic Acids Res}, volume = {49}, year = {2021}, month = {11/2021}, pages = {11459-11475}, abstract = {

Eukaryotic genome and methylome encode DNA fragments{\textquoteright} propensity to form nucleosome particles. Although the mechanical properties of DNA possibly orchestrate such encoding, the definite link between {\textquoteright}omics{\textquoteright} and DNA energetics has remained elusive. Here, we bridge the divide by examining the sequence-dependent energetics of highly bent DNA. Molecular dynamics simulations of 42 intact DNA minicircles reveal that each DNA minicircle undergoes inside-out conformational transitions with the most likely configuration uniquely prescribed by the nucleotide sequence and methylation of DNA. The minicircles{\textquoteright} local geometry consists of straight segments connected by sharp bends compressing the DNA{\textquoteright}s inward-facing major groove. Such an uneven distribution of the bending stress favors minimum free energy configurations that avoid stiff base pair sequences at inward-facing major grooves. Analysis of the minicircles{\textquoteright} inside-out free energy landscapes yields a discrete worm-like chain model of bent DNA energetics that accurately account for its nucleotide sequence and methylation. Experimentally measuring the dependence of the DNA looping time on the DNA sequence validates the model. When applied to a nucleosome-like DNA configuration, the model quantitatively reproduces yeast and human genomes{\textquoteright} nucleosome occupancy. Further analyses of the genome-wide chromatin structure data suggest that DNA bending energetics is a fundamental determinant of genome architecture.

}, keywords = {DNA Methylation, DNA, Circular, Molecular Dynamics Simulation, Nucleic Acid Conformation}, issn = {1362-4962}, doi = {10.1093/nar/gkab967}, author = {Yoo, Jejoong and Park, Sangwoo and Maffeo, Christopher and Ha, Taekjip and Aleksei Aksimentiev} } @article {362, title = {DNA Origami Voltage Sensors for Transmembrane Potentials with Single-Molecule Sensitivity}, journal = {Nano Letters}, volume = {21}, year = {2021}, month = {10/2021}, pages = {8634-8641}, chapter = {8634}, abstract = {

Signal transmission in neurons goes along with changes in the transmembrane potential. To report them, different approaches, including optical voltage-sensing dyes and genetically encoded voltage indicators, have evolved. Here, we present a DNA nanotechnology-based system and demonstrate its functionality on liposomes. Using DNA origami, we incorporated and optimized different properties such as membrane targeting and voltage sensing modularly. As a sensing unit, we used a hydrophobic red dye anchored to the membrane and an anionic green dye at the DNA to connect the nanostructure and the membrane dye anchor. Voltage-induced displacement of the anionic donor unit was read out by fluorescence resonance energy transfer (FRET) changes of single sensors attached to liposomes. A FRET change of \~{}5\% for ΔΨ = 100 mV was observed. The working mechanism of the sensor was rationalized by molecular dynamics simulations. Our approach holds potential for an application as nongenetically encoded membrane sensors.

}, doi = {10.1021/acs.nanolett.1c02584}, url = {https://pubs.acs.org/doi/10.1021/acs.nanolett.1c02584?fig=tgr1\&ref=pdf}, author = {Ochmann, Sarah E and Joshi, Himanshu and Büber, Ece and Franquelim, Henri G and Stegemann, Pierre and Sacc{\`a}, Barbara and Keyser, Ulrich F and Aleksei Aksimentiev and Tinnefeld, Philip} } @article {360, title = {Synthetic Macrocycle Nanopore for Potassium-Selective Transmembrane Transport}, journal = {Journal of the American Chemical Society}, volume = {143}, year = {2021}, month = {08/2021}, pages = {15975-15983}, chapter = {15975}, abstract = {

Reproducing the structure and function of biological membrane channels, synthetic nanopores have been developed for applications in membrane filtration technologies and biomolecular sensing. Stable stand-alone synthetic nanopores have been created from a variety of materials, including peptides, nucleic acids, synthetic polymers, and solid-state membranes. In contrast to biological nanopores, however, furnishing such synthetic nanopores with an atomically defined shape, including deliberate placement of each and every chemical group, remains a major challenge. Here, we introduce a chemosynthetic macromolecule,\ extended pillararene macrocycle (EPM) as a chemically defined transmembrane nanopore that exhibits selective transmembrane transport. Our ionic current measurements reveal stable insertion of individual EPM nanopores into a lipid bilayer membrane and remarkable cation type-selective transport, with up to a 21-fold selectivity for potassium over sodium ions. Taken together, direct chemical synthesis offers a path to de novo design of a new class of synthetic nanopores with custom transport functionality imprinted in their atomically defined chemical structure.\ 

}, keywords = {Electrical conductivity, MD Simulations, Nanopores, Potassium Ions Selectivity}, doi = {10.1021/jacs.1c04910}, author = {Qiao, Dan and Joshi, Himanshu and Zhu, Huangtianzhi and Wang, Fushi and Xu, Yang and Gao, Jia and Huang, Feihe and Aleksei Aksimentiev and Feng, Jiandong} } @article {351, title = {Foldamer-Based Ultrapermeable and Highly Selective Artificial Water Channels that Exclude Protons}, journal = {Nature Nanotechnology}, volume = {16}, year = {2021}, month = {08/2021}, pages = {911-917}, chapter = {911}, abstract = {

The outstanding capacity of aquaporins (AQPs) for mediating highly selective superfast water transport has inspired the recent development of supramolecular monovalent ion-excluding artificial water channels (AWCs). AWC-based bioinspired membranes are proposed for desalination, water purification, and other separation applications. While some recent progress has been made in synthesizing AWCs that approach the water permeability and ion selectivity of AQPs, a hallmark feature of AQPs{\textemdash}high water transport while excluding protons-has not been reproduced. We report a class of biomimetic, helically folded pore-forming polymeric foldamers that can serve as long-sought-after highly selective ultrafast water-conducting channels with performance exceeding those of AQPs (1.1 {\texttimes} 1010 water molecules per second for AQP1, with high water-over- monovalent-ion transport selectivity (~108 water molecules over Cl-\ ion) conferred by the modularly tunable hydrophobicity of the interior pore surface. The best-performing AWC reported here delivers water transport at an exceptionally high rate, namely, 2.5 times that of AQP1, while concurrently rejecting salts (NaCl and KCl) and even protons.

}, doi = {10.1038/s41565-021-00915-2}, author = {Roy, Arundhati and Shen, Jie and Joshi, Himanshu and Song, Woochul and Tu, Yu-Ming and Chowdhury, Ratul and Ruijuan, Ye and Li, Ning and Ren, Changliang and Kumar, Manish and Aleksei Aksimentiev and Zeng, Huaqiang} } @article {356, title = {The emerging landscape of single-molecule protein sequencing technologies}, journal = {Nature Methods}, volume = {18}, year = {2021}, month = {06/2021}, chapter = {604-617}, abstract = {

Single-cell profiling methods have had a profound impact on the understanding of cellular heterogeneity. While genomes and transcriptomes can be explored at the single-cell level, single-cell profiling of proteomes is not yet established. Here we describe new single-molecule protein sequencing and identification technologies alongside innovations in mass spectrometry that will eventually enable broad sequence coverage in single-cell profiling. These technologies will in turn facilitate biological discovery and open new avenues for ultrasensitive disease diagnostics.

}, doi = {10.1038/s41592-021-01143-1}, url = {https://doi.org/10.1038/s41592-021-01143-1}, author = {Javier Antonio Alfaro and Peggy Bohl{\"a}nder and Mingjie Dai and Mike Filius and Cecil J. Howard and Xander F. van Kooten and Shilo Ohayon and Adam Pomorski and Sonja Schmid and Aleksei Aksimentiev and Eric V. Anslyn and Georges Bedran and Chan Cao and Mauro Chinappi and Etienne Coyaud and Cees Dekker and Gunnar Dittmar and Nicholas Drachman and Rienk Eelkema and David Goodlett and S{\'e}bastien Hentz and Umesh Kalathiya and Neil L. Kelleher and Ryan T. Kelly and Zvi Kelman and Sung Hyun Kim and Bernhard Kuster and David Rodriguez-Larrea and Stuart Lindsay and Giovanni Maglia and Edward M. Marcotte and John P. Marino and Christophe Masselon and Michael Mayer and Patroklos Samaras and Kumar Sarthak and Lusia Sepiashvili and Derek Stein and Meni Wanunu and Mathias Wilhelm and Peng Yin and Amit Meller and Chirlmin Joo} } @article {355, title = {The Manipulation of the Internal Hydrophobicity of FraC Nanopores Augments Peptide Capture and Recognition}, journal = {ACS Nano}, year = {2021}, month = {06/2021}, abstract = {

The detection of analytes and the sequencing of DNA using biological nanopores have seen major advances over recent years. The analysis of proteins and peptides with nanopores, however, is complicated by the complex physicochemical structure of polypeptides and the lack of understanding of the mechanism of capture and recognition of polypeptides by nanopores. In this work, we show that introducing aromatic amino acids at precise positions within the lumen of α-helical fragaceatoxin C (FraC) nanopores increased the capture frequency of peptides and largely improved the discrimination among peptides of similar size. Molecular dynamics simulations determined the sensing region of the nanopore, elucidated the microscopic mechanism enabling accurate characterization of the peptides\ via\ ionic current blockades in FraC, and characterized the effect of the pore modification on peptide discrimination. This work provides insights to improve the recognition and to augment the capture of peptides by nanopores, which is important for developing a real-time and single-molecule size analyzer for peptide recognition and identification.

}, doi = {10.1021/acsnano.0c09958}, url = {https://doi.org/10.1021/acsnano.0c09958}, author = {Florian Leonardus Rudolfus Lucas and Kumar Sarthak and Erica Mariska Lenting and David Coltan and Nieck Jordy van der Heide and Roderick Corstiaan Abraham Versloot and Aleksei Aksimentiev and Giovanni Maglia} } @article {350, title = {Cations Regulate Membrane Attachment and Functionality of DNA Nanostructures}, journal = {Journal of the American Chemical Society}, volume = {143}, year = {2021}, month = {05/2021}, pages = {7358-7367}, chapter = {7358}, abstract = {

The interplay between nucleic acids and lipids\ underpins several key processes in molecular biology, synthetic biotechnology, vaccine technology, and nanomedicine. These interactions are often electrostatic in nature, and much of their rich phenomenology remains unexplored in view of the chemical diversity of lipids, the heterogeneity of their phases, and the broad range of relevant solvent conditions. Here we unravel the electrostatic interactions between zwitterionic lipid membranes and DNA nanostructures in the presence of physiologically relevant\ cations, with the purpose of identifying new routes to program DNA-lipid complexation and membrane-active nanodevices. We demonstrate that this interplay is influenced by both the phase of the lipid membranes and the valency of the ions and observe divalent cation bridging between nucleic acids and gel-phase bilayers. Furthermore, even in the presence of hydrophobic modifications on the DNA, we find that cations are still required to enable DNA adhesion to liquid-phase membranes. We show that the latter mechanism can be exploited to control the degree of attachment of cholesterol-modified DNA nanostructures by modifying their overall hydrophobicity and charge. Besides their biological relevance, the interaction mechanisms we explored hold great practical potential in the design of biomimetic nanodevices, as we show by constructing an ion-regulated DNA-based synthetic enzyme.

}, doi = {10.1021/jacs.1c00166}, url = {https://doi.org/10.1021/jacs.1c00166}, author = {Morzy, Diana and Rubio-S{\'a}nchez, Roger and Joshi, Himanshu and Aleksei Aksimentiev and Di Michele, Lorenzo and Keyser, Ulrich F.} } @article {354, title = {Hydrophobic Interactions between DNA Duplexes and Synthetic and Biological Membranes.}, journal = {Journal of the American Chemical Society}, volume = {143}, year = {2021}, month = {05/2021}, pages = {8305-8313}, chapter = {8305}, abstract = {

Equipping DNA with hydrophobic anchors enables targeted interaction with lipid bilayers for applications in biophysics, cell biology, and synthetic biology. Understanding DNA-membrane interactions is crucial for rationally designing functional DNA. Here we study the interactions of hydrophobically tagged DNA with synthetic and cell membranes using a combination of experiments and atomistic molecular dynamics (MD) simulations. The DNA duplexes are rendered hydrophobic by conjugation to a terminal cholesterol anchor or by chemical synthesis of a charge-neutralized alkyl-phosphorothioate (PPT) belt. Cholesterol-DNA tethers to lipid vesicles of different lipid compositions and charges, while PPT DNA binding strongly depends on alkyl length, belt position, and headgroup charge. Divalent cations in the buffer can also influence binding. Our MD simulations directly reveal the complex structure and energetics of PPT DNA within a lipid membrane, demonstrating that longer alkyl-PPT chains provide the most stable membrane anchoring but may disrupt DNA base paring in solution. When tested on cells, cholesterol-DNA is homogeneously distributed on the cell surface, while alkyl-PPT DNA accumulates in clustered structures on the plasma membrane. DNA tethered to the outside of the cell membrane is distinguished from DNA spanning the membrane by nuclease and sphingomyelinase digestion assays. The gained fundamental insight on DNA-bilayer interactions will guide the rational design of membrane-targeting nanostructures.

}, issn = {1520-5126}, doi = {10.1021/jacs.0c13235}, author = {Jones, Sioned F and Joshi, Himanshu and Terry, Stephen J and Burns, Jonathan R and Aleksei Aksimentiev and Eggert, Ulrike S and Howorka, Stefan} } @article {346, title = {Electrical unfolding of cytochrome during translocation through a nanopore constriction.}, journal = {Proceedings of the National Academy of Sciences}, volume = {118}, year = {2021}, month = {04/2021}, abstract = {

Many small proteins move across cellular compartments through narrow pores. In order to thread a protein through a constriction, free energy must be overcome to either deform or completely unfold the protein. In principle, the diameter of the pore, along with the effective driving force for unfolding the protein, as well as its barrier to translocation, should be critical factors that govern whether the process proceeds via squeezing, unfolding/threading, or both. To probe this for a well-established protein system, we studied the electric-field-driven translocation behavior of cytochrome (cyt ) through ultrathin silicon nitride (SiN) solid-state nanopores of diameters ranging from 1.5 to 5.5 nm. For a 2.5-nm-diameter pore, we find that, in a threshold electric-field regime of \~{}30 to 100 MV/m, cyt is able to squeeze through the pore. As electric fields inside the pore are increased, the unfolded state of cyt is thermodynamically stabilized, facilitating its translocation. In contrast, for 1.5- and 2.0-nm-diameter pores, translocation occurs only by threading of the fully unfolded protein after it transitions through a higher energy unfolding intermediate state at the mouth of the pore. The relative energies between the metastable, intermediate, and unfolded protein states are extracted using a simple thermodynamic model that is dictated by the relatively slow (\~{}ms) protein translocation times for passing through the nanopore. These experiments map the various modes of protein translocation through a constriction, which opens avenues for exploring protein folding structures, internal contacts, and electric-field-induced deformability.

}, issn = {1091-6490}, doi = {10.1073/pnas.2016262118}, author = {Tripathi, Prabhat and Benabbas, Abdelkrim and Mehrafrooz, Behzad and Yamazaki, Hirohito and Aleksei Aksimentiev and Champion, Paul M and Wanunu, Meni} } @article {343, title = {Determining the In-Plane Orientation and Binding Mode of Single Fluorescent Dyes in DNA Origami Structures}, journal = {ACS Nano}, volume = {15}, year = {2021}, month = {03/2021}, pages = {5109-5117}, chapter = {5109}, abstract = {

We present a technique to determine the orientation of single fluorophores attached to DNA origami structures based on two measurements. First, the orientation of the absorption transition dipole of the molecule is determined through a polarization-resolved excitation measurement. Second, the orientation of the DNA origami structure is obtained from a DNA-PAINT nanoscopy measurement. Both measurements are performed consecutively on a fluorescence wide-field microscope. We employed this approach to study the orientation of single ATTO 647N, ATTO 643, and Cy5 fluorophores covalently attached to a 2D rectangular DNA origami structure with different nanoenvironments, achieved by changing both the fluorophores{\textquoteright} binding position and immediate vicinity. Our results show that when fluorophores are incorporated with additional space, for example, by omitting nucleotides in an elsewise doublestranded environment, they tend to stick to the DNA and to adopt a preferred orientation that depends more on the specific molecular environment than on the fluorophore type. With the aid of all-atom molecular dynamics simulations, we rationalized our observations and provide insight into the fluorophores{\textquoteright} probable binding modes. We believe this work constitutes an important step toward manipulating the orientation of single fluorophores in DNA origami structures, which is vital for the development of more efficient and reproducible self-assembled nanophotonic devices.\ 

}, keywords = {DNA Nanotechnology, DNA-PAINT, Single-molecule fluorescence polarization-resolved microscopy, Super-resolution microscopy}, doi = {https://doi.org/10.1021/acsnano.0c10259}, url = {https://pubs.acs.org/doi/10.1021/acsnano.0c10259}, author = {Hübner, Kristina and Joshi, Himanshu and Aleksei Aksimentiev and Stefani, Fernando D and Tinnefeld, Philip and Acuna, Guillermo P} } @article {341, title = {Translocation of DNA through Ultrathin Nanoslits}, journal = {Advanced Materials}, volume = {33}, year = {2021}, month = {02/2021}, pages = {2007682}, chapter = {2007682}, abstract = {

2D nanoslit devices, where two crystals with atomically flat surfaces are separated by only a few nanometers, have attracted considerable attention because their tunable control over the confinement allows for the discovery of unusual transport behavior of gas, water, and ions. Here, the passage of double-stranded DNA molecules is studied through nanoslits fabricated from exfoliated 2D materials, such as graphene or hexagonal boron nitride, and the DNA polymer behavior is examined in this tight confinement. Two types of events are observed in the ionic current: long current blockades that signal DNA translocation and short spikes where DNA enters the slits but withdraws. DNA translocation events exhibit three distinct phases in their current-blockade traces{\textemdash}loading, translation, and exit. Coarse-grained molecular dynamics simulation allows the different polymer configurations of these phases to be identified. DNA molecules, including folds and knots in their polymer structure, are observed to slide through the slits with near-uniform velocity without noticeable frictional interactions of DNA with the confining graphene surfaces. It is anticipated that this new class of 2D-nanoslit devices will provide unique ways to study polymer physics and enable lab-on-a-chip biotechnology.

}, keywords = {2D nanoslits, biopolymers, DNA translocation, graphene, Nanofluidics}, doi = {https://doi.org/10.1002/adma.202007682}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/adma.202007682}, author = {Yang, Wayne and Radha, Boya and Choudhary, Adnan and You, Yi and Mettela, Gangaiah and Geim, Andre K. and Aleksei Aksimentiev and Keerthi, Ashok and Dekker, Cees} } @article {357, title = {A tetrahedral DNA nanorobot with conformational change in response to molecular trigger}, journal = {Nanoscale}, year = {2021}, month = {01/2021}, abstract = {

Dynamic DNA origami nanostructures that respond to external stimuli are promising platforms for cargo delivery and nanoscale sensing. However, the low stability of such nanostructures under physiological conditions presents a major obstacle for their use in biomedical applications. This article describes a stable tetrahedral DNA nanorobot (TDN) programmed to undergo a controlled conformational change in response to epithelial cell adhesion molecule (EpCAM), a molecular biomarker specifically expressed on the circulating tumor cells. Multiresolution molecular dynamics simulations verified the overall stability of the folded TDN design and characterized local distortions in the folded structure. Atomic force microscopy and gel electrophoresis results showed that tetragonal structures are more stable than unfolded DNA origami sheets. Live cell experiments demonstrated the low cytotoxicity and target specificity of TDN. In summary, the proposed TDN can not only effectively resist nuclease catalysis but also has the potential to monitor EpCAM-positive cells precisely.

}, issn = {2040-3364}, doi = {10.1039/D1NR02757C}, url = {http://xlink.rsc.org/?DOI=D1NR02757Chttp://pubs.rsc.org/en/content/articlepdf/2021/NR/D1NR02757Chttp://pubs.rsc.org/en/content/articlepdf/2021/NR/D1NR02757C}, author = {Liu, Fengyu and Liu, Xiaoming and Shi, Qing and Maffeo, Christopher and Kojima, Masaru and Dong, Lixin and Aleksei Aksimentiev and Huang, Qiang and Fukuda, Toshio and Arai, Tatsuo} } @article {340, title = {Chiral Systems Made from DNA}, journal = {Advanced Science}, volume = {8}, year = {2021}, month = {01/2021}, pages = {2003113}, type = {Progress Report}, chapter = {2003113}, abstract = {

The very chemical structure of DNA that enables biological heredity and evolution has non-trivial implications for the self-organization of DNA molecules into larger assemblies and provides limitless opportunities for building functional nanostructures. This progress report discusses the natural organization of DNA into chiral structures and recent advances in creating synthetic chiral systems using DNA as a building material. How nucleic acid chirality naturally comes into play in a diverse array of situations is considered first, at length scales ranging from an individual nucleotide to entire chromosomes. Thereafter, chiral liquid crystal phases formed by dense DNA mixtures are discussed, including the ongoing efforts to understand their origins. The report then summarizes recent efforts directed toward building chiral structures, and other structures of complex topology, using the principle of DNA self-assembly. Discussed last are existing and proposed functional man-made nanostructures designed to either probe or harness DNA{\textquoteright}s chirality, from plasmonics and spintronics to\ biosensing.

}, doi = {10.1002/advs.202003113}, url = {https://doi.org/10.1002/advs.202003113}, author = {D Winogradoff and Pin-Yi Li and H Joshi and L Quednau and C Maffeo and Aleksei Aksimentiev} } @article {367, title = {Netting proteins, one at a time}, journal = {Nature Nanotechnology}, volume = {16}, year = {2021}, month = {01/2021}, pages = {1178 - 1179}, abstract = {

Ever tried catching fish by hand? Fast and slippery, the fish easily escapes {\textemdash}unless, of course, the hand is holding a fishing net. Catching single proteins has been an outstanding technological challenge because of their small size (about 10 nm) and the stochastic Brownian forces that dominate protein motion at the nanoscale. Methods have been devised to adsorb proteins onto surfaces or to target specific proteins for analysis using antibodies, but such approaches typically produce permanent attachment of the proteins to their macroscopic handles. Writing in Nature Nanotechnology, Schmid and co-workers report a catch-and-release nanopore trap capable of holding single proteins for hours, giving ample time for single-molecule characterization of the protein shape.

}, issn = {1748-3387}, doi = {10.1038/s41565-021-00968-3}, url = {https://www.nature.com/articles/s41565-021-00968-3https://www.nature.com/articles/s41565-021-00968-3.pdfhttps://www.nature.com/articles/s41565-021-00968-3.pdfhttps://www.nature.com/articles/s41565-021-00968-3}, author = {Aleksei Aksimentiev} } @article {338, title = {High-Fidelity Capture, Threading, and Infinite-Depth Sequencing of Single DNA Molecules with a Double-Nanopore System}, journal = {ACS Nano}, volume = {14}, year = {2020}, month = {11/2020}, pages = {15566-15576}, chapter = {15566}, abstract = {

Nanopore sequencing of nucleic acids has an illustrious history of innovations that eventually made commercial nanopore sequencing possible. Nevertheless, the present nanopore sequencing technology leaves much room for improvement, especially with respect to accuracy of raw reads and detection of nucleotide modifications. Double-nanopore sequencing{\textemdash}an approach where a DNA molecule is pulled back and forth by a tug-of-war of two nanopores{\textemdash}could potentially improve single-molecule read accuracy and modification detection by offering multiple reads of the same DNA fragment. One principle difficulty in realizing such a technology is threading single-stranded DNA through both nanopores. Here, we describe and demonstrate through simulations a nanofluidic system for loading and threading DNA strands through a double-nanopore setup with nearly 100\% fidelity. The high-efficiency loading is realized by using hourglass-shaped side channels that not only deliver the molecules to the nanopore but also retain molecules that missed the nanopore at the first passage to attempt the nanopore capture again. The second nanopore capture is facilitated by an orthogonal microfluidic flow that unravels the molecule captured by the first nanopore and delivers it to the capture volume of the second nanopore. We demonstrate the potential utility of our double-nanopore system for DNA sequencing by simulating repeat back-and-forth motion{\textemdash}flossing{\textemdash}of a DNA strand through the double-nanopore system. We show that repeat exposure of the same DNA fragments to the nanopore sensing volume considerably increases accuracy of the nucleotide sequence determination and that correlated displacement of ssDNA through the two nanopores may facilitate recognition of homopolymer fragments.

}, keywords = {Gene delivery, Genetics, Molecules, Monomers, Nanopores}, doi = {10.1021/acsnano.0c06191}, url = {https://doi.org/10.1021/acsnano.0c06191}, author = {Choudhary, Adnan and Joshi, Himanshu and Chou, Han-Yi and Sarthak, Kumar and Wilson, James and Maffeo, Christopher and Aleksei Aksimentiev} } @article {334, title = {Molecular dynamics simulations of DNA--DNA and DNA--protein interactions}, journal = {Current Opinion in Structural Biology}, volume = {64}, year = {2020}, month = {10/2020}, pages = {88--96}, chapter = {88}, abstract = {

The all-atom molecular dynamics method can characterize the molecular-level interactions in DNA and DNA--protein systems with unprecedented resolution. Recent advances in computational technologies have allowed the method to reveal the unbiased behavior of such systems at the microseconds time scale, whereas enhanced sampling approaches have matured enough to characterize the interaction free energy with quantitative precision. Here, we describe recent progress toward increasing the realism of such simulations by refining the accuracy of the molecular dynamics force field, and we highlight recent application of the method to systems of outstanding biological interest.

}, doi = {https://doi.org/10.1016/j.sbi.2020.06.007}, url = {https://doi.org/10.1016/j.sbi.2020.06.007}, author = {Jejoong Yoo and David Winogradoff and Aleksei Aksimentiev} } @article {335, title = {Scalable molecular dynamics on CPU and GPU architectures with NAMD}, journal = {J. Chem. Phys.}, volume = {153}, year = {2020}, month = {07/2020}, chapter = {044130}, abstract = {

NAMD is a molecular dynamics program designed for high-performance simulations of very large biological objects on CPU- and GPU- based architectures. NAMD offers scalable performance on petascale parallel supercomputers consisting of hundreds of thousands of cores, as well as on inexpensive commodity clusters commonly found in academic environments. It is written in C++ and leans on Charm++ parallel objects for optimal performance on low-latency architectures. NAMD is a versatile, multipurpose code that gathers state-of-the-art algorithms to carry out simulations in apt thermodynamic ensembles, using the widely popular CHARMM, AMBER, OPLS, and GROMOS biomolec- ular force fields. Here, we review the main features of NAMD that allow both equilibrium and enhanced-sampling molecular dynamics\ simulations with numerical efficiency. We describe the underlying concepts utilized by NAMD and their implementation, most notably for handling long-range electrostatics; controlling the temperature, pressure, and pH; applying external potentials on tailored grids; leveraging massively parallel resources in multiple-copy simulations; and hybrid quantum-mechanical/molecular-mechanical descriptions. We detail the variety of options offered by NAMD for enhanced-sampling simulations aimed at determining free-energy differences of either alchem- ical or geometrical transformations and outline their applicability to specific problems. Last, we discuss the roadmap for the development of NAMD and our current efforts toward achieving optimal performance on GPU-based architectures, for pushing back the limitations that have prevented biologically realistic billion-atom objects to be fruitfully simulated, and for making large-scale simulations less expensive and easier to set up, run, and analyze. NAMD is distributed free of charge with its source code at www.ks.uiuc.edu.

}, doi = {10.1063/5.0014475}, author = {James C. Phillips and David J. Hardy and Julio D. C. Maia and John E. Stone and Jo{\~a}o V. Ribeiro and Rafael C. Bernardi and Ronak Buch and Giacomo Fiorin and J{\'e}r{\^o}me H{\'e}nin and Wei Jiang and Ryan McGreevy and Marcelo C. R. Melo and Brian K. Radak and Robert D. Skeel and Abhishek Singharoy and Yi Wang and Beno{\^\i}t Roux and Aleksei Aksimentiev and Zaida Luthey-Schulten and Laxmikant V. Kal{\'e} and Klaus Schulten and Christophe Chipot and Emad Tajkhorshid} } @article {336, title = {Molecular Transport across the Ionic Liquid-Aqueous Electrolyte Interface in a MoS2 Nanopore}, journal = {ACS Appl. Mater. Interfaces}, volume = {12}, year = {2020}, month = {05/2020}, pages = {26624 - 26634}, chapter = {26624}, abstract = {

Nanopore sequencing of DNA has been enabled by the use of a biological enzyme to thread DNA through an engineered biological nanopore while recording the ionic current flowing through the nanopore. Efforts to realize a similar concept using a solid-state nanopore have been met with several technical challenges, one of which is the high speed of DNA translocation and the other the low ionic current contrast among individual nucleotides. A promising avenue to addressing both problems is using an ionic liquid to slow DNA translocation and a tiny nanopore in the MoS2 membrane to distinguish individual nucleotides. The physical mechanisms enabling these technical advances have remained elusive. Here, we characterize the ion and DNA transport through the ionic liquid/aqueous electrolyte interface, with and without a MoS2 nanopore, using the all-atom molecular dynamics method. We find that the partial miscibility of the ionic liquid and the aqueous electrolyte considerably alters the physics of the nanopore translocation process. Thus, the interface of the two phases generates a contact potential of 600 mV, the ionic current is dominated by the motion of ionic liquid molecules through the aqueous solution phase, and the DNA nucleotides exhibit preferential partitioning into the aqueous electrolyte, which leads to spontaneous transport of DNA polymers from the ionic liquid to the aqueous solution compartment in the absence of external voltage bias. The complex physics of the two-phase nanopore system offers a multitude of opportunities for extending the functionality of nanopore-sensing platforms.

}, doi = {10.1021/acsami.0c04523}, author = {Manish Shankla and Aleksei Aksimentiev} } @article {331, title = {Tailoring interleaflet lipid transfer with a DNA-based synthetic enzyme}, journal = {Nano Letters}, volume = {20}, year = {2020}, month = {05/2020}, pages = {4306-4311}, chapter = {4306}, abstract = {

Lipid membranes, enveloping all living systems, are of crucial importance, and control over their structure and composition is a highly desirable functionality of artificial structures. However, the rational design of protein-inspired systems is still challenging. Here we have developed a highly functional nucleic acid construct that self-assembles and inserts into membranes, enabling lipid transfer between inner and outer leaflets. By designing the structure to account for interactions between the DNA, its hydrophobic modifications, and the lipids, we successfully exerted control over the rate of interleaflet lipid transfer induced by our DNA-based enzyme. Furthermore, we can regulate the level of lipid transfer by altering the concentration of divalent ions, similar to stimuli-responsive lipid-flipping proteins.

}, keywords = {DNA Nanotechnology, dodecane, lipid flipping, lipid membranes, Molecular dynamics, synthetic ion channel}, doi = {10.1021/acs.nanolett.0c00990}, author = {Sobota, Diana and Joshi, Himanshu and Ohmann, Alexander and Aleksei Aksimentiev and Keyser, Ulrich F} } @article {337, title = {Single-Protein Collapse Determines Phase Equilibria of a Biological Condensate}, journal = {J. Phys. Chem. Lett. }, volume = {11}, year = {2020}, month = {05/2020}, pages = {4923 - 4929}, chapter = {4923}, abstract = {

Recent advances in microscopy of living cells have established membraneless organelles as critical elements of diverse
biological processes. The body of experimental work suggests that formation of such organelles is driven by liquid-liquid phase separation, a physical process that has been studied extensively for both simple liquids and mixtures of polymers. Here, we combine molecular dynamics simulations with polymer theory to show that the thermodynamic behavior of one particular biomolecular condensate--fused in sarcoma (FUS)--can be quantitatively accounted for at the level of the chain collapse theory. First, we show that a particle-based molecular dynamics model can reproduce known phase separation properties of a FUS condensate, including its critical concentration and susceptibility to mutations. Next, we obtain a polymer physics representation of a FUS condensate by examining the behavior of a single FUS protein as a function of temperature. We use the chain collapse theory to determine the thermodynamic properties of the condensate and to characterize changes in the single-chain conformation at the onset of phase separation. Altogether, our findings suggest that the phase behavior of FUS condensates can be explained by the properties of individual FUS proteins and that the change in the FUS conformation is the main force driving for the phase separation

}, author = {Han-Yi Chou and Aleksei Aksimentiev} } @article {324, title = {Protein unfolding by SDS: the microscopic mechanisms and the properties of the SDS-protein assembly}, journal = {Nanoscale}, volume = {12}, year = {2020}, month = {02/2020}, pages = {5422--5434}, chapter = {5422}, abstract = {

The effects of detergent sodium dodecyl sulfate (SDS) on protein structure and dynamics are fundamental to the most common laboratory technique used to separate proteins and determine their molecular weights: polyacrylamide gel electrophoresis. However, the mechanism by which SDS induces protein unfolding and the microstructure of protein{\textendash}SDS complexes remain largely unknown. Here, we report a detailed account of SDS-induced unfolding of two proteins{\textemdash}I27 domain of titin and β-amylase{\textemdash}obtained through all-atom molecular dynamics simulations. Both proteins were found to spontaneously unfold in the presence of SDS at boiling water temperature on the time scale of several microseconds. The protein unfolding was found to occur via two distinct mechanisms in which specific interactions of individual SDS molecules disrupt the protein{\textquoteright}s secondary structure. In the final state of the unfolding process, the proteins are found to wrap around SDS micelles in a fluid necklace-and-beads configuration, where the number and location of bound micelles changes dynamically. The global conformation of the protein was found to correlate with the number of SDS micelles bound to it, whereas the number of SDS molecules directly bound to the protein was found to define the relaxation time scale of the unfolded protein. Our microscopic characterization of SDS{\textendash}protein interactions sets the stage for future refinement of SDS{\textendash}enabled protein characterization methods, including protein fingerprinting and sequencing using a solid-state nanopore.

}, doi = {10.1039/c9nr09135a}, author = {David Winogradoff and Shalini John and Aleksei Aksimentiev} } @article {317, title = {Electrical recognition of the twenty proteinogenic amino acids using an aerolysin nanopore}, journal = {Nature Biotechnology}, volume = {38}, year = {2020}, month = {02/2020}, pages = {176-181}, chapter = {176}, abstract = {

Efforts to sequence single protein molecules in nanopores have been hampered by the lack of techniques with sufficient sensitivity to discern the subtle molecular differences among all twenty amino acids. Here we report ionic current detection of all twenty proteinogenic amino acids in an aerolysin nanopore with the help of a short polycationic carrier. Application of molecular dynamics simulations revealed that the aerolysin nanopore has a built-in single-molecule trap that fully confines a polycationic carrier-bound amino acid inside the sensing region of the aerolysin. This structural feature means that each amino acid spends sufficient time in the pore for sensitive measurement of the excluded volume of the amino acid. We show that distinct current blockades in wild-type aerolysin can be used to identify 13 of the 20 natural amino acids. Furthermore, we show that chemical modifications, instrumentation advances and nanopore engineering offer a route toward identification of the remaining seven amino acids. These findings may pave the way to nanopore protein sequencing.

Research Highlights

1.\ Tang, Lei. "Sensing proteinogenic amino acids." Nature Methods 17(2):126 (2020) DOI:\ 10.1038/s41592-020-0741-z

2.\ Howorka, Stefan, and Zuzanna S. Siwy. "Reading amino acids in a nanopore." Nature Biotechnology 38(2):159 (2020) DOI:\ 10.1038/s41587-019-0401-y

3.\ Nanopores can identify the amino acids in proteins, the first step to sequencing, Highlight by Illinois news bureau.\ \ 

}, isbn = {1546-1696}, doi = {10.1038/s41587-019-0345-2}, url = {https://doi.org/10.1038/s41587-019-0345-2}, author = {Ouldali, Hadjer and Sarthak, Kumar and Ensslen, Tobias and Piguet, Fabien and Manivet, Philippe and Pelta, Juan and Behrends, Jan C. and Aleksei Aksimentiev and Oukhaled, Abdelghani} } @article {320, title = {Polyhydrazide-based organic nanotubes as extremely efficient and highly selective artificial iodide channels}, journal = {Angewandte Chemie International Edition}, volume = {12}, year = {2020}, month = {02/2020}, pages = {4806-4813}, chapter = {4806}, abstract = {

We report herein a series of pore-containing polymeric nanotubes based on an H-bonded hydrazide backbone. Nanotubes of suitable lengths, possessing a hollow cavity of ~ 6.5 {\r A} in diameter, are found to mediate highly efficient transport of diverse types of anions, rather than cations, across the lipid membrane. Polymer channel 1a, having an averaged molecular weight of 18.2 KDa and 3.6 nm in helical height, exhibits the highest anion transport activities with iodide (EC50 = 0.042 micromolar\ or 0.028 mol \% relative to lipid) being transported 10 times more efficiently than chlorides (EC50 = 0.47 micromolar). Notably, even in the cholesterol-rich environment, iodide transport activity still remains high with EC50\ \ of 0.37 micromolar. Molecular dynamics simulation studies confirm that the channel is highly selective for anions and that such anion selectivity arises from a positive electrostatic potential of the central lumen rendered by the interior-pointing methyl groups.

}, doi = { https://doi.org/10.1002/anie.201916287}, author = {Roy, Arundhati and Joshi, Himanshu and Ye, Ruijuan and Shen, Jie and Chen, Feng and Aleksei Aksimentiev and Zeng, Huaqiang} } @article {319, title = {Rosette Nanotube Porins as Ion Selective Transporters and Single-Molecule Sensors}, journal = {Journal of the American Chemical Society}, volume = {142}, year = {2020}, month = {01/2020}, pages = {1680-1685}, chapter = {1680}, abstract = {

Rosette nanotubes (RNTs) are a class of materials formed by molecular self-assembly of a fused guanine-cytosine base (G^C base). An important feature of these self-assembled nanotubes is their precise atomic structure, intriguing for rational design and optimization as synthetic transmembrane porins. Here, we present experimental observations of ion transport across 1.1 nm inner diameter RNT porins (RNTPs) of various lengths in the range 5-200 nm. In a typical experiment, custom lipophilic RNTPs were first inserted into lipid vesicles; the vesicles then spontaneously fused with a planar lipid bilayer, which produced stepwise increases of ion current across the bilayer. Our measurements in 1 M KCl solution indicate ion transport rates of ~50 ions s-1 V-1 m, which for short channels amounts to conductance values of\  ~1 nS, commensurate with naturally occurring toxin channels such as α-hemolysin. Measurements of interaction times of α-cyclodextrin with RNTPs reveal two distinct unbinding time scales, which suggest that interactions of either face of α-cyclodextrin with the RNTP face are differentiable, backed with all-atom molecular dynamics simulations. Our results highlight the potential of RNTPs as self-assembled nonproteinaceous single-molecule sensors and selective nanofilters with tunable functionality through chemistry.

}, doi = {https://doi.org/10.1021/jacs.9b10993}, author = {Tripathi, Prabhat and Shuai, Liang and Joshi, Himanshu and Yamazaki, Hirohito and Fowle, William H and Aleksei Aksimentiev and Fenniri, Hicham and Wanunu, Meni} } @article {318, title = {Artificial Water Channels Enable Fast and Selective Water Permeation Through Water-wire Networks}, journal = {Nature Nanotechnology.}, volume = {15,}, year = {2020}, month = {01/2020}, pages = {73-79}, chapter = {73}, abstract = {

Artificial water channels are synthetic molecules that aim to mimic the structural and functional features of biological water channels (aquaporins). Here we report on a cluster-forming organic nanoarchitecture, peptide-appended hybrid[4]arene (PAH[4]), as a new class of artificial water channels. Fluorescence experiments and simulations demonstrated that PAH[4]s can form, through lateral diffusion, clusters in lipid membranes that provide synergistic membrane-spanning paths for rapid and selective water permeation through water-wire networks. Quantitative transport studies revealed that PAH[4]s can transport \>109\ water molecules per second per molecule, which is comparable to aquaporin water channels. The performance of these channels exceeds the upper bound limit of current desalination membranes by a factor of ~104, as illustrated by the water/NaCl permeability{\textendash}selectivity trade-off curve. PAH[4]{\textquoteright}s unique properties of a high water/solute permselectivity via cooperative water-wire formation could usher in an alternative design paradigm for permeable membrane materials in separations, energy production, and barrier applications.

}, doi = {https://doi.org/10.1038/s41565-019-0586-8}, author = {Woochul Song and Himanshu Joshi and Ratul Chowdhury and Joseph S. Najem and Yue-xiao Shen and Chao Lang and Codey B. Henderson and Yu-Ming Tu and Megan Farell and Megan E. Pitz and Costas D. Maranas and Paul S. Cremer and Robert J. Hickey and Stephen A. Sarles and Jun-li Hou and Aleksei Aksimentiev and Manish Kumar} } @article {325, title = {MrDNA: a multi-resolution model for predicting the structure and dynamics of DNA systems}, journal = {Nucleic Acids Research}, year = {2020}, abstract = {

Although the field of structural DNA nanotechnology has been advancing with an astonishing pace, de novo design of complex 3D nanostructures and functional devices remains a laborious and time-consuming process. One reason for that is the need for multiple cycles of experimental characterization to elucidate the effect of design choices on the actual shape and function of the self-assembled objects. Here, we demonstrate a multi-resolution simulation framework, mrdna, that, in 30 min\ or less, can produce an atomistic-resolution structure of a self-assembled DNA nanosystem. We demonstrate fidelity of our mrdna framework through direct comparison of the simulation results with the results of cryo-electron microscopy (cryo-EM) reconstruction of multiple 3D DNA origami objects. Furthermore, we show that our approach can characterize an ensemble of conformations adopted by dynamic DNA nanostructures, the equilibrium structure and dynamics of DNA objects constructed using off-lattice self-assembly principles, i.e.\ wireframe DNA objects, and to study the properties of DNA objects under a variety of environmental conditions, such as applied electric field. Implemented as an open source Python package, our framework can be extended by the community and integrated with DNA design and molecular graphics tools.

}, doi = {10.1093/nar/gkaa200}, url = {https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkaa200/5814051}, author = {Maffeo, Christopher and Aleksei Aksimentiev} } @article {308, title = {Atoms to Phenotypes: Molecular Design Principles of Cellular Energy Metabolism}, journal = {Cell}, volume = {179}, year = {2019}, month = {11/2019}, pages = {1098 - 1111.e23}, abstract = {

We report a 100-million atom-scale model of an entire cell organelle, a photosynthetic chromatophore vesicle from a purple bacterium, that reveals the cascade of energy conversion steps culminating in the generation of ATP from sunlight. Molecular dynamics simulations of this vesicle elucidate how the integral membrane complexes influence local curvature to tune photoexcitation of pigments. Brownian dynamics of small molecules within the chromatophore probe the mechanisms of directional charge transport under various pH and salinity conditions. Reproducing phenotypic properties from atomistic details, a kinetic model evinces that low-light adaptations of the bacterium emerge as a spontaneous outcome of optimizing the balance between the chromatophore{\textquoteright}s structural integrity and robust energy conversion. Parallels are drawn with the more universal\ mitochondrial bioenergetic machinery, from whence molecular-scale insights into the mechanism of cellular aging are inferred. Together, our integrative method and spectroscopic experiments pave the way to first-principles modeling of whole living cells.

}, keywords = {bioenergetics, biological membranes, charge transport, chromatophore, integrative model, MD, mitochondria, Molecular Dynamics Simulation, optical spectroscopy, photosynthesis}, issn = {0092-8674}, doi = {10.1016/j.cell.2019.10.021}, url = {http://www.sciencedirect.com/science/article/pii/S0092867419311717}, author = {Abhishek Singharoy and Christopher Maffeo and Karelia H. Delgado-Magnero and David J.K. Swainsbury and Melih Sener and Ulrich Kleinekath{\"o}fer and John W. Vant and Jonathan Nguyen and Andrew Hitchcock and Barry Isralewitz and Ivan Teo and Danielle E. Chandler and John E. Stone and James C. Phillips and Taras V. Pogorelov and M. Ilaria Mallus and Christophe Chipot and Zaida Luthey-Schulten and D. Peter Tieleman and C. Neil Hunter and Emad Tajkhorshid and Aleksei Aksimentiev and Klaus Schulten} } @article {306, title = {Controlling aggregation of cholesterol-modified DNA nanostructures}, journal = {Nucleic Acid Research }, volume = {47}, year = {2019}, month = {11/2019}, pages = {11441-11451}, chapter = {11441}, abstract = {

DNA nanotechnology allows for the design of programmable DNA-built nanodevices which controllably interact with biological membranes and even mimic the function of natural membrane proteins. Hydrophobic modifications, covalently linked to the DNA, are essential for targeted interfacing of DNA nanostructures with lipid membranes. However, these hydrophobic tags typically induce undesired aggregation eliminating structural control, the primary advantage of DNA nanotechnology. Here, we study the aggregation of cholesterol-modified DNA nanostructures using a combined approach of non-denaturing polyacrylamide gel electrophoresis, dynamic light scattering, confocal microscopy and atomistic molecular dynamics simulations. We show that the aggregation of cholesterol-tagged ssDNA is sequence-dependent, while for assembled DNA constructs, the number and position of the cholesterol tags are the dominating factors. Molecular dynamics simulations of cholesterol-modified ssDNA reveal that the nucleotides wrap around the hydrophobic moiety, shielding it from the environment. Utilizing this behavior, we demonstrate experimentally that the aggregation of cholesterol-modified DNA nanostructures can be controlled by the length of ssDNA overhangs positioned adjacent to the cholesterol. Our easy-to-implement method for tuning cholesterol-mediated aggregation allows for increased control and a closer structure{\textendash}function relationship of membrane-interfacing DNA constructs - a fundamental prerequisite for employing DNA nanodevices in research and biomedicine.

}, keywords = {cholesterol-modified DNA nanostructures,, DNA Nanotechnology}, doi = {https://doi.org/10.1093/nar/gkz914}, url = {https://doi.org/10.1093/nar/gkz914}, author = {Ohmann, Alexander and G{\"o}pfrich, Kerstin and Joshi, Himanshu and Thompson, Rebecca F and Sobota, Diana and Ranson, Neil A and Aleksei Aksimentiev and Keyser, Ulrich F} } @article {294, title = {Molecular Mechanism of Spontaneous Nucleosome Unraveling}, journal = {Journal of Molecular Biology}, volume = {431}, year = {2019}, month = {11/2018}, pages = {323--335}, abstract = {

Meters of DNA wrap around histone proteins to form nucleosomes and fit inside the micron-diameter nucleus. For the genetic information encoded in the DNA to become available for transcription, replication and repair, the DNA--histone assembly must be disrupted. Experiment has indicated that the outer stretches of nucleosomal DNA "breathe"\ by spontaneously detaching from and reattaching to the histone core. Here, we report direct observation of spontaneous DNA breathing in atomistic molecular dynamics simulations, detailing a microscopic mechanism of the DNA breathing process. According to our simulations, the outer stretches of nucleosomal DNA detach in discrete steps involving five or ten base pairs, with the detachment process being orchestrated by the motion of several conserved histone residues. The inner stretches of nucleosomal DNA are found to be more stably associated with the histone core by more abundant nonspecific DNA--protein contacts, providing a microscopic interpretation of nucleosome unraveling experiments. The CG content of nucleosomal DNA is found to anticorrelate with the extent of unwrapping, supporting the possibility that AT-rich segments may signal the start of transcription by forming less stable nucleosomes.

}, doi = {10.1016/j.jmb.2018.11.013}, author = {David Winogradoff and Aleksei Aksimentiev} } @article {307, title = {Single molecule analysis of structural fluctuations in DNA nanostructures}, journal = {Nanoscale}, volume = {11}, year = {2019}, month = {10/2019}, pages = {18475 - 18482}, abstract = {

DNA origami is an excellent tool for building complex artificial nanostructures. Functionalization of these structures provides the possibility of precise organization of matter at the nanoscale. In practice, efforts in this endeavour can be impeded by electrostatic repulsion or other dynamics at the molecular scale, resulting in uncompliant local structures. Using single molecule FRET microscopy combined with coarse-grained Brownian dynamics simulations, we investigated here the local structure around the lid of a DNA origami box, which can be opened by specific DNA keys. We found that FRET signals for the closed box depend on buffer ion concentrations and small changes to the DNA structure design. Simulations provided a view of the global and local structure and showed that the distance between the box wall and lid undergoes fluctuations. These results provide methods to vizualise and improve the local structure of three-dimensional DNA origami assemblies and offer guidance for exercising control over placement of chemical groups and ligands.

}, issn = {2040-3364}, doi = {10.1039/C9NR03826D}, url = {http://xlink.rsc.org/?DOI=C9NR03826Dhttp://pubs.rsc.org/en/content/articlepdf/2019/NR/C9NR03826Dhttp://pubs.rsc.org/en/content/articlepdf/2019/NR/C9NR03826D}, author = {Jepsen, Mette D. E. and S{\o}rensen, Rasmus Sch{\o}ler and Maffeo, Christopher and Aleksei Aksimentiev and Kjems, J{\o}rgen and Birkedal, Victoria} } @article {302, title = {Step-defect guided delivery of DNA to a graphene nanopore}, journal = {Nature Nanotechnology}, year = {2019}, month = {08/2019}, abstract = {

Precision placement and transport of biomolecules are critical to many single-molecule manipulation and detection methods. One such method is nanopore sequencing, in which the delivery of biomolecules towards a nanopore controls the method{\textquoteright}s throughput. Using all-atom molecular dynamics, here we show that the precision transport of biomolecules can be realized by utilizing ubiquitous features of graphene surface-step defects that separate multilayer domains. Subject to an external force, we found that adsorbed DNA moved much faster down a step defect than up, and even faster along the defect edge, regardless of whether the motion was produced by a mechanical force or a solvent flow. We utilized this direction dependency to demonstrate a mechanical analogue of an electric diode and a system for delivering DNA molecules to a nanopore. The defect-guided delivery principle can be used for the separation, concentration and storage of scarce biomolecular species, on-demand chemical reactions and nanopore sensing.

}, isbn = {1748-3395}, doi = {10.1038/s41565-019-0514-y}, url = {https://doi.org/10.1038/s41565-019-0514-y}, author = {Shankla, Manish and Aleksei Aksimentiev} } @article {297, title = {Effect of temperature and hydrophilic ratio on the structure of poly(N-vinylcaprolactam)-block-poly(dimethylsiloxane)-block-poly(N-vinylcaprolactam) polymersomes}, journal = {ACS Applied Polymer Materials}, volume = {1}, year = {2019}, month = {04/2019}, pages = {722--736}, chapter = {722}, abstract = {

Nanosized polymeric vesicles (polymersomes) assembled from ABA triblock copolymers of poly(N-vinylcaprolactam)-poly(dimethylsiloxane)-poly(N-vinylcaprolactam) (PVCL-PDMS-PVCL) are a promising platform for biomedical applications, as the temperature-responsiveness of the PVCL blocks enables reversible vesicle shrinkage and permeability of the polymersome shell at elevated temperatures. Herein, we explore the effects of molecular weight, polymer block weight ratios, and temperature on the structure of these polymersomes via electron microscopy, dynamic light scattering, small angle neutron scattering (SANS), and all-atom molecular dynamic methods. We show that the shell structure and overall size of the polymersome can be tuned by varying the hydrophilic (PVCL) weight fraction of the polymer: at room temperature, polymers of smaller hydrophilic ratios form larger vesicles that have thinner shells, whereas polymers with higher PVCL content exhibit interchain aggregation of PVCL blocks within the polymersome shell above 50 {\textdegree}C. Model fitting and model-free analysis of the SANS data reveals that increasing the mass ratio of PVCL to the total copolymer weight from 0.3 to 0.56 reduces the temperature-induced change in vesicle diameter by a factor of 3 while simultaneously increasing the change in shell thickness by a factor of 1.5. Finally, by analysis of the shell structures and overall size of polymersomes with various PVCL weight ratios and those without temperature-dependent polymer components, we bring into focus the mechanism of temperature-triggered drug release reported in a previous study. This work provides new fundamental perspectives on temperature-responsive polymersomes and elucidates important structure-property relationships of their constituent polymers.

}, doi = {10.1021/acsapm.8b00259}, url = {https://pubs.acs.org/doi/pdf/10.1021/acsapm.8b00259}, author = {Yiming Yang and Aaron Alford and Kozlovskaya, Veronika and Zhao, Shidi and Joshi, Himanshu and Kim, Eunjung and Qian, Shuo and Urban, Volker and Cropek, Donald and Aleksei Aksimentiev and Kharlampieva, Eugenia} } @article {300, title = {Characterization of the Lipid Structure and Fluidity of Lipid Membranes on Epitaxial Graphene and Their Correlation to Graphene Features}, journal = {Langmuir}, volume = {35}, year = {2019}, month = {03/2019}, pages = {4726-4735}, abstract = {

Graphene has been recognized as an enhanced platform for biosensors because of its high electron mobility. To integrate active membrane proteins into graphene-based materials for such applications, graphene{\textquoteright}s surface must be functionalized with lipids to mimic the biological environment of these proteins. Several studies have examined supported lipids on various types of graphene and obtained conflicting results for the lipid structure. Here, we present a correlative characterization technique based on fluorescence measurements in a Raman spectroscopy setup to study the lipid structure and dynamics on epitaxial graphene. Compared to other graphene variations, epitaxial graphene is grown on a substrate more conducive to production of electronics and offers unique topographic features. On the basis of experimental and computational results, we propose that a lipid sesquilayer (1.5 bilayer) forms on epitaxial graphene and demonstrate that the distinct surface features of epitaxial graphene affect the structure and diffusion of supported lipids.

}, doi = {10.1021/acs.langmuir.9b00164}, url = {https://doi.org/10.1021/acs.langmuir.9b00164}, author = {Farell, Megan and Wetherington, Maxwell and Shankla, Manish and Chae, Inseok and Subramanian, Shruti and Kim, Seong H. and Aleksei Aksimentiev and Robinson, Joshua and Kumar, Manish} } @article {298, title = {Rapid and Accurate Determination of Nanopore Ionic Current Using a Steric Exclusion Model}, journal = {ACS sensors}, volume = {4}, year = {2019}, month = {03/2019}, pages = {634--644}, abstract = {

Nanopore sensing has emerged as a versatile approach to detection and identification of biomolecules. Presently, researchers rely on experience and intuition for choosing or modifying the nanopores to detect a target analyte. The field would greatly benefit from a computational method that could relate the atomic-scale geometry of the nanopores and analytes to the blockade nanopore currents they produce. Existing computational methods are either computationally too expensive to be used routinely in experimental laboratories or not sensitive enough to account for the atomic structure of the pore and the analytes. Here, we demonstrate a robust and inexpensive computational approach{\textemdash}the steric exclusion model (SEM) of nanopore conductance{\textemdash}that is orders of magnitude more efficient than all-atom MD and yet is sensitive enough to account for the atomic structure of the nanopore and the analyte. The method combines the computational efficiency of a finite element solver with the atomic precision of a nanopore conductance map to yield unprecedented speed and accuracy of ionic current prediction. We validate our SEM approach through comparison with the current blockades computed using the all-atom molecular dynamics method for a range of proteins confined to a solid-state nanopore, biological channels embedded in a lipid bilayer membranes, and blockade currents produced by DNA homopolymers in MspA. We illustrate potential applications of SEM by computing blockade currents produced by nucleosome proteins in a solid-state nanopore, individual amino acids in MspA, and by testing the effect of point mutations on amino acid distinguishability. We expect our SEM approach to become an integral part of future development of the nanopore sensing field.

}, doi = {10.1021/acssensors.8b01375}, url = {https://pubs.acs.org/doi/full/10.1021/acssensors.8b01375}, author = {Wilson, James and Sarthak, Kumar and Si, Wei and Gao, Luyu and Aleksei Aksimentiev} } @article {295, title = {Electro-Mechanical Conductance Modulation of a Nanopore Using a Removable Gate}, journal = {ACS Nano}, volume = {13}, year = {2019}, month = {02/2019}, pages = {2398--2409}, chapter = {2398}, abstract = {

Ion channels form the basis of information processing in livings cells by facilitating exchange of electrical signals across and along cellular membranes. Applying the same principles to man-made systems requires development of synthetic ion channels that can alter their conductance in response to a variety of external manipulations. By combining single-molecule electrical recordings with all-atom molecular dynamics simulations, we here demonstrate a new hybrid nanopore system that allows for both a stepwise change of its conductance and a non-linear current-voltage dependence. The conductance modulation is realized by using a short flexible peptide gate that carries opposite electric charge at its ends. We show that a constant transmembrane bias can position, and in a later stage remove, the peptide gate right at the most sensitive sensing region of a biological nanopore FraC, thus partially blocking its channel and producing a stepwise change in the conductance. Increasing or decreasing the bias while having the peptide gate trapped in the pore stretches or compresses the peptide within the nanopore, thus modulating its conductance in a non-linear but reproducible manner. We envision a range of applications of this removable-gate nanopore system, e.g. from an element of biological computing circuits to a test bed for probing the elasticity of intrinsically disordered proteins.

}, doi = {10.1021/acsnano.8b09266}, url = {https://doi.org/10.1021/acsnano.8b09266}, author = {Shidi Zhao and Restrepo-Perez, Laura and Maglia, Giovanni and Misha Soskine and Chirlmin Joo and Cees Dekker and Aleksei Aksimentiev} } @article {296, title = {Molecular Mechanisms of DNA Replication and Repair Machinery: Insights from Microscopic Simulations}, journal = {Advanced Theory and Simulations}, volume = {2}, year = {2019}, month = {02/2019}, pages = {1800191}, abstract = {

Reproduction, the hallmark of biological activity, requires making an accurate copy of the genetic material to allow the progeny to inherit parental traits. In all living cells, the process of DNA replication is carried out by a concerted action of multiple protein species forming a loose protein{\textendash}nucleic acid complex, the replisome. Proofreading and error correction generally accompany replication but also occur independently, safeguarding genetic information through all phases of the cell cycle. Advances in biochemical characterization of intracellular processes, proteomics, and the advent of single-molecule biophysics have brought about a treasure trove of information awaiting to be assembled into an accurate mechanistic model of the DNA replication process. This review describes recent efforts to model elements of DNA replication and repair processes using computer simulations, an approach that has gained immense popularity in many areas of molecular biophysics but has yet to become mainstream in the DNA metabolism community. It highlights the use of diverse computational methods to address specific problems of the fields and discusses unexplored possibilities that lie ahead for the computational approaches in these areas.

}, keywords = {coarse-grained simulation, DNA damage, DNA repair, homologous recombination, Molecular dynamics, nucleic acids, QM/MM, replisome}, doi = {10.1002/adts.201800191}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/adts.201800191}, author = {Maffeo, Christopher and Chou, Han-Yi and Aleksei Aksimentiev} } @article {293, title = {Dynamic Interactions between Lipid-Tethered DNA and Phospholipid Membranes}, journal = {Langmuir}, volume = {34}, year = {2018}, month = {11/2018}, pages = {15084-15092}, chapter = {15084}, abstract = {

Lipid-anchored DNA can attach functional cargo to bilayer membranes in DNA nanotechnology, synthetic biology, and cell biology research. To optimize DNA anchoring, an understanding of DNA-membrane interactions in terms of binding strength, extent, and structural dynamics is required. Here we use experiments and molecular dynamics (MD) simulations to determine how the membrane binding of cholesterol-modified DNA depends on electrostatic and steric factors involving the lipid headgroup charge, duplexed or single-stranded DNA, and the buffer composition. The experiments distinguish between free and membrane vesicle-bound DNA and thereby reveal the surface density of anchored DNA and its binding affinity, something which had previously not been known. The Kd values range from 8.5 {\textpm} 4.9 to 466 {\textpm} 134 μM whereby negatively charged headgroups led to weak binding due to the electrostatic repulsion with respect to the negatively charged DNA. Atomistic MD simulations explain the findings and elucidate the dynamic nature of anchored DNA such as the mushroom-like conformation of single-stranded DNA hovering over the bilayer surface in contrast to a straight-up conformation of double-stranded DNA. The biophysical insight into the binding strength to membranes as well as the molecular accessibility of DNA for hybridization to molecular cargo is expected to facilitate the\  creation of biomimetic DNA versions of natural membrane nanopores and cytoskeletons for research and nanobiotechnology.

}, keywords = {DNA Nanotechnology, Lipid Bilayer anchored DNA, Lipid-DNA binding affinity}, doi = {10.1021/acs.langmuir.8b02271}, url = {https://doi.org/10.1021/acs.langmuir.8b02271}, author = {Arnott, Patrick M. and Joshi, Himanshu and Aleksei Aksimentiev and Howorka, Stefan} } @article {292, title = {Sequence-Dependent DNA Condensation as a Driving Force of DNA Phase Separation}, journal = {Nucleic Acids Research}, volume = {46}, year = {2018}, month = {10/2018}, pages = {9401--9413}, abstract = {

The physical properties of DNA have been suggested to play a central role in spatio-temporal organization of eukaryotic chromosomes. Experimental correlations have been established between the local nucleotide content of DNA and the frequency of inter- and intra-chromosomal contacts but the underlying physical mechanism remains unknown. Here, we combine fluorescence resonance energy transfer (FRET) measurements, precipitation assays, and molecular dynamics simulations to characterize the effect of DNA nucleotide content, sequence, and methylation on inter-DNA association and its correlation with DNA looping. First, we show that the strength of DNA condensation mediated by poly-lysine peptides as a reduced model of histone tails depends on the DNA{\textquoteright}s global nucleotide content but also on the local nucleotide sequence, which turns out to be qualitatively same as the condensation by spermine. Next, we show that the presence and spatial arrangement of C5 methyl groups determines the strength of inter-DNA attraction, partially explaining why RNA resists condensation. Interestingly, multi-color single molecule FRET measurements reveal strong anti-correlation between DNA looping and DNA{\textendash}DNA association, suggesting that a common biophysical mechanism underlies them. We propose that the differential affinity between DNA regions of varying sequence pattern may drive the phase separation of chromatin into chromosomal subdomains.

}, doi = {10.1093/nar/gky639 }, author = {Hyunju Kang and Jejoong Yoo and Hong Soo Lee and Byeong-Kwon Sohn and Seung-Won Lee and Wenjie Ma and Jung-Min Kee and Aleksei Aksimentiev and Hajin Kim} } @article {290, title = {PoreDesigner for tuning solute selectivity in a robust and highly permeable outer membrane pore}, journal = {Nature Communications}, volume = {9}, year = {2018}, month = {09/2018}, pages = {3661}, abstract = {

Monodispersed angstrom-size pores embedded in a suitable matrix are promising for highly selective membrane-based separations. They can provide substantial energy savings in water treatment and small molecule bioseparations. Such pores present as membrane proteins (chiefly aquaporin-based) are commonplace in biological membranes but difficult to implement in synthetic industrial membranes and have modest selectivity without tunable selectivity. Here we present PoreDesigner, a design workflow to redesign the robust beta-barrel Outer Membrane Protein F as a scaffold to access three specific pore designs that exclude solutes larger than sucrose (\>360 Da), glucose (\>180 Da), and salt (\>58 Da) respectively. PoreDesigner also enables us to design any specified pore size (spanning 3{\textendash}10 {\r A}), engineer its pore profile, and chemistry. These redesigned pores may be ideal for conducting sub-nm aqueous separations with permeabilities exceeding those of classical biological water channels,\ aquaporins, by more than an order of magnitude at over 10 billion water molecules per channel per second.

}, issn = {2041-1723}, doi = {10.1038/s41467-018-06097-1}, url = {https://doi.org/10.1038/s41467-018-06097-1}, author = {Chowdhury, Ratul and Ren, Tingwei and Shankla, Manish and Decker, Karl and Grisewood, Matthew and Prabhakar, Jeevan and Baker, Carol and Golbeck, John H and Aleksei Aksimentiev and Kumar, Manish and Maranas, Costas D} } @article {291, title = {Dynamics of a Molecular Plug Docked onto a Solid-State Nanopore}, journal = {The Journal of Physical Chemistry Letters}, volume = {9}, year = {2018}, month = {08/2018}, pages = {4686-4694}, chapter = {4686}, abstract = {

Docking of a protein- DNA complex onto a nanopore can provide ample observation time, and has enabled collection of analytic applications of biological nanopores, including DNA sequencing. However, the application of the same principle to solid-state nanopores is tempered by poor understanding of the docking process. Here, we elucidate the behavior of individual protein- DNA complexes docked onto a solid-state nanopore by monitoring the nanopore ionic current. Repeat docking of monovalent streptavidin- DNA complexes is found to produce ionic current blockades that fluctuate between discrete levels. We elucidate the roles of the protein plug and the DNA tether in the docking process, finding the docking configurations to determine the multitude of the current blockade levels, whereas the frequency of the current level switching is determined by the interactions between the molecules and the solid-state membrane. Finally, we prove the feasibility of using the nanopore docking principle for single-molecule sensing using solid-state nanopores by detecting conformational changes of a tethered DNA molecule from a random coil to an i-motif state.

}, doi = {10.1021/acs.jpclett.8b01755}, author = {Xin Shi and Qiao Li and Rui Gao and Wei Si and Shao-Chuang Liu and Aleksei Aksimentiev and Yi-Tao Long} } @article {286, title = {A synthetic enzyme built from DNA flips 10$^{7}$ lipids per second in biological membranes}, journal = {Nature Communications}, volume = {9}, year = {2018}, month = {07/2018}, pages = {2426}, abstract = {

Mimicking enzyme function and increasing performance of naturally evolved proteins is one of the most challenging and intriguing aims of nanoscience. Here, we employ DNA nanotechnology to design a synthetic enzyme that substantially outperforms its biological archetypes. Consisting of only eight strands, our DNA nanostructure spontaneously inserts into biological membranes by forming a toroidal pore that connects the membrane{\textquoteright}s inner and outer leaflets. The membrane insertion catalyzes spontaneous transport of lipid molecules between the bilayer leaflets, rapidly equilibrating the lipid composition. Through a combination of microscopic simulations and fluorescence microscopy we find the lipid transport rate catalyzed by the DNA nanostructure exceeds 107 molecules per second, which is three orders of magnitude higher than the rate of lipid transport catalyzed by biological enzymes. Furthermore, we show that our DNA-based enzyme can control the composition of human cell membranes, which opens new avenues for applications of membrane-interacting DNA systems in medicine.

}, keywords = {Computational biophysics, DNA nanostructures, Membrane biophysics, Nanobiotechnology}, doi = {10.1038/s41467-018-04821-5}, url = {http://www.nature.com/articles/s41467-018-04821-5}, author = {Ohmann, Alexander and Li, Chen-Yu and Maffeo, Christopher and Al Nahas, Kareem and Baumann, Kevin N. and G{\"o}pfrich, Kerstin and Yoo, Jejoong and Keyser, Ulrich F. and Aleksei Aksimentiev} } @article {287, title = {Water-compression gating of nanopore transport}, journal = {Physical Review Letters}, volume = {120}, year = {2018}, month = {06/2018}, pages = {268101}, abstract = {

Electric field-driven motion of biomolecules is a process essential to many analytics methods, in particular, to nanopore sensing, where a transient reduction of nanopore ionic current indicates the passage of a biomolecule through the nanopore. However, before any molecule can be examined by a nanopore, the molecule must first enter the nanopore from the solution. Previously, the rate of capture by a nanopore was found to increase with the strength of the applied electric field. Here, we theoretically show that, in the case of narrow pores in graphene membranes, increasing the strength of the electric field can not only decrease the rate of capture, but also repel biomolecules from the nanopore. As the strong electric field polarizes water near and within the nanopore, the high gradient of the field also produces a strong dielectrophoretic force that compresses the water. The pressure difference caused by the sharp water density gradient produces a hydrostatic force that repels DNA or proteins from the nanopore, preventing, in certain conditions, their capture. We show that such local compression of fluid can regulate the transport of biomolecules through nanoscale passages in the absence of physical gates and sort proteins according to their phosphorylated states.

}, author = {James Wilson and Aleksei Aksimentiev} } @article {285, title = {Inchworm movement of two rings switching onto a thread by biased Brownian diffusion represent a three-body problem}, journal = {Proceedings of the National Academy of Sciences}, year = {2018}, month = {05/2018}, abstract = {

This article describes a molecular realization of the classical three-body problem, where the motion of three or more bodies is directed by a set of pairwise forces. Surprisingly, motion of the components of the three-body molecular systems is found to be highly choreographed by differences in strength of intercomponent interactions, promoting a rare inchworm-like loading of molecular rings onto a molecular thread. Our work demonstrates the utility of an integrative approach to design and develop functional molecular machines.The coordinated motion of many individual components underpins the operation of all machines. However, despite generations of experience in engineering, understanding the motion of three or more coupled components remains a challenge, known since the time of Newton as the {\textquotedblleft}three-body problem.{\textquotedblright} Here, we describe, quantify, and simulate a molecular three-body problem of threading two molecular rings onto a linear molecular thread. Specifically, we use voltage-triggered reduction of a tetrazine-based thread to capture two cyanostar macrocycles and form a [3]pseudorotaxane product. As a consequence of the noncovalent coupling between the cyanostar rings, we find the threading occurs by an unexpected and rare inchworm-like motion where one ring follows the other. The mechanism was derived from controls, analysis of cyclic voltammetry (CV) traces, and Brownian dynamics simulations. CVs from two noncovalently interacting rings match that of two covalently linked rings designed to thread via the inchworm pathway, and they deviate considerably from the CV of a macrocycle designed to thread via a stepwise pathway. Time-dependent electrochemistry provides estimates of rate constants for threading. Experimentally derived parameters (energy wells, barriers, diffusion coefficients) helped determine likely pathways of motion with rate-kinetics and Brownian dynamics simulations. Simulations verified intercomponent coupling could be separated into ring{\textendash}thread interactions for kinetics, and ring{\textendash}ring interactions for thermodynamics to reduce the three-body problem to a two-body one. Our findings provide a basis for high-throughput design of molecular machinery with multiple components undergoing coupled motion.

}, issn = {0027-8424}, doi = {10.1073/pnas.1719539115}, url = {http://www.pnas.org/content/early/2018/05/03/1719539115}, author = {Benson, Christopher R. and Maffeo, Christopher and Fatila, Elisabeth M. and Liu, Yun and Sheetz, Edward G. and Aleksei Aksimentiev and Singharoy, Abhishek and Flood, Amar H.} } @article {282, title = {New tricks for old dogs: Improving the accuracy of biomolecular force fields by pair-specific corrections to non-bonded interactions}, journal = {Physical Chemistry Chemical Physics}, volume = {20}, year = {2018}, month = {03/2018}, pages = {8432-8449}, abstract = {

In contrast to ordinary polymers, the vast majority of biological macromolecules adopt highly ordered three-dimensional structures that define their functions. The key to folding of a biopolymer into a unique 3D structure or to assembly of several biopolymers into a functional unit is a delicate balance between the attractive and repulsive forces that also makes such self-assembly reversible under physiological conditions. The all-atom molecular dynamics (MD) method has emerged as a powerful tool for studies of individual biomolecules and their functional assemblies, encompassing systems of ever increasing complexity. However, advances in parallel computing technology have outpaced development of the underlying theoretical models{\textemdash}the molecular force fields, pushing the MD method into untested territory. Recent tests of the MD method have found the most commonly used molecular force fields to be out of balance, overestimating attractive interactions between charged and hydrophobic groups, which can promote artificial aggregation in MD simulations of multi-component protein, nucleic acid, and lipid systems. One route to improving the force fields is through the NBFIX corrections method, in which the intermolecular forces are calibrated against experimentally measured quantities such as osmotic pressure by making atom pair-specific adjustments to the non-bonded interactions. In this article, we review development of the NBFIX corrections to the AMBER and CHARMM force fields and discuss their implications for MD simulations of electrolyte solutions, dense DNA systems, Holliday junctions, protein folding, and lipid bilayer membranes.

}, doi = {10.1039/C7CP08185E}, author = {Jejoong Yoo and Aleksei Aksimentiev} } @article {281, title = {Optical voltage sensing using DNA origami}, journal = {Nano Letters}, volume = {18}, year = {2018}, pages = {1962-1971}, abstract = {

We explore the potential of DNA nanotechnology for developing novel optical voltage sensing nano-devices that convert a local change of electric potential into optical signals. As a proof-of-concept of the sensing mechanism, we assembled voltage responsive DNA origami structures labelled with a single pair of FRET dyes. The DNA structures were reversibly immobilised on a nanocapillary tip and underwent controlled structural changes upon application of an electric field. The applied field was monitored through a change in FRET efficiency. By exchanging the position of a single dye, we could tune the voltage sensitivity of our DNA origami structure, demonstrating the flexibility and versatility of our approach. The experimental studies were complemented by coarse-grained simulations that characterised voltage-dependent elastic deformation of the DNA nanostructures and the associated change in the distance between the FRET pair. Our work opens a novel pathway for determining the mechanical properties of DNA origami structures, and highlights potential applications of dynamic DNA nanostructures as voltage sensors.

}, doi = {10.1021/acs.nanolett.7b05354}, url = {https://doi.org/10.1021/acs.nanolett.7b05354}, author = {Hemmig, Elisa Alina and Fitzgerald, Clare and Maffeo, Christopher and Hecker, Lisa and Ochmann, Sarah Elisabeth and Aleksei Aksimentiev and Tinnefeld, Philip and Keyser, Ulrich F} } @inbook {277, title = {A Practical Guide to Molecular Dynamics Simulations of DNA Origami Systems}, booktitle = {DNA Nanotechology: Methods and Protocols}, series = {Methods in Molecular Biology}, volume = {1811}, year = {2018}, pages = {209-229}, publisher = {Humana Press}, organization = {Humana Press}, edition = {2}, chapter = {A Practical Guide to Molecular Dynamics Simulations of DNA Origami Systems}, address = {New York}, abstract = {

The DNA origami method exploits the self-assembly property of nucleic acids to build diverse nanoscale systems. The all-atom molecular dynamics (MD) method has emerged as a powerful computational tool for atomic-resolution characterization of the in situ structure and physical properties of DNA origami objects. This chapter provides step-by-step instructions for building atomic-scale models of DNA origami systems, using the MD method to simulate the models, and performing basic analyses of the resulting MD trajectories.\ 

}, issn = {978-1-4939-8581-4}, doi = {10.1007/978-1-4939-8582-1_15}, url = {https://link.springer.com/protocol/10.1007/978-1-4939-8582-1_15}, author = {Jejoong Yoo and Chen-Yu Li and Scott Michael Slone and Christopher Maffeo and Aleksei Aksimentiev}, editor = {Giampaolo Zuccheri} } @article {273, title = {Molecular mechanism of DNA association with single-stranded DNA binding protein}, journal = {Nucleic Acids Research}, volume = {45}, year = {2017}, month = {12/2017}, pages = {12125{\textendash}12139}, chapter = {12125}, abstract = {

During DNA replication, the single-stranded DNA binding protein (SSB) wraps single-stranded DNA (ssDNA) with high affinity to protect it from degradation and prevent secondary structure formation. Although SSB binds ssDNA tightly, it can be repositioned along ssDNA to follow the advancement of the replication fork. Using all-atom molecular dynamics simulations, we characterized the molecular mechanism of ssDNA association with SSB. Placed in solution, ssDNA{\textendash}SSB assemblies were observed to change their structure spontaneously; such structural changes were suppressed in the crystallographic environment. Repeat simulations of the SSB{\textendash}ssDNA complex under mechanical tension revealed a multitude of possible pathways for ssDNA to come off SSB punctuated by prolonged arrests at reproducible sites at the SSB surface. Ensemble simulations of spontaneous association of short ssDNA fragments with SSB detailed a three-dimensional map of local affinity to DNA; the equilibrium amount of ssDNA bound to SSB was found to depend on the electrolyte concentration but not on the presence of the acidic tips of the SSB tails. Spontaneous formation of ssDNA bulges and their diffusive motion along SSB surface was directly observed in multiple 10-{\textmu}s-long simulations. Such reptation-like motion was confined by DNA binding to high-affinity spots, suggesting a two-step mechanism for SSB diffusion.

}, doi = {10.1093/nar/gkx917}, url = {http://dx.doi.org/10.1093/nar/gkx917}, author = {Maffeo, Christopher and Aleksei Aksimentiev} } @article {279, title = {Porphyrin-Assisted Docking of a Thermophage Portal Protein into Lipid Bilayers: Nanopore Engineering and Characterization}, journal = {ACS Nano}, volume = {11}, year = {2017}, month = {12/2017}, pages = {11931-11945}, abstract = {

Nanopore-based sensors for nucleic acid sequencing and single-molecule detection typically employ pore-forming membrane proteins with hydrophobic external surfaces, suitable for insertion into a lipid bilayer. In contrast, hydrophilic pore-containing molecules such as DNA origami, have been shown to require chemical modification to favor insertion into a lipid environment. In this work, we describe a strategy for inserting polar proteins with an inner pore into lipid membranes, focusing here on a circular 12-subunit assembly of the thermophage G20c portal protein. X-ray crystallography, electron microscopy, molecular dynamics and thermal/chaotrope denaturation experiments all find the G20c portal protein to have a highly stable structure, favorable for nanopore sensing applications. Porphyrin conjugation to a cysteine mutant in the protein facilitates the protein{\textquoteright}s insertion into lipid bilayers, allowing us to probe ion transport through the pore. Finally, we probed the portal interior size and shape using a series of cyclodextrins of varying sizes, revealing asymmetric transport that possibly originates from the portal{\textquoteright}s DNA-ratchet function.

}, doi = {10.1021/acsnano.7b06980}, url = {http://pubs.acs.org/doi/abs/10.1021/acsnano.7b06980}, author = {Cressiot*, Benjamin and Greive*, Sandra J. and Si*, Wei and Pascoa, Tomas and Mojtabavi, Mehrnaz and Chechik, Maria and Jenkins, Huw Thomas and Lu, Xueguang and Zhang, Ke and Aleksei Aksimentiev and Antson, Alfred A. and Wanunu, Meni} } @article {274, title = {Quantification of Membrane Protein-Detergent Complex Interactions}, journal = {The Journal of Physical Chemistry B}, volume = {121}, year = {2017}, month = {11/2017}, pages = {10228-10241}, chapter = {10228}, abstract = {

Although fundamentally significant in structural, chemical, and membrane biology, the interfacial protein-detergent complex (PDC) interactions have been modestly examined because of the complicated behavior of both detergents and membrane proteins in aqueous phase. Membrane proteins are prone to unproductive aggregation resulting from poor detergent solvation, but the participating forces in this phenomenon remain ambiguous. Here, we show that using rational membrane protein design, targeted chemical modification, and steady-state fluorescence polarization spectroscopy, the detergent desolvation of membrane proteins can be quantitatively evaluated. We demonstrate that depleting the detergent in the sample well produced a two-state transition of membrane proteins between a fully detergent-solvated state and a detergent-desolvated state, the nature of which depended on the interfacial PDC interactions. Using a panel of six membrane proteins of varying hydrophobic topography, structural fingerprint, and charge distribution on the solvent-accessible surface, we provide direct experimental evidence for the contributions of the electrostatic and hydrophobic interactions to the protein solvation properties. Moreover, all-atom molecular dynamics simulations report the major contribution of the hydrophobic forces exerted at the PDC interface. This semi-quantitative approach might be extended in the future to include studies of the interfacial PDC interactions of other challenging membrane protein systems of unknown structure. This would have practical importance in protein extraction, solubilization, stabilization, and crystallization.

}, doi = {10.1021/acs.jpcb.7b08045}, url = {http://pubs.acs.org/doi/abs/10.1021/acs.jpcb.7b08045}, author = {Wolfe, Aaron John and Si, Wei and Zhang, Zhengqi and Blanden, Adam R and Hsueh, Yi-Ching and Gugel, Jack Fredrick and Pham, Bach and Chen, Min and Loh, Stewart N and Rozovsky, Sharon and Aleksei Aksimentiev and Movileanu, Liviu} } @article {268, title = {Nanoscale Ion Pump Derived from a Biological Water Channel}, journal = {The Journal of Physical Chemistry B }, volume = {121}, year = {2017}, month = {08/2017}, pages = {7899{\textendash}7906 }, abstract = {

Biological molecular machines perform the\ work of supporting life at the smallest of scales, including\ the work of shuttling ions across cell boundaries and against\ chemical gradients. Systems of artifi cial channels at the\ nanoscale can likewise control ionic concentration by way of\ ionic current rectifi cation, species selectivity, and voltage\ gating mechanisms. Here, we theoretically show that a voltagegated,\ ion species-selective, and rectifying ion channel can be\ built using the components of a biological water channel\ aquaporin. Through all-atom molecular dynamics simulations,\ we show that the ionic conductance of a truncated aquaporin\ channel nonlinearly increases with the bias magnitude, depends on the channel{\textquoteright} s orientation, and is highly cation specific but only\ for one polarity of the transmembrane bias. Further, we show that such an unusually complex response of the channel to\ transmembrane bias arises from mechanical motion of a positively charged gate that blocks cation transport. By combining two\ truncated aquaporins, we demonstrate a molecular system that pumps ions against their chemical gradients when subject to an\ alternating transmembrane bias. Our work sets the stage for future biomimicry eff orts directed toward reproducing the function\ of biological ion pumps using synthetic components.

}, doi = {10.1021/acs.jpcb.7b05568}, author = {Karl Decker and Martin Page and Aleksei Aksimentiev} } @article {258, title = {Picomolar Fingerprinting of Nucleic Acid Nanoparticles Using Solid-State Nanopores}, journal = {ACS Nano}, volume = {11}, year = {2017}, month = {07/2017}, pages = {9701-9710}, abstract = {

Nucleic acid nanoparticles (NANPs) are an emerging class of programmable structures with tunable shape and function. Their promise as tools for fundamental biophysics studies, molecular sensing, and therapeutic applications necessitates methods for their detection and characterization at the single-particle level. In this work, we study electrophoretic transport of individual ring-shaped and cube-shaped NANPs through solid-state nanopores. In the optimal nanopore size range, the particles must deform to pass through, which considerably increases their residence time within the pore. Such anomalously long residence times permit detection of picomolar amounts of NANPs when nanopore measurements are carried out at a high transmembrane bias. In the case of a NANP mixture, the type of individual particle passing through nanopores can be efficiently determined from analysis of a single electrical pulse. Molecular dynamics simulations provide insight into the mechanical barrier to transport of the NANPs and corroborate the difference in the signal amplitudes observed for the two types of particles. Our study serves as a basis for label-free analysis of soft programmable-shape nanoparticles.

}, doi = {10.1021/acsnano.7b04923}, url = {http://dx.doi.org/10.1021/acsnano.7b04923}, author = {Alibakhshi, Mohammad Amin and Halman, Justin R. and Wilson, James and Aleksei Aksimentiev and Afonin, Kirill A. and Wanunu, Meni} } @article {270, title = {Nanopore Sensing of Protein Folding}, journal = {ACS Nano}, volume = {11, 7091-7100}, year = {2017}, month = {05/2017}, abstract = {

Single-molecule studies of protein folding\ hold keys to unveiling protein folding pathways and elusive intermediate folding states-attractive pharmaceutical targets. Although conventional single-molecule approaches can detect folding intermediates, they presently lack throughput and require elaborate labeling. Here, we theoretically show that measurements of ionic current through a nanopore containing a protein can report on the protein{\textquoteright}s folding state. Our all-atom molecular dynamics (MD) simulations show that the unfolding of a protein lowers the nanopore ionic current, an effect that originates from the reduction of ion mobility in proximity to a protein. Using a theoretical model, we show that the average change in ionic current produced by a folding-unfolding transition is detectable despite the orientational and conformational heterogeneity of the folded and unfolded states. By analyzing millisecond-long all-atom MD simulations of multiple protein transitions, we show that a nanopore ionic current recording can detect folding-unfolding transitions in real time and report on the structure of folding intermediates.

}, doi = {10.1021/acsnano.7b02718}, url = {http://pubs.acs.org/doi/abs/10.1021/acsnano.7b02718}, author = {Si, Wei and Aleksei Aksimentiev} } @article {266, title = {SDS-assisted protein transport through solid-state nanopores}, journal = {Nanoscale}, volume = {9}, year = {2017}, month = {05/2017}, pages = {11685-11693}, abstract = {

Using nanopores for single-molecule sequencing of proteins - similar to nanopore-based sequencing of DNA - faces multiple challenges, including unfolding of the complex tertiary structure of the proteins and enforcing their unidirectional translocation through nanopores. Here, we combine molecular dynamics (MD) simulations with single-molecule experiments to investigate the utility of SDS (Sodium Dodecyl Sulfate) to unfold proteins for solid-state nanopore translocation, while simultaneously endowing them with a stronger electrical charge. Our simulations and experiments prove that SDS-treated proteins show a considerable loss of the protein structure during the nanopore translocation. Moreover, SDS-treated proteins translocate through the nanopore in the direction prescribed by the electrophoretic force due to the negative charge impaired by SDS. In summary, our results suggest that SDS causes protein unfolding while facilitating protein translocation in the direction of the electrophoretic force; both characteristics being advantageous for future protein sequencing applications using solid-state nanopores.

}, doi = {10.1039/C7NR02450A}, url = {http://dx.doi.org/10.1039/C7NR02450A}, author = {Restrepo-Perez*, Laura and John*, Shalini and Aleksei Aksimentiev and Joo, Chirlmin and Dekker, Cees} } @article {252, title = {Modulation of Molecular Flux Using a Graphene Nanopore Capacitor}, journal = {The Journal of Physical Chemistry B}, volume = {121}, year = {2017}, month = {02/2017}, pages = {3724-3733}, chapter = {3724}, abstract = {

Modulation of ionic current flowing through nanoscale pores is one of the fundamental biological processes. Inspired by nature, nanopores in synthetic solid-state membranes are being developed to enable rapid analysis of biological macromolecules and to serve as elements of nanofludic circuits. Here, we \ theoretically investigate ion and water transport through a graphene-insulator-graphene membrane containing a single, electrolyte-filled nanopore. By means of all-atom molecular dynamics simulations we show \ that the charge state of such a graphene nanopore capacitor \ can \ regulate both the selectivity and the magnitude of the nanopore ionic current. At a fixed transmembrane bias, the ionic current can be switched from being carried by an equal mixture of cations and anions to being carried almost exclusively by either cationic or anionic species, depending on the the sign of the charge assigned to both plates of the capacitor. \  Assigning the plates of the capacitor opposite sign charges can either increase the nanopore current or reduce it substantially, depending on the polarity of the \ bias driving the transmembrane current. Facilitated by dynamic inversion of the nanopore surface charge, such ionic current modulations are found to occur despite the physical dimensions of the nanopore being an order of magnitude larger than the screening length of the electrolyte. The \ ionic current rectification is accompanied by a pronounced electro-osmotic effect that can transport neutral molecules such as proteins and drugs across the solid-state membrane and thereby serve as an interface between electronic and chemical signals.

}, issn = {1520-6106}, doi = {10.1021/acs.jpcb.6b10574}, author = {Manish Shankla and Aleksei Aksimentiev} } @article {251, title = {Selective Permeability of Truncated Aquaporin 1 in Silico}, journal = {ACS Biomaterials Science \& Engineering}, volume = {3}, year = {2017}, month = {02/2017}, pages = {342-348}, chapter = {342}, abstract = {

Aquaporin (AQP) proteins function as highly efficient water transport channels that support homeostasis in many types of living cells. Their structure-function relationships have been characterized extensively in fundamental and applied research, primarily via structural analysis, mutational studies, and computational approaches. The present study evaluates the effects of progressive truncations on the permeability and ionic conductivity of AQP-1 (bovine). The use of truncations to determine critical features has not been considered previously, as physical truncation of AQP is likely not technically feasible due to the ornate arrangement of six interwoven alpha helices in a single pore structure. However, structures not obtainable through protein assembly can be realized via synthetic chemistry approaches and studied using molecular dynamics (MD) simulations. Here, we apply the MD method to characterize the permeability of AQP variants truncated along the pore axis from both cytoplasmic and extracellular sides of the channel. The simulation results suggest that AQP-1 can retain its function even after deletion of up to 50\% of the channel{\textquoteright}s length, representing 50\% of proteins{\textquoteright}s molecular mass. Deletions such as these are expected to greatly simplify future biomimicry efforts of reproducing the AQP functionality using synthetic macromolecules. This study demonstrates the potential of in silico approaches to support the creation of streamlined functional analogs of biological molecular machines.

}, doi = {10.1021/acsbiomaterials.6b00583 }, author = {Karl Decker and Martin Page and Ashley Boyd and Irene MacAllister and Mark Ginsberg and Aleksei Aksimentiev} } @article {253, title = {Interference-free detection of genetic biomarkers using synthetic dipole-facilitated nanopore dielectophoresis.}, journal = {ACS Nano}, volume = {11}, year = {2017}, month = {01/2017}, pages = {1204-1213}, chapter = {1204}, abstract = {

The motion of polarizable particles in a non-uniform electric field, i.e., dielectrophoresis, has been extensively used for concentration, separation, sorting, and transport of biological particles, from cancer cells and viruses to biomolecules such as DNAs and proteins. However, current approaches to dielectrophoretic manipulation are not sensitive enough to selectively target individual molecular species. Here we describe the application of the dielectrophoretic principle for selective detection of DNA and RNA molecules using an engineered biological nanopore. The key element of our approach is a synthetic polycationic nanocarrier that selectively binds to the target biomolecules, dramatically increasing their dielectrophoretic response to the electric field gradient generated by the nanopore. The dielectrophoretic capture of the nanocarrier-target complexes is detected as a transient blockade of the nanopore ionic current while any non-target nucleic acids are repelled from the nanopore by electrophoresis and thus do not interfere with the signal produced by the target{\textquoteright}s capture. Strikingly, we show that even modestly charged nanocarriers can be used to capture DNA or RNA molecules of any length or secondary structure and simultaneously detect several molecular targets. Such selective, multiplex molecular detection technology would be highly desirable for real-time analysis of complex clinical samples.

}, doi = {10.1021/acsnano.6b07570}, author = {Kai Tian and Karl Decker and Aleksei Aksimentiev and Li-Qun Gu} } @article {250, title = {Mechanical Trapping of DNA in a Double-Nanopore System}, journal = {Nano Letters}, volume = {16}, year = {2016}, month = {11/2016}, pages = {8021-8028 }, abstract = {

Nanopores have become ubiquitous components of systems for single-molecule manipulation and detection, in particular DNA sequencing where electric field driven translocation of DNA through a nanopore is used to read out the DNA molecule. Here, we present a double-pore system where two nanopores are drilled in parallel through the same solid-state membrane, which offers new opportunities for DNA manipulation. Our experiments and molecular dynamics simulations show that simultaneous electrophoretic capture of a DNA molecule by the two nanopores mechanically traps the molecule, increasing its residence time within the nanopores by orders of magnitude. Remarkably, by using two unequal-sized nanopores, the pore of DNA entry and exit can be discerned from the ionic current blockades, and the translocation direction can be precisely controlled by small differences in the effective force applied to DNA. The mechanical arrest of DNA translocation using a double-pore system can be straightforwardly integrated into any solid-state nanopore platform, including those using optical or transverse-current readouts.

}, doi = {10.1021/acs.nanolett.6b04642}, author = {Sergii Pud and Shu-Han Chao and Maxim Belkin and Daniel Verschueren and Teun Huijben and Casper van Engelenburg and Cees Dekker and Aleksei Aksimentiev} } @article {239, title = {Refined Parameterization of Nonbonded Interactions Improves Conformational Sampling and Kinetics of Protein Folding Simulations}, journal = {Journal of Physical Chemistry Letters}, volume = {7}, year = {2016}, month = {09/2016}, pages = {3812{\textendash}3818}, chapter = {3812}, abstract = {

Recent advances in computational technology have enabled brute-force molecular dynamics (MD) simulations of protein folding using physics-based molecular force fields. The extensive sampling of protein conformations afforded by such simulations revealed, however, considerable compaction of the protein conformations in the unfolded state, which is inconsistent with experiment. Here, we show that a set of surgical corrections to nonbonded interactions between amine nitrogen{\textendash}carboxylate oxygen and aliphatic carbon{\textendash}carbon atom pairs can considerably improve the realism of protein folding simulations. Specifically, we show that employing our corrections in \~{}500 μs all-atom replica-exchange MD simulations of the WW domain and villin head piece proteins increases the size of the denatured proteins{\textquoteright} conformations and does not destabilize the native conformations of the proteins. In addition to making the folded conformations a global minimum of the respective free energy landscapes at room temperature, our corrections also make the free energy landscape smoother, considerably accelerating the folding kinetics and, hence, reducing the computational expense of a protein folding simulation.

}, doi = {10.1021/acs.jpclett.6b01747}, author = {Jejoong Yoo and Aleksei Aksimentiev} } @article {237, title = {Large-Conductance Transmembrane Porin Made from DNA Origami}, journal = {ACS Nano}, volume = {10}, year = {2016}, month = {08/2016}, pages = {8207--8214}, abstract = {

DNA nanotechnology allows for the creation of three-dimensional structures at nanometer scale. Here, we use DNA to build the largest synthetic pore in a lipid membrane to date, approaching the dimensions of the nuclear pore complex and increasing the pore-area and the conductance tenfold compared to previous man-made channels. In our design, nineteen cholesterol-tags anchor a megadalton funnel-shaped DNA origami porin in a lipid bilayer membrane (see equilibration trajectory, require login to nanoHUB). Confocal imaging and ionic current recordings reveal spontaneous insertion of the DNA porin into the lipid membrane, creating a transmembrane pore of tens of nanosiemens conductance (see ionic current trajectory). All-atom molecular dynamics simulations characterize the conductance mechanism at the atomic level and independently confirm the DNA porins{\textquoteright} large ionic conductance.

}, doi = {10.1021/acsnano.6b03759}, author = {Kerstin G{\"o}pfrich* and Chen-Yu Li* and Maria Ricci and Satya Prathyusha Bhamidimarri and Jejoong Yoo and Bertalan Gyenes and Alexander Ohmann and Mathias Winterhalter and Aleksei Aksimentiev and Ulrich F Keyser} } @article {218, title = {Improved model of hydrated calcium ion for molecular dynamics simulations using classical biomolecular force fields}, journal = {Biopolymers}, volume = {105}, year = {2016}, month = {07/2016}, pages = {752-763}, chapter = {752}, abstract = {
Calcium ions (Ca2+) play key roles in various fundamental biological processes such as cell signaling and brain function . Molecular dynamics (MD) simulations have been used to study such interactions, however, the accuracy of the Ca2+ models provided by the standard M D force fields has not been rigorously tested. Here, we assess the performance of the Ca2+ models from the most popular classical force fields AMBER and CHARMM by computing the osmotic pressure of model compounds and the free energy of DNA{\textendash}DNA inter act i on s. In the simulations performed using the two standard models, Ca2+ ions are seen to form artificial clusters with chloride, acetate, and phosphate species; the osmotic pressure of CaAc2and CaCl2solutions is a small fraction of the experimental values for both force fields. Using the standard parameterization of Ca2+ ions in the simulations of Ca2+-mediated DNA-DNA interact ions leads to qualitatively wrong outcomes: both AMBER and CHARMM simulations suggest strong inter-DNA attraction whereas, in experiment, DNA molecules repel one another. The artificial attraction of Ca2+to DNA phosphate is strong enough to affect the direction of the electric field-driven translocation of DNA through a solid-state nanopore. To address these shortcomings of the standard Ca2+ model, we introduce a custom model of a hydrated Ca2+ ion and show that using our model brings the results of the above MD simulations in quantitative agreement with experiment. Our improved model of Ca2+ can be readily applied to MD simulations of various biomolecular systems, including nucleic acids, proteins and lipid bilayer membranes.
}, doi = {10.1002/bip.22868}, author = {Jejoong Yoo and James Wilson and Aleksei Aksimentiev} } @article {235, title = {Graphene Nanopores for Protein Sequencing}, journal = {Advanced Functional Materials}, volume = {26}, year = {2016}, month = {06/2016}, pages = {4830-4838}, chapter = {4830}, abstract = {

An inexpensive, reliable method for protein sequencing is essential to unraveling the biological mechanisms governing cellular behavior and disease. Current protein sequencing methods suffer from limitations associated with the size of proteins that can be sequenced, the time, and the cost of the sequencing procedures. This study reports the results of all-atom molecular dynamics simulations that investigated the feasibility of using graphene nanopores for protein sequencing. The study is focused on the biologically significant phenylalanine-glycine repeat peptides (FG-nups){\textemdash}parts of the nuclear pore transport machinery. Surprisingly, FG-nups are found to behave similarly to single stranded DNA: The peptides adhere to graphene and exhibit stepwise translocation when subject to a transmembrane bias or a hydrostatic pressure gradient. Reducing the peptide{\textquoteright}s charge density or increasing the peptide{\textquoteright}s hydrophobicity is found to decrease the translocation speed. Yet, unidirectional and stepwise translocation driven by a transmembrane bias is observed even when the ratio of charged to hydrophobic amino acids is as low as 1:8. The nanopore transport of the peptides is found to produce stepwise modulations of the nanopore ionic current correlated with the type of amino acids present in the nanopore, suggesting that protein sequencing by measuring ionic current blockades may be possible.

}, keywords = {graphene, ionic current, nanopore sequencing, transmembrane transport}, issn = {1616-3028}, doi = {10.1002/adfm.201601272}, url = {http://dx.doi.org/10.1002/adfm.201601272}, author = {Wilson, James and Sloman, Leila and He, Zhiren and Aleksei Aksimentiev} } @article {236, title = {Ion Channels Made from a Single Membrane-Spanning DNA Duplex}, journal = {Nano Letters}, volume = {16}, year = {2016}, month = {06/2016}, pages = {4665--4669}, abstract = {

Due to their hollow interior, transmembrane channels are capable of opening up pathways for ions across lipid membranes of living cells. Here, we demonstrate ion conduction induced by a single DNA duplex that lacks a hollow central channel. Decorated with six porpyrin-tags, our duplex is designed to span lipid membranes. Combining electrophysiology measurements with all-atom molecular dynamics simulations, we elucidate the microscopic conductance pathway\ (see\ water channel\ trajectory, require login to nanoHUB). Ions flow (see ion transport\ trajectory)\ at the DNA-lipid interface as the lipid head groups tilt towards the amphiphilic duplex forming a toroidal pore filled with water and ions. Ionic current traces produced by the DNA-lipid channel show well-defined insertion steps, closures and gating similar to those observed for traditional protein channels or synthetic pores. Ionic conductances obtained through simulations and experiments are in excellent quantitative agreement. The conductance mechanism realized here, with the smallest possible DNA-based ion channel, offers a route to design a new class of synthetic ion channels with maximum simplicity.

}, doi = {10.1021/acs.nanolett.6b02039}, author = {Kerstin G{\"o}pfrich and Chen-Yu Li and Iwona Mames and Satya Prathyusha Bhamidimarri and Maria Ricci and Jejoong Yoo and Adam Mames and Alexander Ohmann and Mathias Winterhalter and Eugen Stulz and Aleksei Aksimentiev and Ulrich F Keyser} } @article {226, title = {Molecular mechanics of DNA bricks: in situ structure, mechanical properties and ionic conductivity}, journal = {New Journal of Physics}, volume = {18}, year = {2016}, month = {05/2016}, pages = {055012}, abstract = {

The DNA bricks method exploits self-assembly of short DNA fragments to produce custom three-dimensional objects with subnanometer precision. In contrast to DNA origami, the DNA brick method permits a variety of different structures to be realized using the same library of DNA strands. As a consequence of their design, however, assembled DNA brick structures have fewer interhelical connections in comparison to equivalent DNA origami structures. Although the overall shape of the DNA brick objects has been characterized and found to conform to the features of the target designs, the microscopic properties of DNA brick objects remain yet to be determined. Here, we use the all-atom molecular dynamics method to directly compare the structure, mechanical properties and ionic conductivity of DNA brick and DNA origami structures different only by internal connectivity of their consistituent DNA strands. In comparison to equivalent DNA origami structures, the DNA brick structures are found to be less rigid and less dense and have a larger cross-section area normal to the DNA helix direction. At the microscopic level, the junction in the DNA brick structures are found to be right-handed, similar to the structure of individual Holliday junctions (HJ) in solution, which contrasts with the left-handed structure of HJ in DNA origami. Subject to external electric field, a DNA brick plate is more leaky to ions than an equivalent DNA origami plate because of its lower density and larger cross-section area. Overall, our results indicate that the structures produced by the DNA brick method are fairly similar in their overall appearance to those created by the DNA origami method but are more compliant when subject to external forces, which likely is a consequence of their single crossover design.

}, doi = {10.1088/1367-2630/18/5/055012}, url = {http://dx.doi.org/10.1088/1367-2630/18/5/055012}, author = {Scott Michael Slone and Chen-Yu Li and Jejoong Yoo and Aleksei Aksimentiev} } @article {BELK2016, title = {Molecular Dynamics Simulation of DNA Capture and Transport in Heated Nanopores}, journal = {ACS Applied Materials and Interfaces}, volume = {8}, year = {2016}, note = {PMID: 26963065}, month = {05/2016}, pages = {12599{\textendash}12608}, type = {Research}, abstract = {

The integration of local heat sources with solid-state nanopores offers new means for controlling the transmembrane transport of charged biomacromolecules. In the case of electrophoretic transport of DNA, recent experimental studies revealed unexpected temperature dependences of the DNA capture rate, the DNA translocation velocity, and the ionic current blockades produced by the presence of DNA in the nanopore.\  Here, we report the results of all-atom molecular dynamics (MD) simulations that elucidated the effect of temperature on the key microscopic processes governing\  electric field-driven transport of DNA through nanopores. Mimicking the experimental setup, we simulated the capture and subsequent translocation of short DNA duplexes through a locally heated nanopore at several temperature and electrolyte conditions. The temperature dependence of ion mobility at the DNA surface was found to cause\  the dependence of the relative conductance blockades on temperature. To the first order, the effective force on DNA in the nanopore was found to be independent of temperature, despite a considerable reduction of solution viscosity. The temperature dependence of the solution viscosity was found to make DNA translocations faster for a\  uniformly heated system but not in the case of local heating that does not affect viscosity of solution surrounding the untranslocated part of the molecule. Increasing solution temperature was also found to reduce the lifetime of bonds formed between cations and DNA. Using a flow suppression algorithm, we were able to separate the effects of electro-osmotic flow and direct ion binding, finding the reduced durations of DNA--ion bonds to increase, albeit weakly, the effective force experienced by DNA in an electric field. Unexpectedly, our simulations revealed a considerable temperature dependence of\  solvent velocity at the DNA surface---slip velocity, an effect that can alter hydrodynamic coupling between the motion of DNA and the surrounding fluid.

}, doi = {10.1021/acsami.6b00463}, url = {http://dx.doi.org/10.1021/acsami.6b00463}, author = {Maxim Belkin and Aleksei Aksimentiev} } @article {246, title = {DNA sequence-dependent ionic currents in ultra-small solid-state nanopores}, journal = {Nanoscale}, volume = {18}, year = {2016}, month = {04/2016}, pages = {9600-9613}, abstract = {

Measurements of ionic currents through nanopores partially blocked by DNA have emerged as a powerful method for characterization of the DNA nucleotide sequence. Although the effect of the nucleotide sequence on the nanopore blockade current has been experimentally demonstrated, prediction and interpretation of such measurements remain a formidable challenge. Using atomic resolution computational approaches, here we show how the sequence, molecular conformation, and pore geometry affect the blockade ionic current in model solid-state nanopores. We demonstrate that the blockade current from a DNA molecule is determined by the chemical identities and conformations of at least three consecutive nucleotides. We find the blockade currents produced by the nucleotide triplets to vary considerably with their nucleotide sequence despite having nearly identical molecular conformations. Encouragingly, we find blockade current differences as large as 25\% for single-base substitutions in ultra small (1.6 nm x 1.1 nm cross section; 2 nm length) solid-state nanopores. \ Despite the complex dependence of the blockade current on the sequence and conformation of the DNA triplets, we find that, under many conditions, the number of thymine bases is positively correlated with the current, whereas the number of purine bases and the presence of both purine and pyrimidines in the triplet \ are negatively correlated with the current. Based on these observations, we construct a simple theoretical model that relates the ion current to the base content of a solid-state nanopore. Furthermore, we show that compact \ conformations of DNA in narrow pores provide the greatest signal-to-noise ratio for single base detection, whereas reduction of the nanopore length \ increases the ionic current noise.\ Thus, the sequence dependence of nanopore blockade current can be theoretically rationalized, although the predictions will likely need to be customized for each nanopore type.

}, doi = {10.1039/C6NR01061J}, url = {http://pubs.rsc.org/en/content/articlehtml/2016/nr/c6nr01061j}, author = {Jeffrey Comer and Aleksei Aksimentiev} } @article {247, title = {Water Mediates Recognition of DNA Sequence via Ionic Current Blockade in a Biological Nanopore}, journal = {ACS Nano}, volume = {10}, year = {2016}, month = {04/2016}, pages = {4644{\textendash}4651}, abstract = {

Electric field-driven translocation of DNA strands through biological nanopores has been shown to produce blockades of the nanopore ionic current that depend on the nucleotide composition of the strands. Coupling a biological nanopore MspA to a DNA processing enzyme has made DNA sequencing \ via\ measurement of \ ionic current blockades \ possible. Nevertheless, the physical mechanism enabling the DNA sequence readout has remained undetermined. Here, we report the results of all-atom molecular dynamics simulations that elucidated the physical mechanism of ionic current blockades in the biological nanopore MspA. We find that the amount of water displaced from the nanopore by the DNA strand determines the nanopore ionic current, whereas the steric and base-stacking properties of the DNA nucleotides determine the amount of water displaced. \ Unexpectedly, we \ find the effective force on DNA in MspA to undergo large fluctuations, which may produce insertion errors in the DNA sequence readout.

}, doi = {10.1021/acsnano.6b00940}, author = {Swati Bhattacharya and Jejoong Yoo and Aleksei Aksimentiev} } @article {214, title = {De Novo Reconstruction of DNA Origami Structures through Atomistic Molecular Dynamics Simulation}, journal = {Nucleic Acids Research}, volume = {44}, year = {2016}, month = {04/2016}, pages = {3013-3019}, chapter = {3013}, abstract = {

The DNA origami method has brought nanometer-precision fabrication to molecular biology labs, offering myriads of potential applications in the fields of synthetic biology, biomolecular medicine, molecular computation, etc. Advancing the method further requires controlling self-assembly down to the atomic scale. Here we demonstrate a computational method that allows the equilibrium structure of a large, complex DNA origami object to be determined to atomic resolution. Through direct comparison with the results of cryo-electron microscopy, we demonstrate de novo reconstruction of a 4.7 megadalton pointer structure by means of fully atomistic molecular dynamics simulations. Furthermore, we show that elastic network-guided simulations performed without solvent can yield similar accuracy at a fraction of the computational cost, making this method an attractive approach for prototyping and validation of self-assembled DNA nanostructures.

}, doi = {10.1093/nar/gkw155}, url = {http://nar.oxfordjournals.org/content/early/2016/03/14/nar.gkw155}, author = {Christopher Maffeo and Jejoong Yoo and Aleksei Aksimentiev} } @article {211, title = {Direct evidence for sequence-dependent attraction between double-stranded DNA controlled by methylation}, journal = {Nature Communications}, volume = {7}, year = {2016}, month = {03/2016}, pages = {11045}, abstract = {

Although proteins mediate highly ordered DNA organization\ in vivo, theoretical studies suggest that homologous DNA duplexes can preferentially associate with one another even in the absence of proteins. Here we combine molecular dynamics simulations with single-molecule fluorescence resonance energy transfer experiments to examine the interactions between duplex DNA in the presence of spermine, a biological polycation. We find that AT-rich DNA duplexes associate more strongly than GC-rich duplexes, regardless of the sequence homology. Methyl groups of thymine acts as a steric block, relocating spermine from major grooves to interhelical regions, thereby increasing DNA{\textendash}DNA attraction. Indeed, methylation of cytosines makes attraction between GC-rich DNA as strong as that between AT-rich DNA. Recent genome-wide chromosome organization studies showed that remote contact frequencies are higher for AT-rich and methylated DNA, suggesting that direct DNA{\textendash}DNA interactions that we report here may play a role in the chromosome organization and gene regulation.

}, doi = {10.1038/ncomms11045}, author = {Jejoong Yoo and Hajin Kim and Aleksei Aksimentiev and Taekjip Ha} } @article {207, title = {Hydroxymethyluracil modifications enhance the flexibility and hydrophilicity of double-stranded DNA}, journal = {Nucleic Acids Research}, volume = {44}, year = {2016}, month = {03/2016}, pages = {2085--2092}, chapter = {2085}, abstract = {

Oxidation of a DNA thymine to 5-hydroxymethyluracil is one of several recently discovered epigenetic modifications. Here, we report the results of nanopore translocation experiments and molecular dynamics simulations that provide insight into the impact of this modification on the structure and dynamics of DNA. When transported through ultrathin solid-state nanopores, short DNA fragments containing thymine modifications were found to exhibit distinct, reproducible features in their transport characteristics that differentiate them from unmodified molecules. Molecular dynamics simulations suggest that 5-hydroxymethyluracil alters the flexibility and hydrophilicity of the DNA molecules, which may account for the differences observed in our nanopore translocation experiments. The altered physico-chemical properties of DNA produced by the thymine modifications may have implications for recognition and processing of such modifications by regulatory DNA-binding proteins.

}, doi = {10.1093/nar/gkv1199}, url = {http://nar.oxfordjournals.org/content/early/2015/11/16/nar.gkv1199.abstract}, author = {Carson, Spencer and Wilson, James and Aleksei Aksimentiev and Weigele, Peter R. and Wanunu, Meni} } @article {216, title = {The Hinge Region Strengthens the Nonspecific Interaction between Lac-Repressor and DNA: A Computer Simulation Study}, journal = {PLoS ONE}, volume = {11}, year = {2016}, month = {02/2016}, pages = {e0152002}, abstract = {

LacI is commonly used as a model to study the protein-DNA interaction and gene regulation. The headpiece of the lac-repressor (LacI) protein is an ideal system for investigation of nonspecific binding of the whole LacI protein to DNA. The hinge region of the headpiece has been known to play a key role in the specific binding of LacI to DNA, whereas its role in nonspecific binding process has not been elucidated. Here, we report the results of explicit solvent molecular dynamics simulation and continuum electrostatic calculations suggesting that the hinge region strengthens the nonspecific interaction, accounting for up to 50\% of the micro-dissociation free energy of LacI from DNA. Consequently, the rate of microscopic dissociation of LacI from DNA is reduced by 2~3 orders of magnitude in the absence of the hinge region. We find the hinge region makes an important contribution to the electrostatic energy, the salt dependence of electrostatic energy, and the number of salt ions excluded from binding of the LacI-DNA complex.

}, doi = {10.1371/journal.pone.0152002}, url = {http://journals.plos.org/plosone/article?id=10.1371\%2Fjournal.pone.0152002}, author = {Lili Sun and Marcin Tabaka and Sen Hou and Lin Li and Krzysztof Burdzy and Aleksei Aksimentiev and Christopher Maffeo and Xuzhu Zhang and Robert Holyst} } @article {209, title = {Improved Parameterization of Amine{\textendash}Carboxylate and Amine{\textendash}Phosphate Interactions for Molecular Dynamics Simulations Using the CHARMM and AMBER Force Fields}, journal = {Journal of Chemical Theory and Computation}, volume = {12}, year = {2016}, pages = {430{\textendash}443}, abstract = {

Over the past decades, molecular dynamics (MD) simulations of biomolecules have become a mainstream biophysics technique. As the length and time scales amenable to the MD method increase, shortcomings of the empirical force fields, which have been developed and validated using relatively short simulations of small molecules, become apparent. One common artifact is aggregation of water-soluble biomolecules driven by artificially strong charge{\textendash}charge interactions. Here, we report a systematic atom pair-specific refinement of Lennard-Jones parameters (NBFIX) describing amine{\textendash}carboxylate and amine{\textendash}phosphate interactions, which bring MD simulations of basic peptide-mediated nucleic acid assemblies and lipid bilayer membranes into better agreement with experimental data. As our refinement does not affect the existing parametrization of bonded interactions or alter the solvation free energies, it improves the realism of an MD simulation without introducing additional artifacts.

}, doi = {10.1021/acs.jctc.5b00967}, author = {Jejoong Yoo and Aleksei Aksimentiev} } @article {210, title = {Effect of Cytosine Modifications on DNA Flexibility and Nucleosome Mechanical Stability}, journal = {Nature Communications}, volume = {7}, year = {2016}, pages = {10813}, chapter = {10813}, abstract = {

Cytosine can undergo modifications, forming 5-methylcytosine (5-mC) and its oxidized products 5-hydroxymethylcytosine (5-hmC), 5-formylcytosine (5-fC) and 5-carboxylcytosine (5-caC). Despite their importance as epigenetic markers and as central players in cellular processes, it is not well understood how these modifications influence physical properties of DNA and chromatin. Here we report a comprehensive survey of the effect of cytosine modifications on DNA flexibility. We find that even a single copy of 5-fC increases DNA flexibility markedly. 5-mC reduces and 5-hmC enhances flexibility, and 5-caC does not have a measurable effect. Molecular dynamics simulations show that these modifications promote or dampen structural fluctuations, likely through competing effects of base polarity and steric hindrance, without changing the average structure. The increase in DNA flexibility increases the mechanical stability of the nucleosome and vice versa, suggesting a gene regulation mechanism where cytosine modifications change the accessibility of nucleosomal DNA through their effects on DNA flexibility.

}, doi = {10.1038/ncomms10813}, author = {Thuy Ngo and Jejoong Yoo and Dai, Q and Zhang, Q and He, C and Aleksei Aksimentiev and Taekjip Ha} } @article {212, title = {The structure and intermolecular forces of DNA condensates}, journal = {Nucleic Acids Research}, volume = {44}, year = {2016}, pages = {2036{\textendash}2046}, abstract = {

Spontaneous assembly of DNA molecules into compact structures is ubiquitous in biological systems. Experiment has shown that polycations can turn electrostatic self-repulsion of DNA into attraction, yet the physical mechanism of DNA condensation has remained elusive. Here, we report the results of atomistic molecular dynamics simulations that elucidated the microscopic structure of dense DNA assemblies and the physics of interactions that makes such assemblies possible. Reproducing the setup of the DNA condensation experiments, we measured the internal pressure of DNA arrays as a function of the DNA{\textendash}DNA distance, showing a quantitative agreement between the results of our simulations and the experimental data. Analysis of the MD trajectories determined the DNA{\textendash}DNA force in a DNA condensate to be pairwise, the DNA condensation to be driven by electrostatics of polycations and not hydration, and the concentration of bridging cations, not adsorbed cations, to determine the magnitude and the sign of the DNA{\textendash}DNA force. Finally, our simulations quantitatively characterized the orientational correlations of DNA in DNA arrays as well as diffusive motion of DNA and cations.

}, doi = {10.1093/nar/gkw081}, author = {Jejoong Yoo and Aleksei Aksimentiev} } @article {206, title = {Molecular Dynamics of Membrane-Spanning DNA Channels: Conductance Mechanism, Electro-Osmotic Transport, and Mechanical Gating}, journal = {The Journal of Physical Chemistry Letters}, volume = {6}, year = {2015}, month = {11/2015}, pages = {4680-4687}, abstract = {

DNA self-assembly has emerged as a new paradigm for design of biomimetic membrane channels. Several experimental groups have already demonstrated assembly and insertion of DNA channels into lipid bilayer membranes; however, the structure of the channels and their conductance mechanism have remained undetermined. Here, we report the results of molecular dynamics simulations that characterized the biophysical properties of the DNA membrane channels with atomic precision. We show that, while overall remaining stable, the local structure of the channels undergoes considerable fluctuations, departing from the idealized design. The transmembrane ionic current flows both through the central pore of the channel as well as along the DNA walls and through the gaps in the DNA structure. Surprisingly, we find that the conductance of DNA channels depend on the membrane tension, making them potentially suitable for force-sensing applications. Finally, we show that electro-osmosis governs the transport of druglike molecules through the DNA channels.

}, doi = {10.1021/acs.jpclett.5b01964}, url = {http://dx.doi.org/10.1021/acs.jpclett.5b01964}, author = {Jejoong Yoo and Aleksei Aksimentiev} } @article {204, title = {Plasmonic Nanopores for Trapping, Controlling Displacement, and Sequencing of DNA}, journal = {ACS Nano}, volume = {9}, year = {2015}, month = {09/2015}, pages = {10598--10611}, type = {Article}, abstract = {

\ \ \ \ \ \ With the aim of developing a DNA sequencing methodology, we theoretically examine the feasibility of using nanoplasmonics to control the translocation of a DNA molecule through a solid-state nanopore and to read off sequence information using surface-enhanced Raman spectroscopy. Using molecular dynamics\ simulations, we show that high-intensity optical hot spots produced by a metallic nanostructure can arrest DNA translocation through a solid-state nanopore, thus providing a physical knob for controlling the DNA speed. Switching the plasmonic field on and off can displace the DNA molecule in discrete steps, sequentially exposing neighboring fragments of a DNA molecule to the pore as well as to the plasmonic hot spot. Surface-enhanced Raman scattering from the exposed DNA fragments contains information about their nucleotide composition, possibly allowing the identification of the nucleotide sequence of a DNA molecule transported through the hot spot. The principles of plasmonic nanopore sequencing can be extended to detection of DNA modifications and RNA characterization.

}, doi = {10.1021/acsnano.5b04173}, url = {http://pubs.acs.org/doi/10.1021/acsnano.5b04173}, author = {Maxim Belkin and Shu-Han Chao and Magnus P. Jonsson and Cees Dekker and Aleksei Aksimentiev} } @article {202, title = {Highly permeable artificial water channels that self-assemble into two-dimensional arrays}, journal = {Proceedings of the National Academy of Science}, volume = {112}, year = {2015}, month = {07/2015}, pages = {9810-9815}, chapter = {9810}, abstract = {

Bioinspired artificial water channels aim to combine the high permeability and selectivity of biological aquaporin (AQP) water channels with chemical stability. We characterized a new architecture of artificial water channels, peptide-appended pillar[5]arenes (PAPs). The average single-channel osmotic water permeability for PAPs is 1.0({\textpm} 0.3){\texttimes}10-14\ cm3/s or 3.5({\textpm} 1.0){\texttimes}108\ water molecules/s, which is in the range of AQPs (3.4~40.3{\texttimes}108\ water molecules/s) and their current synthetic analogs, carbon nanotubes (CNTs, 9.0{\texttimes}108\ water molecules/s). This permeability is an order of magnitude higher than first-generation artificial water channels (20 to ~107\ water molecules/s). Furthermore, within lipid bilayers, PAP channels can self-assemble into two-dimensional arrays. Importantly for permeable membrane design, the pore density of PAP channel arrays (~2.6{\texttimes}105\ pores/μm2) is two orders of magnitude higher than CNT membranes (0.1~2.5{\texttimes}103\ pores/μm2). PAP channels thus combine the advantages of biological channels and CNTs and improve upon them through their relatively simple synthesis, chemical stability and propensity to form arrays.

}, keywords = {membrane, nanochannel, permeation}, doi = {10.1073/pnas.1508575112}, author = {Yue-xiao Shen and Wen Si and Mustafa Erbakan and Karl Decker and Rita De Zorzi and Patrick O. Saboe and You Jung Kang and Sheereen Majd and Peter J. Butler and Thomas Walz and Aleksei Aksimentiev and Jun-li Hou and Manish Kumar} } @article {160, title = {Slowing DNA Transport Using Graphene{\textendash}DNA Interactions}, journal = {Advanced Functional Materials}, volume = {25}, year = {2015}, month = {02/2015}, pages = {936{\textendash}946}, abstract = {

Slowing down DNA translocation speed in a nanopore is essential to ensuring reliable resolution of individual bases. Thin membrane materials enhance spatial resolution but simultaneously reduce the temporal resolution as the molecules translocate far too quickly. In this study, the effect of exposed graphene layers on the transport dynamics of both single (ssDNA) and double-stranded DNA (dsDNA) through nanopores is examined. Nanopore devices with various combinations of graphene and Al2O3 dielectric layers in stacked membrane structures are fabricated. Slow translocations of ssDNA in nanopores drilled in membranes with layers of graphene are reported. The increased hydrophobic interactions between the ssDNA and the graphene layers could explain this phenomenon. Further confirmation of the hydrophobic origins of these interactions is obtained through reporting significantly faster translocations of dsDNA through these graphene layered membranes. Molecular dynamics simulations confirm the preferential interactions of DNA with the graphene layers as compared to the dielectric layer verifying the experimental findings. Based on our findings, we propose that the integration of multiple stacked graphene layers could slow down DNA enough to enable the identification of nucleobases.

}, keywords = {graphene, graphene{\textendash}DNA interactions, Molecular dynamics, Nanopores, stacked membranes}, issn = {1616-3028}, doi = {10.1002/adfm.201403719}, url = {http://dx.doi.org/10.1002/adfm.201403719}, author = {Banerjee, Shouvik and James Wilson and Shim, Jiwook and Shankla, Manish and Corbin, Elise A. and Aleksei Aksimentiev and Rashid Bashir} } @article {LI2015, title = {Ionic Conductivity, Structural Deformation, and Programmable Anisotropy of DNA Origami in Electric Field}, journal = {ACS Nano}, volume = {9}, year = {2015}, note = {PMID: 25623807}, month = {01/2015}, pages = {1420-1433}, abstract = {

The DNA origami technique can enable functionalization of inorganic structures for single-molecule electric current recordings. Experiments have shown that several layers of DNA molecules, a DNA origami plate, placed on top of a solid-state nanopore is permeable to ions. Here, we report a comprehensive characterization of the ionic conductivity of DNA origami plates by means of all-atom molecular dynamics (MD) simulations and nanocapillary electric current recordings. Using the MD method, we characterize the ionic conductivity of several origami constructs, revealing the local distribution of ions, the distribution of the electrostatic potential and contribution of different molecular species to the current. The simulations determine the dependence of the ionic conductivity on the applied voltage, the number of DNA layers, the nucleotide content and the lattice type of the plates. We demonstrate that increasing the concentration of Mg2+\ ions makes the origami plates more compact, reducing their conductivity. The conductance of a DNA origami plate on top of a solid-state nanopore is determined by the two competing effects: bending of the DNA origami plate that reduces the current and separation of the DNA origami layers that increases the current. The latter is produced by the electro-osmotic flow and is reversible at the time scale of a hundred nanoseconds. The conductance of a DNA origami object is found to depend on its orientation, reaching maximum when the electric field aligns with the direction of the DNA helices. Our work demonstrates feasibility of programming the electrical properties of a self-assembled nanoscale object using DNA.

}, doi = {10.1021/nn505825z}, url = {http://dx.doi.org/10.1021/nn505825z}, author = {Li, Chen-Yu and Hemmig, Elisa A. and Kong, Jinglin and Yoo, Jejoong and Hern{\'a}ndez-Ainsa, Silvia and Keyser, Ulrich F. and Aleksei Aksimentiev} } @article {139, title = {Close encounters with DNA}, journal = {J Phys Condens Matter}, volume = {26}, year = {2014}, month = {10/2014}, pages = {413101}, abstract = {

Over the past ten years, the all-atom molecular dynamics method has grown in the scale of both systems and processes amenable to it and in its ability to make quantitative predictions about the behavior of experimental systems. The field of computational DNA research is no exception, witnessing a dramatic increase in the size of systems simulated with atomic resolution, the duration of individual simulations and the realism of the simulation outcomes. In this topical review, we describe the hallmark physical properties of DNA from the perspective of all-atom simulations. We demonstrate the amazing ability of such simulations to reveal the microscopic physical origins of experimentally observed phenomena. We also discuss the frustrating limitations associated with imperfections of present atomic force fields and inadequate sampling. The review is focused on the following four physical properties of DNA: effective electric charge, response to an external mechanical force, interaction with other DNA molecules and behavior in an external electric field.

}, keywords = {Review}, issn = {1361-648X}, doi = {10.1088/0953-8984/26/41/413101}, author = {Christopher Maffeo and Yoo, J and Jeffrey Comer and Wells, D B and Luan, B and Aleksei Aksimentiev} } @article {123, title = {A Coarse-Grained Model of Unstructured Single-Stranded DNA Derived from Atomistic Simulation and Single-Molecule Experiment}, journal = {Journal of Chemical Theory and Computation}, volume = {10}, year = {2014}, month = {08/2014}, pages = {2891{\textendash}2896}, abstract = {

A simple coarse-grained model of single-stranded DNA (ssDNA) was developed, featuring only two sites per nucleotide that represent the centers of mass of the backbone and sugar/base groups. In the model, the interactions between sites are described using tabulated bonded potentials optimized to reproduce the solution structure of DNA observed in atomistic molecular dynamics simulations. Isotropic potentials describe nonbonded interactions, implicitly taking into account the solvent conditions to match the experimentally determined radius of gyration of ssDNA. The model reproduces experimentally measured force{\textendash}extension dependence of an unstructured DNA strand across 2 orders of magnitude of the applied force. The accuracy of the model was confirmed by measuring the end-to-end distance of a dT14 fragment via FRET while stretching the molecules using optical tweezers. The model offers straightforward generalization to systems containing double-stranded DNA and DNA binding proteins.

}, doi = {10.1021/ct500193u}, url = {http://pubs.acs.org/doi/abs/10.1021/ct500193u}, author = {Christopher Maffeo and Ngo, Thuy T. M. and Ha, Taekjip and Aleksei Aksimentiev} } @article {119, title = {Two Structural Scenarios for Protein Stabilization by PEG.}, journal = {J Phys Chem B}, volume = {118}, year = {2014}, month = {05/2014}, pages = {8388{\textendash}8395}, abstract = {

PEGylation, or addition of poly(ethylene glycol) chains to proteins, is widely used to improve delivery in pharmaceutical applications. Recent studies suggest that stabilization of a protein by PEG, and hence its proteolytic degradability, are sequence-dependent and require only short PEG chains. Here we connect stabilization by short PEG chains directly to the structural dynamics of the protein and PEG chain. We measured the stability of human Pin1 WW domain with PEG-4 at asparagine 19 for a full mutant cycle at two positions thought to influence PEG-protein interaction: Ser16Ala and Tyr23Phe. We then performed explicit solvent molecular dynamics simulations on all PEGylated and PEG-free mutants. The mutant cycle yields a non-additive stabilization effect where the pseudo wild type and double mutant are more stabilized relative to unPEGylated proteins than are the two single mutants. The simulation reveals why: the double mutant suffers loss of beta sheet structure, which PEGylation restores even though the PEG extends as a coil into the solvent. In contrast, in one of the single mutants PEG preferentially interacts with the protein surface while disrupting the interactions of its asparagine host with a nearby methionine side chain. Thus PEG attachment can stabilize a protein differentially depending on the local sequence, and either by interacting with the surface, or by extending into the solvent. A simulation with PEG-45 attached to asparagine 19 shows that PEG even can do both in the same context.

}, issn = {1520-5207}, doi = {10.1021/jp502234s}, author = {Shu-Han Chao and Matthews, Sam S and Paxman, Ryan and Aleksei Aksimentiev and Martin Gruebele and Price, Joshua L} } @article {14, title = {A Stabilized Finite Element Method for Modified Poisson-Nernst-Planck Equations to Determine Ion Flow Through a Nanopore}, journal = {Commun Comput Phys}, volume = {15}, year = {2014}, month = {01/2014}, pages = {93-125}, abstract = {

The conventional Poisson-Nernst-Planck equations do not account for the finite size of ions explicitly. This leads to solutions featuring unrealistically high ionic concentrations in the regions subject to external potentials, in particular, near highly charged surfaces. A modified form of the Poisson-Nernst-Planck equations accounts for steric effects and results in solutions with finite ion concentrations. Here, we evaluate numerical methods for solving the modified Poisson-Nernst-Planck equations by modeling electric field-driven transport of ions through a nanopore. We describe a novel, robust finite element solver that combines the applications of the Newton{\textquoteright}s method to the nonlinear Galerkin form of the equations, augmented with stabilization terms to appropriately handle the drift-diffusion processes. To make direct comparison with particle-based simulations possible, our method is specifically designed to produce solutions under periodic boundary conditions and to conserve the number of ions in the solution domain. We test our finite element solver on a set of challenging numerical experiments that include calculations of the ion distribution in a volume confined between two charged plates, calculations of the ionic current though a nanopore subject to an external electric field, and modeling the effect of a DNA molecule on the ion concentration and nanopore current.

}, issn = {1815-2406}, doi = {10.4208/cicp.101112.100413a}, author = {Chaudhry, Jehanzeb Hameed and Jeffrey Comer and Aleksei Aksimentiev and Olson, Luke N} } @article {133, title = {Modeling thermophoretic effects in solid-state nanopores}, journal = {Journal of Computational Electronics}, volume = {13}, year = {2014}, pages = {826-838}, publisher = {Springer US}, abstract = {

Local modulation of temperature has emerged as a new mechanism for regulation of molecular transport through nanopores. Predicting the effect of such modulations on nanopore transport requires simulation protocols capable of reproducing non-uniform temperature gradients observed in experiment. Conventional molecular dynamics (MD) method typically employs a single thermostat for maintaining a uniform distribution of temperature in the entire simulation domain, and, therefore, can not model local temperature variations. In this article, we describe a set of simulation protocols that enable modeling of nanopore systems featuring non-uniform distributions of temperature. First, we describe a method to impose a temperature gradient in all-atom MD simulations based on a boundary-driven non-equilibrium MD protocol. Then, we use this method to study the effect of temperature gradient on the distribution of ions in bulk solution (the thermophoretic effect). We show that DNA nucleotides exhibit differential response to the same temperature gradient. Next, we describe a method to directly compute the effective force of a thermal gradient on a prototypical biomolecule {\textemdash} a fragment of double-stranded DNA. Following that, we demonstrate an all-atom MD protocol for modeling thermophoretic effects in solid-state nanopores. We show that local heating of a nanopore volume can be used to regulate the nanopore ionic current. Finally, we show how continuum calculations can be coupled to a coarse-grained model of DNA to study the effect of local temperature modulation on electrophoretic motion of DNA through plasmonic nanopores. The computational methods described in this article are expected to find applications in rational design of temperature-responsive nanopore systems.

}, keywords = {Boundary-driven MD, Molecular dynamics, Nanofluidics, Non-equilibrium MD, Plasmonic heating, Soret coefficient, Thermodiffusion, Thermophoresis}, issn = {1569-8025}, doi = {10.1007/s10825-014-0594-8}, url = {http://dx.doi.org/10.1007/s10825-014-0594-8}, author = {Maxim Belkin and Shu-Han Chao and Giannetti, Gino and Aleksei Aksimentiev} } @article {Carson20142381, title = {Smooth DNA Transport through a Narrowed Pore Geometry}, journal = {Biophysical Journal}, volume = {107}, number = {10}, year = {2014}, pages = {2381 - 2393}, abstract = {

Voltage-driven transport of double-stranded DNA through nanoscale pores holds much potential for applications in quantitative molecular biology and biotechnology, yet the microscopic details of translocation have proven to be challenging to decipher. Earlier experiments showed strong dependence of transport kinetics on pore size: fast regular transport in large pores (\> 5 nm diameter), and slower yet heterogeneous transport time distributions in sub-5 nm pores, which imply a large positional uncertainty of the DNA in the pore as a function of the translocation time. In this work, we show that this anomalous transport is a result of DNA self-interaction, a phenomenon that is strictly pore-diameter dependent. We identify a regime in which DNA transport is regular, producing narrow and well-behaved dwell-time distributions that fit a simple drift-diffusion theory. Furthermore, a systematic study of the dependence of dwell time on DNA length reveals a single power-law scaling of 1.37 in the range of 35{\textendash}20,000 bp. We highlight the resolution of our nanopore device by discriminating via single pulses 100 and 500 bp fragments in a mixture with \>98\% accuracy. When coupled to an appropriate sequence labeling method, our observation of smooth DNA translocation can pave the way for high-resolution DNA mapping and sizing applications in genomics.

}, issn = {0006-3495}, doi = {10.1016/j.bpj.2014.10.017}, url = {http://www.sciencedirect.com/science/article/pii/S0006349514010686}, author = {Spencer Carson and James Wilson and Aleksei Aksimentiev and Meni Wanunu} } @article {147, title = {Conformational transitions and stop-and-go nanopore transport of single-stranded DNA on charged graphene}, journal = {Nature Communications}, volume = {5}, year = {2014}, pages = {5171}, abstract = {

Control over interactions with biomolecules holds the key to applications of graphene in biotechnology. One such application is nanopore sequencing, where a DNA molecule is electrophoretically driven through a graphene nanopore. Here we investigate how interactions of single-stranded DNA and a graphene membrane can be controlled by electrically biasing the membrane. The results of our molecular dynamics simulations suggest that electric charge on graphene can force a DNA homopolymer to adopt a range of strikingly different conformations. The conformational response is sensitive to even very subtle nucleotide modifications, such as DNA methylation. The speed of DNA motion through a graphene nanopore is strongly affected by the graphene charge: a positive charge accelerates the motion, whereas a negative charge arrests it. As a possible application of the effect, we demonstrate stop-and-go transport of DNA controlled by the charge of graphene. Such on-demand transport of DNA is essential for realizing nanopore sequencing.

}, issn = {2041-1723}, doi = {10.1038/ncomms6171}, url = {http://www.nature.com/ncomms/2014/141009/ncomms6171/full/ncomms6171.html}, author = {Shankla, Manish and Aleksei Aksimentiev} } @article {doi:10.1021/jp501492g, title = {Rectification of Ion Current in Nanopores Depends on the Type of Monovalent Cations: Experiments and Modeling}, journal = {The Journal of Physical Chemistry C}, volume = {118}, number = {18}, year = {2014}, pages = {9809-9819}, abstract = {Rectifying nanopores feature ion currents that are higher for voltages of one polarity compared to the currents recorded for corresponding voltages of the opposite polarity. Rectification of nanopores has been found to depend on the pore opening diameter and distribution of surface charges on the pore walls as well as pore geometry. Very little is known, however, on the dependence of ionic rectification on the type of transported ions of the same charge. We performed experiments with single conically shaped nanopores in a polymer film and recorded current-voltage curves in three electrolytes: LiCl, NaCl, and KCl. Rectification degrees of the pores, quantified as the ratio of currents recorded for voltages of opposite polarities, were the highest for KCl and the lowest for LiCl. The experimental observations could not be explained by a continuum modeling based on the Poisson-Nernst-Planck equations. All-atom molecular dynamics simulations revealed differential binding between Li+, Na+, and K+ ions and carboxyl groups on the pore walls, resulting in changes to both the effective surface charge of the nanopore and cation mobility within the pore.}, doi = {10.1021/jp501492g}, url = {http://dx.doi.org/10.1021/jp501492g}, author = {Gamble, Trevor and Karl Decker and Plett, Timothy S. and Pevarnik, Matthew and Pietschmann, Jan-Frederik and Vlassiouk, Ivan and Aleksei Aksimentiev and Siwy, Zuzanna S.} } @article {90, title = {In situ structure and dynamics of DNA origami determined through molecular dynamics simulations.}, journal = {Proc Natl Acad Sci U S A}, volume = {110}, year = {2013}, month = {12/2013}, pages = {20099-104}, abstract = {

The DNA origami method permits folding of long single-stranded DNA into complex 3D structures with subnanometer precision. Transmission electron microscopy, atomic force microscopy, and recently cryo-EM tomography have been used to characterize the properties of such DNA origami objects, however their microscopic structures and dynamics have remained unknown. Here, we report the results of all-atom molecular dynamics simulations that characterized the structural and mechanical properties of DNA origami objects in unprecedented microscopic detail. When simulated in an aqueous environment, the structures of DNA origami objects depart from their idealized targets as a result of steric, electrostatic, and solvent-mediated forces. Whereas the global structural features of such relaxed conformations conform to the target designs, local deformations are abundant and vary in magnitude along the structures. In contrast to their free-solution conformation, the Holliday junctions in the DNA origami structures adopt a left-handed antiparallel conformation. We find the DNA origami structures undergo considerable temporal fluctuations on both local and global scales. Analysis of such structural fluctuations reveals the local mechanical properties of the DNA origami objects. The lattice type of the structures considerably affects global mechanical properties such as bending rigidity. Our study demonstrates the potential of all-atom molecular dynamics simulations to play a considerable role in future development of the DNA origami field by providing accurate, quantitative assessment of local and global structural and mechanical properties of DNA origami objects.

}, keywords = {DNA, Single-Stranded, Models, Molecular, Molecular Dynamics Simulation, Nanotechnology, Nucleic Acid Conformation, Water}, issn = {1091-6490}, doi = {10.1073/pnas.1316521110}, author = {Yoo, Jejoong and Aleksei Aksimentiev} } @article {20, title = {Stretching and controlled motion of single-stranded DNA in locally heated solid-state nanopores}, journal = {ACS Nano}, volume = {7}, year = {2013}, month = {08/2013}, pages = {6816-24}, abstract = {

Practical applications of solid-state nanopores for DNA detection and sequencing require the electrophoretic motion of DNA through the nanopores to be precisely controlled. Controlling the motion of single-stranded DNA presents a particular challenge, in part because of the multitude of conformations that a DNA strand can adopt in a nanopore. Through continuum, coarse-grained and atomistic modeling, we demonstrate that local heating of the nanopore volume can be used to alter the electrophoretic mobility and conformation of single-stranded DNA. In the nanopore systems considered, the temperature near the nanopore is modulated via a nanometer-size heater element that can be radiatively switched on and off. The local enhancement of temperature produces considerable stretching of the DNA fragment confined within the nanopore. Such stretching is reversible, so that the conformation of DNA can be toggled between compact (local heating is off) and extended (local heating is on) states. The effective thermophoretic force acting on single-stranded DNA in the vicinity of the nanopore is found to be sufficiently large (4-8 pN) to affect such changes in the DNA conformation. The local heating of the nanopore volume is observed to promote single-file translocation of DNA strands at transmembrane biases as low as 10 mV, which opens new avenues for using solid-state nanopores for detection and sequencing of DNA.

}, issn = {1936-086X}, doi = {10.1021/nn403575n}, author = {Maxim Belkin and Christopher Maffeo and David B Wells and Aleksei Aksimentiev} } @article {25, title = {Competitive binding of cations to duplex DNA revealed through molecular dynamics simulations}, journal = {J Phys Chem B}, volume = {116}, year = {2012}, month = {2012 Nov 1}, pages = {12946-54}, abstract = {

The concept of "ion atmosphere" is prevalent in both theoretical and experimental studies of nucleic acid systems, yet the spatial arrangement and the composition of ions in the ion atmosphere remain elusive, in particular when several ionic species (e.g., Na(+), K(+), and Mg(2+)) compete to neutralize the charge of a nucleic acid polyanion. Complementing the experimental study of Bai and co-workers (J. Am. Chem. Soc.2007, 129, 14981), here we characterize ion atmosphere around double-stranded DNA through all-atom molecular dynamics simulations. We demonstrate that our improved parametrization of the all-atom model can quantitatively reproduce the experimental ion-count data. Our simulations determine the size of the ion atmosphere, the concentration profiles of ionic species competing to neutralize the DNA charge, and the sites of the cations{\textquoteright} preferential binding at the surface of double-stranded DNA. We find that the effective size of the ion atmosphere depends on both the bulk concentration and valence of ions: increasing either reduces the size of the atmosphere. Near DNA, the concentration of Mg(2+) is strongly enhanced compared to monovalent cations. Within the DNA grooves, the relative concentrations of cations depend on their bulk values. Nevertheless, the total charge of competing cations buried in the DNA grooves is constant and compensates for about ~30\% of the total DNA charge.

}, keywords = {Base Pairing, Base Sequence, Binding, Competitive, Cations, DNA, Molecular Dynamics Simulation, Phosphates, Static Electricity}, issn = {1520-5207}, doi = {10.1021/jp306598y}, author = {Yoo, Jejoong and Aleksei Aksimentiev} } @article {27, title = {DNA base-calling from a nanopore using a Viterbi algorithm}, journal = {Biophys J}, volume = {102}, year = {2012}, month = {2012 May 16}, pages = {L37-9}, abstract = {

Nanopore-based DNA sequencing is the most promising third-generation sequencing method. It has superior read length, speed, and sample requirements compared with state-of-the-art second-generation methods. However, base-calling still presents substantial difficulty because the resolution of the technique is limited compared with the measured signal/noise ratio. Here we demonstrate a method to decode 3-bp-resolution nanopore electrical measurements into a DNA sequence using a Hidden Markov model. This method shows tremendous potential for accuracy (~98\%), even with a poor signal/noise ratio.

}, keywords = {Algorithms, Base Sequence, DNA, Electricity, Genome, Human, Humans, Markov Chains, Nanopores, Sequence Analysis, DNA, Signal-To-Noise Ratio}, issn = {1542-0086}, doi = {10.1016/j.bpj.2012.04.009}, author = {Timp, Winston and Jeffrey Comer and Aleksei Aksimentiev} } @article {15, title = {End-to-end attraction of duplex DNA}, journal = {Nucleic Acids Res}, volume = {40}, year = {2012}, month = {2012 May}, pages = {3812-21}, abstract = {

Recent experiments [Nakata, M. et al., End-to-end stacking and liquid crystal condensation of 6 to 20 basepair DNA duplexes. Science 2007; 318:1276-1279] have demonstrated spontaneous end-to-end association of short duplex DNA fragments into long rod-like structures. By means of extensive all-atom molecular dynamic simulations, we characterized end-to-end interactions of duplex DNA, quantitatively describing the forces, free energy and kinetics of the end-to-end association process. We found short DNA duplexes to spontaneously aggregate end-to-end when axially aligned in a small volume of monovalent electrolyte. It was observed that electrostatic repulsion of 5{\textquoteright}-phosphoryl groups promoted the formation of aggregates in a conformation similar to the B-form DNA double helix. Application of an external force revealed that rupture of the end-to-end assembly occurs by the shearing of the terminal base pairs. The standard binding free energy and the kinetic rates of end-to-end association and dissociation processes were estimated using two complementary methods: umbrella sampling simulations of two DNA fragments and direct observation of the aggregation process in a system containing 458 DNA fragments. We found the end-to-end force to be short range, attractive, hydrophobic and only weakly dependent on the ion concentration. The relation between the stacking free energy and end-to-end attraction is discussed as well as possible roles of the end-to-end interaction in biological and nanotechnological systems.

}, keywords = {DNA, Kinetics, Molecular Dynamics Simulation, Nucleic Acid Conformation}, issn = {1362-4962}, doi = {10.1093/nar/gkr1220}, author = {Christopher Maffeo and Luan, Binquan and Aleksei Aksimentiev} } @article {29, title = {Predicting the DNA sequence dependence of nanopore ion current using atomic-resolution Brownian dynamics}, journal = {J Phys Chem C Nanomater Interfaces}, volume = {116}, year = {2012}, month = {2012 Feb 9}, pages = {3376-3393}, abstract = {

It has become possible to distinguish DNA molecules of different nucleotide sequences by measuring ion current passing through a narrow pore containing DNA. To assist experimentalists in interpreting the results of such measurements and to improve the DNA sequence detection method, we have developed a computational approach that has both the atomic-scale accuracy and the computational efficiency required to predict DNA sequence-specific differences in the nanopore ion current. In our Brownian dynamics method, the interaction between the ions and DNA is described by three-dimensional potential of mean force maps determined to a 0.03 nm resolution from all-atom molecular dynamics simulations. While this atomic-resolution Brownian dynamics method produces results with orders of magnitude less computational effort than all-atom molecular dynamics requires, we show here that the ion distributions and ion currents predicted by the two methods agree. Finally, using our Brownian dynamics method, we find that a small change in the sequence of DNA within a pore can cause a large change in the ion current, and validate this result with all-atom molecular dynamics.

}, issn = {1932-7447}, doi = {10.1021/jp210641j}, author = {Jeffrey Comer and Aleksei Aksimentiev} } @article {31, title = {Slowing down DNA translocation through a nanopore in lithium chloride.}, journal = {Nano Lett}, volume = {12}, year = {2012}, month = {2012 Feb 8}, pages = {1038-44}, abstract = {

The charge of a DNA molecule is a crucial parameter in many DNA detection and manipulation schemes such as gel electrophoresis and lab-on-a-chip applications. Here, we study the partial reduction of the DNA charge due to counterion binding by means of nanopore translocation experiments and all-atom molecular dynamics (MD) simulations. Surprisingly, we find that the translocation time of a DNA molecule through a solid-state nanopore strongly increases as the counterions decrease in size from K(+) to Na(+) to Li(+), both for double-stranded DNA (dsDNA) and single-stranded DNA (ssDNA). MD simulations elucidate the microscopic origin of this effect: Li(+) and Na(+) bind DNA stronger than K(+). These fundamental insights into the counterion binding to DNA also provide a practical method for achieving at least 10-fold enhanced resolution in nanopore applications.

}, keywords = {DNA, Lithium Chloride, Models, Molecular, Molecular Dynamics Simulation, Nanopores, Nanotechnology, Particle Size, Surface Properties}, issn = {1530-6992}, doi = {10.1021/nl204273h}, author = {Kowalczyk, Stefan W and David B Wells and Aleksei Aksimentiev and Dekker, Cees} } @article {18, title = {Modeling and simulation of ion channels}, journal = {Chem Rev}, volume = {112}, year = {2012}, month = {2012 Dec 12}, pages = {6250-6284}, abstract = {

Transport of ions through pores in membranes is a process of fundamental importance to cell biology. In living organisms, such transport is facilitated by ion channels that utilize the ionic flux to perform diverse biological functions, such as cell{\textendash}cell communication and signaling, osmotic stress response, muscle contraction, etc. The action of ion channels is responsible for most of what we (humans) perceive as reality in the form of sound, smell, sight, taste, and touch and forms the physiological basis for thought. Biomimetic ion channels are ubiquitous in engineering, with application ranging from water desalination to fuel cells. Here, we review efforts to model and simulate ion channels that occurred within the past 10 years.

}, keywords = {Review}, issn = {1520-6890}, doi = {10.1021/cr3002609}, author = {Christopher Maffeo and Bhattacharya, Swati and Yoo, Jejoong and David B Wells and Aleksei Aksimentiev} } @article {24, title = {Toward detection of DNA-bound proteins using solid-state nanopores: insights from computer simulations}, journal = {Electrophoresis}, volume = {33}, year = {2012}, month = {2012 Dec}, pages = {3466-79}, abstract = {

Through all-atom molecular dynamics simulations, we explore the use of nanopores in thin synthetic membranes for detection and identification of DNA binding proteins. Reproducing the setup of a typical experiment, we simulate electric field driven transport of DNA-bound proteins through nanopores smaller in diameter than the proteins. As model systems, we use restriction enzymes EcoRI and BamHI specifically and nonspecifically bound to a fragment of dsDNA, and streptavidin and NeutrAvidin proteins bound to dsDNA and ssDNA via a biotin linker. Our simulations elucidate the molecular mechanics of nanopore-induced rupture of a protein-DNA complex, the effective force applied to the DNA-protein bond by the electrophoretic force in a nanopore, and the role of DNA-surface interactions in the rupture process. We evaluate the ability of the nanopore ionic current and the local electrostatic potential measured by an embedded electrode to report capture of DNA, capture of a DNA-bound protein, and rupture of the DNA-protein bond. We find that changes in the strain on dsDNA can reveal the rupture of a protein-DNA complex by altering both the nanopore ionic current and the potential of the embedded electrode. Based on the results of our simulations, we suggest a new method for detection of DNA binding proteins that utilizes peeling of a nicked double strand under the electrophoretic force in a nanopore.

}, keywords = {Bacterial Proteins, Deoxyribonuclease BamHI, Deoxyribonuclease EcoRI, DNA, DNA-Binding Proteins, Electrochemical Techniques, Models, Chemical, Molecular Dynamics Simulation, Nanopores, Protein Binding, Spectrum Analysis, Static Electricity}, issn = {1522-2683}, doi = {10.1002/elps.201200164}, author = {Jeffrey Comer and Anthony H. Ho and Aleksei Aksimentiev} } @article {13, title = {Assessing graphene nanopores for sequencing DNA.}, journal = {Nano Letters}, volume = {12}, year = {2012}, month = {2012 Aug 8}, pages = {4117-4123}, abstract = {

Using all-atom molecular dynamics and atomic-resolution Brownian dynamics, we simulate the translocation of single-stranded DNA through graphene nanopores and characterize the ionic current blockades produced by DNA nucleotides. We find that transport of single DNA strands through graphene nanopores may occur in single nucleotide steps. For certain pore geometries, hydrophobic interactions with the graphene membrane lead to a dramatic reduction in the conformational fluctuations of the nucleotides in the nanopores. Furthermore, we show that ionic current blockades produced by different DNA nucleotides are, in general, indicative of the nucleotide type, but very sensitive to the orientation of the nucleotides in the nanopore. Taken together, our simulations suggest that strand sequencing of DNA by measuring the ionic current blockades in graphene nanopores may be possible, given that the conformation of DNA nucleotides in the nanopore can be controlled through precise engineering of the nanopore surface.

}, keywords = {DNA, Graphite, Nanopores, Sequence Analysis, DNA}, issn = {1530-6992}, doi = {10.1021/nl301655d}, author = {David B Wells and Maxim Belkin and Jeffrey Comer and Aleksei Aksimentiev} } @article {26, title = {Molecular dynamics study of MspA arginine mutants predicts slow DNA translocations and ion current blockades indicative of DNA sequence}, journal = {ACS Nano}, volume = {6}, year = {2012}, month = {2012 Aug 28}, pages = {6960-8}, abstract = {

The protein nanopore Mycobacteria smegmatis porin A (MspA), can be used to sense individual nucleotides within DNA, potentially enabling a technique known as nanopore sequencing. In this technique, single-stranded DNA electrophoretically moves through the nanopore and results in an ionic current that is nucleotide-specific. However, with a high transport velocity of the DNA within the nanopore, the ionic current cannot be used to distinguish signals within noise. Through extensive (~100 μs in total) all-atom molecular dynamics simulations, we examine the effect of positively charged residues on DNA translocation rate and the ionic current blockades in MspA. Simulation of several arginine mutations show a ~10-30 fold reduction of DNA translocation speed without eliminating the nucleotide induced current blockages. Comparison of our results with similar engineering efforts on a different nanopore (α-hemolysin) reveals a nontrivial effect of nanopore geometry on the ionic current blockades in mutant nanopores.

}, keywords = {Arginine, Base Sequence, Biosensing Techniques, Computer Simulation, Conductometry, DNA, Electric Conductivity, Ion Channel Gating, Models, Chemical, Models, Genetic, Models, Molecular, Molecular Sequence Data, Mutation, Porins, Sequence Analysis, DNA, Translocation, Genetic}, issn = {1936-086X}, doi = {10.1021/nn3019943}, author = {Bhattacharya, Swati and Derrington, Ian M and Pavlenok, Mikhail and Niederweis, Michael and Gundlach, Jens H and Aleksei Aksimentiev} } @article {30, title = {Optimization of the molecular dynamics method for simulations of DNA and ion transport through biological nanopores}, journal = {Methods Mol Biol}, volume = {870}, year = {2012}, month = {2012}, pages = {165-86}, abstract = {

Molecular dynamics (MD) simulations have become a standard method for the rational design and interpretation of experimental studies of DNA translocation through nanopores. The MD method, however, offers a multitude of algorithms, parameters, and other protocol choices that can affect the accuracy of the resulting data as well as computational efficiency. In this chapter, we examine the most popular choices offered by the MD method, seeking an optimal set of parameters that enable the most computationally efficient and accurate simulations of DNA and ion transport through biological nanopores. In particular, we examine the influence of short-range cutoff, integration timestep and force field parameters on the temperature and concentration dependence of bulk ion conductivity, ion pairing, ion solvation energy, DNA structure, DNA-ion interactions, and the ionic current through a nanopore.

}, keywords = {Biological Transport, DNA, Electric Conductivity, Electroosmosis, Hemolysin Proteins, Ions, Lipid Bilayers, Molecular Dynamics Simulation, Nanopores, Porins, Solvents, Thermodynamics}, issn = {1940-6029}, doi = {10.1007/978-1-61779-773-6_10}, author = {David B Wells and Bhattacharya, Swati and Carr, Rogan and Christopher Maffeo and Anthony H. Ho and Jeffrey Comer and Aleksei Aksimentiev} } @article {91, title = {Improved Parametrization of Li+, Na+, K+, and Mg2+ Ions for All-Atom Molecular Dynamics Simulations of Nucleic Acid Systems}, journal = {The Journal of Physical Chemistry Letters}, volume = {3}, year = {2012}, pages = {45-50}, abstract = {

Atomic-scale modeling of compacted nucleic acids has the ability to reveal the inner workings of spectacular biomolecular machines, yet the outcome of such modeling efforts sensitively depends on the accuracy of the underlying computational models. Our molecular dynamics simulations of an array of 64 parallel duplex DNA revealed considerable artifacts of cation-DNA phosphate interactions in CHARMM and AMBER parameter sets: both the DNA arrangement and the pressure inside the DNA arrays were found to be in considerable disagreement with experiment. To improve the models, we fine-tuned van der Waals interaction parameters for specific ion pairs to reproduce experimental osmotic pressure of binary electrolyte solutions of biologically relevant ions. Repeating the DNA array simulations using our parameters produced results consistent with experiment. Our improved parametrization can be directly applied to molecular dynamics simulations of various charged biomolecular systems, including nucleic acids, proteins, and lipid bilayer membranes.

}, issn = {1948-7185}, doi = {10.1021/jz201501a}, url = {http://pubs.acs.org/doi/abs/10.1021/jz201501a}, author = {Yoo, Jejoong and Aleksei Aksimentiev} } @article {33, title = {Atoms-to-microns model for small solute transport through sticky nanochannels}, journal = {Lab Chip}, volume = {11}, year = {2011}, month = {2011 Nov 21}, pages = {3766-73}, abstract = {

Modeling the transport of solutes through fluidic systems that have adsorbing surfaces is challenging due to the range of length and time scales involved. The components of such systems typically have dimensions from hundreds of nanometres to microns, whereas adsorption of solutes is sensitive to the atomic-scale structure of the solutes and surfaces. Here, we describe an atomic-resolution Brownian dynamics method for modeling the transport of solutes through sticky nanofluidic channels. Our method can fully recreate the results of all-atom molecular dynamics simulations at a fraction of the computational cost of the latter, which makes simulations of micron-size channels at a millisecond time scale possible without losing information about the atomic-scale features of the system. We demonstrate the capability of our method by simulating the rise and fall of solute concentration in sub-micron-long sticky nanochannels, showing that the atomic-scale features of the channels{\textquoteright} surfaces have a dramatic effect on the kinetics of solute transport in and out of the channels. We expect our method to find applications in design and optimization of micro and nanofluidic systems for solute-specific transport and to complement existing approaches to modeling lab-on-a-chip devices by providing atomic scale information at a low computational cost.

}, keywords = {Microfluidic Analytical Techniques, Molecular Conformation, Molecular Dynamics Simulation, Motion, Nanotechnology, Reproducibility of Results, Surface Properties}, issn = {1473-0189}, doi = {10.1039/c1lc20697d}, author = {Carr, Rogan and Jeffrey Comer and Ginsberg, Mark D and Aleksei Aksimentiev} } @article {34, title = {Control of Nanoscale Environment to Improve Stability of Immobilized Proteins on Diamond Surfaces}, journal = {Adv Funct Mater}, volume = {21}, year = {2011}, month = {2011 Mar 21}, pages = {1040-1050}, abstract = {

Immunoassays for detection of bacterial pathogens rely on the selectivity and stability of bio-recognition elements such as antibodies tethered to sensor surfaces. The search for novel surfaces that improve the stability of biomolecules and assay performance has been pursued for a long time. However, the anticipated improvements in stability have not been realized in practice under physiological conditions because the surface functionalization layers on commonly used substrates, silica and gold, are themselves unstable on time scales of days. In this paper, we show that covalent linking of antibodies to diamond surfaces leads to substantial improvements in biological activity of proteins as measured by the ability to selectively capture cells of the pathogenic bacterium Escherichia coli O157:H7 even after exposure to buffer solutions at 37 {\textdegree}C for extended periods of time, approaching 2 weeks. Our results from ELISA, XPS, fluorescence microscopy, and MD simulations suggest that by using highly stable surface chemistry and controlling the nanoscale organization of the antibodies on the surface, it is possible to achieve significant improvements in biological activity and stability. Our findings can be easily extended to functionalization of micro and nanodimensional sensors and structures of biomedical diagnostic and therapeutic interest.

}, issn = {1616-301X}, doi = {10.1002/adfm.201002251}, author = {Radadia, Adarsh D and Courtney J Stavis and Carr, Rogan and Zeng, Hongjun and King, William P and Carlisle, John A and Aleksei Aksimentiev and Hamers, Robert J and Rashid Bashir} } @article {28, title = {Microscopic Perspective on the Adsorption Isotherm of a Heterogeneous Surface}, journal = {J Phys Chem Lett}, volume = {2}, year = {2011}, month = {2011 Jul 2}, pages = {1804-1807}, abstract = {

Adsorption of dissolved molecules onto solid surfaces can be extremely sensitive to the atomic-scale properties of the solute and surface, causing difficulties for the design of fluidic systems in industrial, medical and technological applications. In this communication, we show that the Langmuir isotherm for adsorption of a small molecule to a realistic, heterogeneous surface can be predicted from atomic structures of the molecule and surface through molecular dynamics (MD) simulations. We highlight the method by studying the adsorption of dimethyl-methylphosphonate (DMMP) to amorphous silica substrates and show that subtle differences in the atomic-scale surface properties can have drastic effects on the Langmuir isotherm. The sensitivity of the method presented is sufficient to permit the optimization of fluidic devices and to determine fundamental design rules for controlling adsorption at the nanoscale.

}, issn = {1948-7185}, doi = {10.1021/jz200749d}, author = {Carr, Rogan and Jeffrey Comer and Ginsberg, Mark D and Aleksei Aksimentiev} } @article {40, title = {Surface functionalization of thin-film diamond for highly stable and selective biological interfaces}, journal = {Proc Natl Acad Sci U S A}, volume = {108}, year = {2011}, month = {2011 Jan 18}, pages = {983-8}, abstract = {

Carbon is an extremely versatile family of materials with a wide range of mechanical, optical, and mechanical properties, but many similarities in surface chemistry. As one of the most chemically stable materials known, carbon provides an outstanding platform for the development of highly tunable molecular and biomolecular interfaces. Photochemical grafting of alkenes has emerged as an attractive method for functionalizing surfaces of diamond, but many aspects of the surface chemistry and impact on biological recognition processes remain unexplored. Here we report investigations of the interaction of functionalized diamond surfaces with proteins and biological cells using X-ray photoelectron spectroscopy (XPS), atomic force microscopy, and fluorescence methods. XPS data show that functionalization of diamond with short ethylene glycol oligomers reduces the nonspecific binding of fibrinogen below the detection limit of XPS, estimated as > 97\% reduction over H-terminated diamond. Measurements of different forms of diamond with different roughness are used to explore the influence of roughness on nonspecific binding onto H-terminated and ethylene glycol (EG)-terminated surfaces. Finally, we use XPS to characterize the chemical stability of Escherichia coli K12 antibodies on the surfaces of diamond and amine-functionalized glass. Our results show that antibody-modified diamond surfaces exhibit increased stability in XPS and that this is accompanied by retention of biological activity in cell-capture measurements. Our results demonstrate that surface chemistry on diamond and other carbon-based materials provides an excellent platform for biomolecular interfaces with high stability and high selectivity.

}, keywords = {Antibodies, Bacterial, Avidin, Chemistry, Physical, Diamond, Escherichia coli K12, Ethylene Glycol, Fibrinogen, Fluorescence, Microscopy, Atomic Force, Photoelectron Spectroscopy, Protein Binding, Surface Properties}, issn = {1091-6490}, doi = {10.1073/pnas.1006660107}, author = {Courtney J Stavis and Clare, Tami Lasseter and Butler, James E and Radadia, Adarsh D and Carr, Rogan and Zeng, Hongjun and King, William P and Carlisle, John A and Aleksei Aksimentiev and Rashid Bashir and Hamers, Robert J} } @article {39, title = {Modeling Pressure-Driven Transport of Proteins through a Nanochannel}, journal = {IEEE Trans Nanotechnol}, volume = {10}, year = {2011}, month = {2011 Jan}, pages = {75-82}, abstract = {

Reducing the size of a nanofluidic channel not only creates new opportunities for high-precision manipulation of biological macromolecules, but also makes the performance of the entire nanofluidic system more susceptible to undesirable interactions between the transported biomolecules and the walls of the channel. In this manuscript, we report molecular dynamics simulations of a pressure-driven flow through a silica nanochannel that characterized, with atomic resolution, adsorption of a model protein to its surface. Although the simulated adsorption of the proteins was found to be nonspecific, it had a dramatic effect on the rate of the protein transport. To determine the relative strength of the protein-silica interactions in different adsorbed states, we simulated flow-induced desorption of the proteins from the silica surface. Our analysis of the protein conformations in the adsorbed states did not reveal any simple dependence of the adsorption strength on the size and composition of the protein-silica contact, suggesting that the heterogeneity of the silica surface may be a important factor.

}, issn = {1536-125X}, author = {Carr, Rogan and Jeffrey Comer and Ginsberg, Mark D and Aleksei Aksimentiev} } @article {195, title = {Rectification of the current in alpha-hemolysin pore depends on the cation type: the alkali series probed by MD simulations and experiments}, journal = {The Journal of Physical Chemistry C}, volume = {115}, year = {2011}, month = {2011 Feb 21}, pages = {4255-4264}, abstract = {

A striking feature of the alpha-hemolysin channel-a prime candidate for biotechnological applications-is the dependence of its ionic conductance on the magnitude and direction of the applied bias. Through a combination of lipid bilayer single-channel recording and molecular dynamics (MD) simulations, we characterized the current-voltage relationship of alpha-hemolysin for all alkali chloride salts at neutral pH. The rectification of the ionic current was found to depend on the type of cations and increase from Li(+) to Cs(+). Analysis of the MD trajectories yielded a simple quantitative model that related the ionic current to the electrostatic potential, the concentration and effective mobility of ions in the channel. MD simulations reveal that the major contribution to the current asymmetry and rectification properties originates from the cationic contribution to the current that is significantly reduced in a cationic dependent way when the membrane polarity is reversed. The variation of chloride current was found to be less important. We report that the differential affinity of cations for the charged residues positioned at the channel{\textquoteright}s end modulates the number of ions inside the channel stem thus affecting the current properties. Through direct comparison of simulation and experiment, this study evaluates the accuracy of the MD method for prediction of the asymmetric, voltage dependent conductances of a membrane channel.

}, issn = {1932-7447}, doi = {10.1021/jp111441p}, author = {Bhattacharya, Swati and Muzard, L and Payet, Linda and Math{\'e}, J{\'e}r{\^o}me and Bockelmann, Ulrich and Aleksei Aksimentiev and Viasnoff, Virgile} } @article {32, title = {Nanopore analysis of individual RNA/antibiotic complexes.}, journal = {ACS Nano}, volume = {5}, year = {2011}, month = {2011 Dec 27}, pages = {9345-53}, abstract = {

Nanopores in thin solid-state membranes are used to rapidly analyze individual RNA/drug complexes. The interactions of a truncated A-site RNA model of the prokaryotic ribosome with aminoglycoside antibiotics are characterized by passing individual molecules through a 3-3.5 nm diameter pore fabricated in a 8-10 nm thick silicon nitride membrane. Complexes of the A-site RNA with aminoglycosides can be distinguished from unbound A-site based on the ion current signatures produced as they pass through the nanopores. Counting the fraction of free and drug-bound molecules affords label-free drug-RNA binding isotherms consistent with literature reports and with data generated using independent fluorescence-based assays. Our measurements are supported by molecular dynamics simulations, which illustrate the relationship between the ionic current and complexation of the A-site RNA with paramomycin, a prototypical aminoglycoside antibiotic.

}, keywords = {Anti-Bacterial Agents, Binding Sites, Diffusion, Electroporation, Materials Testing, Membranes, Artificial, Nanostructures, Paromomycin, Porosity, RNA, Semiconductors}, issn = {1936-086X}, doi = {10.1021/nn203764j}, author = {Meni Wanunu and Bhattacharya, Swati and Xie, Yun and Tor, Yitzhak and Aleksei Aksimentiev and Drndic, Marija} } @article {37, title = {Lipid bilayer coated Al(2)O(3) nanopore sensors: towards a hybrid biological solid-state nanopore}, journal = {Biomed Microdevices}, volume = {13}, year = {2011}, month = {2011 Aug}, pages = {671-82}, abstract = {

Solid-state nanopore sensors are highly versatile platforms for the rapid, label-free electrical detection and analysis of single molecules, applicable to next generation DNA sequencing. The versatility of this technology allows for both large scale device integration and interfacing with biological systems. Here we report on the development of a hybrid biological solid-state nanopore platform that incorporates a highly mobile lipid bilayer on a single solid-state Al(2)O(3) nanopore sensor, for the potential reconstitution of ion channels and biological nanopores. Such a system seeks to combine the superior electrical, thermal, and mechanical stability of Al(2)O(3) solid-state nanopores with the chemical specificity of biological nanopores. Bilayers on Al(2)O(3) exhibit higher diffusivity than those formed on TiO(2) and SiO(2) substrates, attributed to the presence of a thick hydration layer on Al(2)O(3), a key requirement to preserving the biological functionality of reconstituted membrane proteins. Molecular dynamics simulations demonstrate that the electrostatic repulsion between the dipole of the DOPC headgroup and the positively charged Al(2)O(3) surface may be responsible for the enhanced thickness of this hydration layer. Lipid bilayer coated Al(2)O(3) nanopore sensors exhibit excellent electrical properties and enhanced mechanical stability (GΩ seals for over 50 h), making this technology ideal for use in ion channel electrophysiology, the screening of ion channel active drugs and future integration with biological nanopores such as α-hemolysin and MspA for rapid single molecule DNA sequencing. This technology can find broad application in bio-nanotechnology.

}, keywords = {Aluminum Oxide, Biosensing Techniques, DNA, Fluorescence Recovery After Photobleaching, Ion Channels, Lipid Bilayers, Models, Biological, Molecular Dynamics Simulation, Nanopores, Nanotechnology, Phosphatidylcholines, Sequence Analysis, DNA, Silicon Dioxide, Staining and Labeling, Titanium}, issn = {1572-8781}, doi = {10.1007/s10544-011-9537-3}, author = {Venkatesan, Bala Murali and Polans, James and Jeffrey Comer and Sridhar, Supriya and Wendell, David and Aleksei Aksimentiev and Rashid Bashir} } @inbook {35, title = {Modeling nanopores for sequencing DNA}, booktitle = {DNA Nanotechnology: Methods and Protocols}, volume = {749}, year = {2011}, month = {2011}, pages = {317-358}, abstract = {

Using nanopores to sequence DNA rapidly and at a low cost has the potential to radically transform the field of genomic research. However, despite all the exciting developments in the field, sequencing DNA using a nanopore has yet to be demonstrated. Among the many problems that hinder development of the nanopore sequencing methods is the inability of current experimental techniques to visualize DNA conformations in a nanopore and directly relate the microscopic state of the system to the measured signal. We have recently shown that such tasks could be accomplished through computation. This chapter provides step-by-step instructions of how to build atomic scale models of biological and solid-state nanopore systems, use the molecular dynamics method to simulate the electric field-driven transport of ions and DNA through the nanopores, and analyze the results of such computational experiments.

}, keywords = {Base Sequence, Computer Simulation, DNA, Hemolysin Proteins, Models, Molecular, Molecular Conformation, Molecular Dynamics Simulation, Nanopores, Nanotechnology, Sequence Analysis, DNA}, issn = {1940-6029}, doi = {10.1007/978-1-61779-142-0_22}, author = {Jeffrey Comer and David B Wells and Aleksei Aksimentiev}, editor = {Giampaolo Zuccheri and Bruno Samori} } @inbook {193, title = {Nanopore Force Spectroscopy: Insights from Molecular Dynamics Simulations}, booktitle = {Nanopores: Sensing and Fundamental Biological Interactions}, year = {2011}, pages = {335{\textendash}356}, publisher = {Springer Science and Business Media, LLC}, organization = {Springer Science and Business Media, LLC}, chapter = {14}, address = {New York}, abstract = {

Nanopore force spectroscopy (NFS) has emerged as a convenient method to characterize the behavior of single biomolecules and biomolecular assemblies under force. NFS has many advantages over conventional single molecule techniques, such as being label-free and high throughput; however, NFS lacks direct control over the force applied to the biomolecules and registers the conformational transitions induced by the force only indirectly, by monitoring changes in the ionic current passing through the pore. In this chapter, we describe how all-atom molecular dynamics simulations can complement NFS experiments by providing information inaccessible to experiment. The chapter illustrates applications of the molecular dynamics (MD) method to interpret the results of NFS measurements, characterize the forces involved and determine the microscopic origin of the observed phenomena. Important technical aspects of the method, as well as its pitfalls and limitations are briefly discussed.

}, isbn = {978-144-198-2-5-1-3}, doi = {10.1007/978-1-4419-8252-0_14}, author = {Jeffrey Comer and Aleksei Aksimentiev}, editor = {Rashid Bashir and Samir Iqbal} } @inbook {192, title = {Third Generation DNA Sequencing with a Nanopore}, booktitle = {Nanopores: Sensing fundamental biological interactions at the single molecule level}, year = {2011}, pages = {287-311}, publisher = {Springer US}, organization = {Springer US}, chapter = {12}, abstract = {

With the advent of Next-Generation-Sequencing (NGS) technologies, an enormous volume of DNA sequencing data can be generated at low cost, placing genomic science within the grasp of everyday medicine. However, mired in this voluminous data, a new problem has emerged: the assembly of the genome from the short reads. In this chapter we examine the prospects for sequencing DNA using a synthetic nanopore. Nanopore sequencing has the potential for very long reads, reducing the computational burden posed by alignment and genome assembly, while at the same time eliminating logistically challenging and error-prone amplification and library formation due to its exquisite single molecule sensitivity. On the other hand, long high fidelity reads demand stringent control over both the DNA configuration in the pore and the translocation kinetics. We examine the prospects for satisfying these specifications with a synthetic nanopore.

}, keywords = {Comparison between biological and synthetic nanopores, Hydrodynamic focusing, Molecular dynamics simulations, Sequencing DNA, Trapping DNA, λ-DNA}, isbn = {978-1-4419-8251-3}, doi = {10.1007/978-1-4419-8252-0_12}, url = {http://dx.doi.org/10.1007/978-1-4419-8252-0_12}, author = {Gregory Timp and Mirsaidov, Utkur and Timp, Winston and Shim, Jiwook and Wang, Deqiang and Valentin Dimitrov and Scrimgeour, Jan and Lin, Chunchen and Jeffrey Comer and Anthony H. Ho and Zou, Xueqing and Aleksei Aksimentiev and Klaus Schulten}, editor = {Iqbal, Samir M. and Rashid Bashir} } @inbook {145, title = {Modeling the Interface between Biological and Synthetic Components in Hybrid Nanosystems}, booktitle = {Simulations in Nanobiotechnology}, year = {2011}, pages = {43-60}, publisher = {CRC Press}, organization = {CRC Press}, chapter = {2}, abstract = {Hybrid structures that combine biological and inorganic materials are ubiquitous in the biosphere, from the carbonated hydroxyapatite that makes up the inorganic structure of bones to the calcium carbonate created by coral polyps and coralline algae that form the structure of coral reefs. The ability to design materials that are bio-compatible, or able to be incorporated into organisms without provoking an immune response, is important for medicine and therapeutics, for example, in prosthetics and implanted medical devices such as pacemakers. However, designing synthetic materials to interact favorably with biological components is made difficult by the fact that many biological processes, including immune response, are dictated by interactions betweeen biomolecules and their environment on the nanometer scale. Therefore, our ability to fabricate materials with nanometer precision would provide hope for a future in which man-made devices can easily interface with the biological world.}, issn = {9781439835043}, url = {http://www.crcpress.com/product/isbn/9781439835043}, author = {Carr, Rogan and Jeffrey Comer and Aleksei Aksimentiev}, editor = {Eom, Kilho} } @article {16, title = {Single molecule force measurements: insights from molecular simulations. Comment on "Biophysical characterization of DNA binding from single molecule force measurements" by Kathy R. Chaurasiya et al.}, journal = {Phys Life Rev}, volume = {7}, year = {2010}, month = {2010 Sep}, pages = {353-4; discussion 358-61}, keywords = {Biophysics, DNA, Microscopy, Atomic Force, Molecular Dynamics Simulation, Nucleic Acid Conformation, Thermodynamics}, issn = {1873-1457}, doi = {10.1016/j.plrev.2010.07.004}, author = {Christopher Maffeo and Aleksei Aksimentiev} } @article {17, title = {DNA-DNA interactions in tight supercoils are described by a small effective charge density}, journal = {Phys Rev Lett}, volume = {105}, year = {2010}, month = {2010 Oct 8}, pages = {158101}, abstract = {

DNA-DNA interactions are important for genome compaction and transcription regulation. In studies of such complex processes, DNA is often modeled as a homogeneously charged cylinder and its electrostatic interactions are calculated within the framework of the Poisson-Boltzmann equation. Commonly, a charge adaptation factor is used to address limitations of this theoretical approach. Despite considerable theoretical and experimental efforts, a rigorous quantitative assessment of this parameter is lacking. Here, we comprehensively characterized DNA-DNA interactions in the presence of monovalent ions by analyzing the supercoiling behavior of single DNA molecules held under constant tension. Both a theoretical model and coarse-grained simulations of this process revealed a surprisingly small effective DNA charge of 40\% of the nominal charge density, which was additionally supported by all-atom molecular dynamics simulations.

}, keywords = {Biomechanical Phenomena, DNA, Superhelical, Molecular Dynamics Simulation, Monte Carlo Method, Salts, Static Electricity}, issn = {1079-7114}, doi = {10.1103/PhysRevLett.105.158101 }, url = {http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.105.158101}, author = {Christopher Maffeo and Sch{\"o}pflin, Robert and Brutzer, Hergen and Stehr, Ren{\'e} and Aleksei Aksimentiev and Wedemann, Gero and Seidel, Ralf} } @article {41, title = {Slowing the translocation of double-stranded DNA using a nanopore smaller than the double helix}, journal = {Nanotechnology}, volume = {21}, year = {2010}, month = {2010 Oct 1}, pages = {395501}, abstract = {

It is now possible to slow and trap a single molecule of double-stranded DNA (dsDNA), by stretching it using a nanopore, smaller in diameter than the double helix, in a solid-state membrane. By applying an electric force larger than the threshold for stretching, dsDNA can be impelled through the pore. Once a current blockade associated with a translocating molecule is detected, the electric field in the pore is switched in an interval less than the translocation time to a value below the threshold for stretching. According to molecular dynamics (MD) simulations, this leaves the dsDNA stretched in the pore constriction with the base-pairs tilted, while the B-form canonical structure is preserved outside the pore. In this configuration, the translocation velocity is substantially reduced from 1 bp/10 ns to approximately 1 bp/2 ms in the extreme, potentially facilitating high fidelity reads for sequencing, precise sorting, and high resolution (force) spectroscopy.

}, keywords = {Bacteriophage lambda, DNA, DNA, Viral, Electrochemical Techniques, Microscopy, Electron, Transmission, Molecular Dynamics Simulation, Nanopores, Nanotechnology, Nucleic Acid Conformation, Particle Size}, issn = {1361-6528}, doi = {10.1088/0957-4484/21/39/395501}, author = {Mirsaidov, Utkur and Jeffrey Comer and Valentin Dimitrov and Aleksei Aksimentiev and Gregory Timp} } @article {38, title = {Control and reversal of the electrophoretic force on DNA in a charged nanopore}, journal = {J Phys Condens Matter}, volume = {22}, year = {2010}, month = {2010 Nov 17}, pages = {454123}, abstract = {

Electric field driven transport of DNA through solid-state nanopores is the key process in nanopore-based DNA sequencing that promises dramatic reduction of genome sequencing costs. A major hurdle in the development of this sequencing method is that DNA transport through the nanopores occurs too quickly for the DNA sequence to be detected. By means of all-atom molecular dynamics simulations, we demonstrate that the velocity of DNA transport through a nanopore can be controlled by the charge state of the nanopore surface. In particular, we show that the charge density of the nanopore surface controls the magnitude and/or direction of the electro-osmotic flow through the nanopore and thereby can significantly reduce or even reverse the effective electrophoretic force on DNA. Our work suggests a physical mechanism to control DNA transport in a nanopore by chemical, electrical or electrochemical modification of the nanopore surface.

}, keywords = {Base Sequence, Computer Simulation, DNA, Electromagnetic Fields, Electrophoresis, Models, Chemical, Molecular Sequence Data, Nanostructures, Porosity, Sequence Analysis, DNA, Static Electricity, Stress, Mechanical}, issn = {1361-648X}, doi = {10.1088/0953-8984/22/45/454123}, author = {Luan, Binquan and Aleksei Aksimentiev} } @article {36, title = {Nanopore Sequencing: Electrical Measurements of the Code of Life}, journal = {IEEE Trans Nanotechnol}, volume = {9}, year = {2010}, month = {2010 May 1}, pages = {281-294}, abstract = {

Sequencing a single molecule of deoxyribonucleic acid (DNA) using a nanopore is a revolutionary concept because it combines the potential for long read lengths (\>5 kbp) with high speed (1 bp/10 ns), while obviating the need for costly amplification procedures due to the exquisite single molecule sensitivity. The prospects for implementing this concept seem bright. The cost savings from the removal of required reagents, coupled with the speed of nanopore sequencing places the $1000 genome within grasp. However, challenges remain: high fidelity reads demand stringent control over both the molecular configuration in the pore and the translocation kinetics. The molecular configuration determines how the ions passing through the pore come into contact with the nucleotides, while the translocation kinetics affect the time interval in which the same nucleotides are held in the constriction as the data is acquired. Proteins like α-hemolysin and its mutants offer exquisitely precise self-assembled nanopores and have demonstrated the facility for discriminating individual nucleotides, but it is currently difficult to design protein structure ab initio, which frustrates tailoring a pore for sequencing genomic DNA. Nanopores in solid-state membranes have been proposed as an alternative because of the flexibility in fabrication and ease of integration into a sequencing platform. Preliminary results have shown that with careful control of the dimensions of the pore and the shape of the electric field, control of DNA translocation through the pore is possible. Furthermore, discrimination between different base pairs of DNA may be feasible. Thus, a nanopore promises inexpensive, reliable, high-throughput sequencing, which could thrust genomic science into personal medicine.

}, keywords = {Review}, issn = {1536-125X}, doi = {10.1109/TNANO.2010.2044418}, author = {Timp, Winston and Mirsaidov, Utkur M and Wang, Deqiang and Jeffrey Comer and Aleksei Aksimentiev and Gregory Timp} } @article {43, title = {Mechanical properties of a complete microtubule revealed through molecular dynamics simulation}, journal = {Biophys J}, volume = {99}, year = {2010}, month = {2010 Jul 21}, pages = {629-37}, abstract = {

Microtubules (MTs) are the largest type of cellular filament, essential in processes ranging from mitosis and meiosis to flagellar motility. Many of the processes depend critically on the mechanical properties of the MT, but the elastic moduli, notably the Young{\textquoteright}s modulus, are not directly revealed in experiment, which instead measures either flexural rigidity or response to radial deformation. Molecular dynamics (MD) is a method that allows the mechanical properties of single biomolecules to be investigated through computation. Typically, MD requires an atomic resolution structure of the molecule, which is unavailable for many systems, including MTs. By combining structural information from cryo-electron microscopy and electron crystallography, we have constructed an all-atom model of a complete MT and used MD to determine its mechanical properties. The simulations revealed nonlinear axial stress-strain behavior featuring a pronounced softening under extension, a possible plastic deformation transition under radial compression, and a distinct asymmetry in response to the two senses of twist. This work demonstrates the possibility of combining different levels of structural information to produce all-atom models suitable for quantitative MD simulations, which extends the range of systems amenable to the MD method and should enable exciting advances in our microscopic knowledge of biology.

}, keywords = {Biomechanical Phenomena, Microtubules, Molecular Dynamics Simulation, Protein Multimerization, Stress, Mechanical, Tubulin}, issn = {1542-0086}, doi = {10.1016/j.bpj.2010.04.038}, author = {David B Wells and Aleksei Aksimentiev} } @article {44, title = {Electric and Electrophoretic Inversion of the DNA Charge in Multivalent Electrolytes}, journal = {Soft Matter}, volume = {6}, year = {2010}, month = {2010 Jan 1}, pages = {243-246}, abstract = {

Counterion-induced inversion of the DNA charge was characterized through extensive molecular dynamics simulations. We observed reversal of the DNA motion in an external electric field upon increasing the concentration of trivalent or quadrivalent counterions. In the case of a divalent electrolyte, inversion of the DNA{\textquoteright}s electric charge was observed at high concentrations of the electrolyte but not reversal of the DNA{\textquoteright} electrophoretic motion. We demonstrate that inversion of the DNA{\textquoteright}s electrophoretic mobility results from a complex interplay of electrostatics and hydrodynamics.

}, issn = {1744-683X}, doi = {10.1039/b917973a}, author = {Luan, Binquan and Aleksei Aksimentiev} } @article {42, title = {Deciphering ionic current signatures of DNA transport through a nanopore}, journal = {Nanoscale}, volume = {2}, year = {2010}, month = {2010 Apr}, pages = {468-83}, abstract = {

Within just a decade from the pioneering work demonstrating the utility of nanopores for molecular sensing, nanopores have emerged as versatile systems for single-molecule manipulation and analysis. In a typical setup, a gradient of the electrostatic potential captures charged solutes from the solution and forces them to move through a single nanopore, across an otherwise impermeable membrane. The ionic current blockades resulting from the presence of a solute in a nanopore can reveal the type of the solute, for example, the nucleotide makeup of a DNA strand. Despite great success, the microscopic mechanisms underlying the functionality of such stochastic sensors remain largely unknown, as it is not currently possible to characterize the microscopic conformations of single biomolecules directly in a nanopore and thereby unequivocally establish the causal relationship between the observables and the microscopic events. Such a relationship can be determined using molecular dynamics-a computational method that can accurately predict the time evolution of a molecular system starting from a given microscopic state. This article describes recent applications of this method to the process of DNA transport through biological and synthetic nanopores.

}, keywords = {Biological Transport, DNA, Escherichia coli Proteins, Hemolysin Proteins, Kinetics, Molecular Dynamics Simulation, Monte Carlo Method, Nanostructures, Nanotubes, Porins, Review}, issn = {2040-3372}, doi = {10.1039/b9nr00275h}, author = {Aleksei Aksimentiev} } @article {46, title = {The effect of calcium on the conformation of cobalamin transporter BtuB}, journal = {Proteins}, volume = {78}, year = {2010}, month = {2010 Apr}, pages = {1153-62}, abstract = {

BtuB is a beta-barrel membrane protein that facilitates transport of cobalamin (vitamin B12) from the extracellular medium across the outer membrane of Escherichia coli. It is thought that binding of B12 to BtuB alters the conformation of its periplasm-exposed N-terminal residues (the TonB box), which enables subsequent binding of a TonB protein and leads to eventual uptake of B12 into the cytoplasm. Structural studies determined the location of the B12 binding site at the top of the BtuB{\textquoteright}s beta-barrel, surrounded by extracellular loops. However, the structure of the loops was found to depend on the method used to obtain the protein crystals, which-among other factors-differed in calcium concentration. Experimentally, calcium concentration was found to modulate the binding of the B12 substrate to BtuB. In this study, we investigate the effect of calcium ions on the conformation of the extracellular loops of BtuB and their possible role in B12 binding. Using all-atom molecular dynamics, we simulate conformational fluctuations of several X-ray structures of BtuB in the presence and absence of calcium ions. These simulations demonstrate that calcium ions can stabilize the conformation of loops 3-4, 5-6, and 15-16, and thereby prevent occlusion of the binding site. Furthermore, binding of calcium ions to extracellular loops of BtuB was found to enhance correlated motions in the BtuB structure, which is expected to promote signal transduction. Finally, we characterize conformation dynamics of the TonB box in different X-ray structures and find an interesting correlation between the stability of the TonB box structure and calcium binding.

}, keywords = {Amino Acid Sequence, Bacterial Outer Membrane Proteins, Calcium, Escherichia coli Proteins, Lipid Bilayers, Membrane Transport Proteins, Models, Molecular, Molecular Dynamics Simulation, Molecular Sequence Data, Protein Binding, Protein Conformation, Vitamin B 12, Vitamin B Complex}, issn = {1097-0134}, doi = {10.1002/prot.22635}, author = {Luan, Binquan and Carr, Rogan and Caffrey, Martin and Aleksei Aksimentiev} } @article {48, title = {Modeling Transport Through Synthetic Nanopores}, journal = {IEEE Nanotechnol Mag}, volume = {3}, year = {2009}, month = {2009 Mar}, pages = {20-28}, abstract = {

Nanopores in thin synthetic membranes have emerged as convenient tools for high-throughput single-molecule manipulation and analysis. Because of their small sizes and their ability to selectively transport solutes through otherwise impermeable membranes, nanopores have numerous potential applications in nanobiotechnology. For most applications, properties of the nanopore systems have to be characterize at the atomic level, which is currently beyond the limit of experimental methods. Molecular dynamics (MD) simulations can provide the desired information, however several technical challenges have to be met before this method can be applied to synthetic nanopore systems. Here, we highlight our recent work on modeling synthetic nanopores of the most common types. First, we describe a novel graphical tool for setting up all-atom systems incorporating inorganic materials and biomolecules. Next, we illustrate the application of the MD method for silica, silicon nitride, and polyethylene terephthalate nanopores. Following that, we describe a method for modeling synthetic surfaces using a bias potential. Future directions for tool development and nanopore modeling are briefly discussed at the end of this article.

}, issn = {1932-4510}, doi = {10.1109/MNANO.2008.931112}, author = {Aleksei Aksimentiev and Robert Brunner and Eduardo Cruz-Ch{\'u} and Jeffrey Comer and Klaus Schulten} } @article {19, title = {Structure, dynamics, and ion conductance of the phospholamban pentamer}, journal = {Biophys J}, volume = {96}, year = {2009}, month = {2009 Jun 17}, pages = {4853-65}, abstract = {

A 52-residue membrane protein, phospholamban (PLN) is an inhibitor of an adenosine-5{\textquoteright}-triphosphate-driven calcium pump, the Ca2+-ATPase. Although the inhibition of Ca2+-ATPase involves PLN monomers, in a lipid bilayer membrane, PLN monomers form stable pentamers of unknown biological function. The recent NMR structure of a PLN pentamer depicts cytoplasmic helices extending normal to the bilayer in what is known as the bellflower conformation. The structure shows transmembrane helices forming a hydrophobic pore 4 {\r A} in diameter, which is reminiscent of earlier reports of possible ion conductance through PLN pentamers. However, recent FRET measurements suggested an alternative structure for the PLN pentamer, known as the pinwheel model, which features a narrower transmembrane pore and cytoplasmic helices that lie against the bilayer. Here, we report on structural dynamics and conductance properties of the PLN pentamers from all-atom (AA) and coarse-grained (CG) molecular dynamics simulations. Our AA simulations of the bellflower model demonstrate that in a lipid bilayer membrane or a detergent micelle, the cytoplasmic helices undergo large structural fluctuations, whereas the transmembrane pore shrinks and becomes asymmetric. Similar asymmetry of the transmembrane region was observed in the AA simulations of the pinwheel model; the cytoplasmic helices remained in contact with the bilayer. Using the CG approach, structural dynamics of both models were investigated on a microsecond timescale. The cytoplasmic helices of the CG bellflower model were observed to fall against the bilayer, whereas in the CG pinwheel model the conformation of the cytoplasmic helices remained stable. Using steered molecular dynamics simulations, we investigated the feasibility of ion conductance through the pore of the bellflower model. The resulting approximate potentials of mean force indicate that the PLN pentamer is unlikely to function as an ion channel.

}, keywords = {Calcium-Binding Proteins, Cell Membrane, Computer Simulation, Cytoplasm, Humans, Hydrophobic and Hydrophilic Interactions, Ions, Lipid Bilayers, Micelles, Models, Molecular, Protein Multimerization, Protein Structure, Quaternary}, issn = {1542-0086}, doi = {10.1016/j.bpj.2009.03.053}, author = {Christopher Maffeo and Aleksei Aksimentiev} } @article {49, title = {Analyzing the forces binding a restriction endonuclease to DNA using a synthetic nanopore}, journal = {Nucleic Acids Res}, volume = {37}, year = {2009}, month = {2009 Jul}, pages = {4170-9}, abstract = {

Restriction endonucleases are used prevalently in recombinant DNA technology because they bind so stably to a specific target sequence and, in the presence of cofactors, cleave double-helical DNA specifically at a target sequence at a high rate. Using synthetic nanopores along with molecular dynamics (MD), we have analyzed with atomic resolution how a prototypical restriction endonuclease, EcoRI, binds to the DNA target sequence--GAATTC--in the absence of a Mg(2+) ion cofactor. We have previously shown that there is a voltage threshold for permeation of DNA bound to restriction enzymes through a nanopore that is associated with a nanonewton force required to rupture the complex. By introducing mutations in the DNA, we now show that this threshold depends on the recognition sequence and scales linearly with the dissociation energy, independent of the pore geometry. To predict the effect of mutation in a base pair on the free energy of dissociation, MD is used to qualitatively rank the stability of bonds in the EcoRI-DNA complex. We find that the second base in the target sequence exhibits the strongest binding to the protein, followed by the third and first bases, with even the flanking sequence affecting the binding, corroborating our experiments.

}, keywords = {Computer Simulation, Deoxyribonuclease EcoRI, DNA, DNA-Binding Proteins, Models, Molecular, Nanostructures, Protein Binding}, issn = {1362-4962}, doi = {10.1093/nar/gkp317}, author = {Dorvel, B and G Sigalov and Zhao, Q and Jeffrey Comer and Valentin Dimitrov and Mirsaidov, U and Aleksei Aksimentiev and Gregory Timp} } @article {50, title = {Microscopic mechanics of hairpin DNA translocation through synthetic nanopores}, journal = {Biophys J}, volume = {96}, year = {2009}, month = {2009 Jan}, pages = {593-608}, abstract = {

Nanoscale pores have proved useful as a means to assay DNA and are actively being developed as the basis of genome sequencing methods. Hairpin DNA (hpDNA), having both double-helical and overhanging coil portions, can be trapped in a nanopore, giving ample time to execute a sequence measurement. In this article, we provide a detailed account of hpDNA interaction with a synthetic nanopore obtained through extensive all-atom molecular dynamics simulations. For synthetic pores with minimum diameters from 1.3 to 2.2 nm, we find that hpDNA can translocate by three modes: unzipping of the double helix and--in two distinct orientations--stretching/distortion of the double helix. Furthermore, each of these modes can be selected by an appropriate choice of the pore size and voltage applied transverse to the membrane. We demonstrate that the presence of hpDNA can dramatically alter the distribution of ions within the pore, substantially affecting the ionic current through it. In experiments and simulations, the ionic current relative to that in the absence of DNA can drop below 10\% and rise beyond 200\%. Simulations associate the former with the double helix occupying the constriction and the latter with accumulation of DNA that has passed through the constriction.

}, keywords = {Cell Membrane Permeability, Computer Simulation, DNA, Ion Transport, Membrane Potentials, Membranes, Artificial, Microelectrodes, Microscopy, Electron, Transmission, Models, Molecular, Monte Carlo Method, Nanostructures, Nucleic Acid Conformation}, issn = {1542-0086}, doi = {10.1016/j.bpj.2008.09.023}, author = {Jeffrey Comer and Valentin Dimitrov and Zhao, Qian and Gregory Timp and Aleksei Aksimentiev} } @article {45, title = {Ionic Current Rectification Through Silica Nanopores}, journal = {J Phys Chem C Nanomater Interfaces}, volume = {113}, year = {2009}, month = {2009 Feb 1}, pages = {1850}, abstract = {

Nanopores immersed in electrolytic solution and under the influence of an electric field can produce ionic current rectification, where ionic currents are higher for one voltage polarity than for the opposite polarity, resulting in an asymmetric current-voltage (I-V) curve. This behavior has been observed in polymer and silicon-based nanopores as well as in theoretically studied continuum models. By means of atomic level molecular dynamics (MD) simulations, we have performed a systematic investigation of KCl conductance in silica nanopores with a total simulation time of 680 ns. We found that ion-binding spots at the silica surfaces, such as dangling atoms, have effects on the ion concentration and electrostatic potential inside the nanopore, producing asymmetric I-V curves. Conversely, silica surfaces without ion-binding spots produce symmetric I-V curves.

}, issn = {1932-7447}, doi = {10.1021/jp804724p}, author = {Eduardo Cruz-Ch{\'u} and Aleksei Aksimentiev and Klaus Schulten} } @article {55, title = {Strain softening in stretched DNA}, journal = {Phys Rev Lett}, volume = {101}, year = {2008}, month = {2008 Sep 12}, pages = {118101}, abstract = {

The microscopic mechanics of DNA stretching was characterized using extensive molecular dynamics simulations. By employing an anisotropic pressure-control method, realistic force-extension dependences of effectively infinite DNA molecules were obtained. A coexistence of B and S DNA domains was observed during the overstretching transition. The simulations revealed that strain softening may occur in the process of stretching torsionally constrained DNA. The latter observation was qualitatively reconciled with available experimental data using a random-field Ising model.

}, keywords = {Computer Simulation, DNA, Elasticity, Kinetics, Models, Molecular, Nucleic Acid Conformation, Thermodynamics}, issn = {0031-9007}, author = {Luan, Binquan and Aleksei Aksimentiev} } @article {53, title = {DNA attraction in monovalent and divalent electrolytes}, journal = {J Am Chem Soc}, volume = {130}, year = {2008}, month = {2008 Nov 26}, pages = {15754-5}, abstract = {

The dependence of the effective force on the distance between two DNA molecules was directly computed from a set of extensive all-atom molecular dynamics simulations. The simulations revealed that in a monovalent electrolyte the effective force is repulsive at short and long distances but can be attractive in the intermediate range. This attractive force is, however, too weak (approximately 5 pN per turn of a DNA helix) to induce DNA condensation in the presence of thermal fluctuations. In divalent electrolytes, DNA molecules were observed to form a bound state, where Mg(2+) ions bridged minor groves of DNA. The effective force in divalent electrolytes was predominantly attractive, reaching a maximum of 42 pN per one turn of a DNA helix.

}, keywords = {Computer Simulation, DNA, Electrolytes, Models, Molecular, Molecular Conformation}, issn = {1520-5126}, doi = {10.1021/ja804802u}, author = {Luan, Binquan and Aleksei Aksimentiev} } @article {58, title = {Synthetic ion channels via self-assembly: a route for embedding porous polyoxometalate nanocapsules in lipid bilayer membranes}, journal = {Nano Lett}, volume = {8}, year = {2008}, month = {2008 Nov}, pages = {3916-21}, abstract = {

Porous polyoxometalate nanocapsules of Keplerate type are known to exhibit the functionality of biological ion channels; however, their use as an artificial ion channel is tempered by the high negative charge of the capsules, which renders their spontaneous incorporation into a lipid bilayer membrane unlikely. In this Letter we report coarse-grained molecular dynamics simulations that demonstrate a route for embedding negatively charged nanocapsules into lipid bilayer membranes via self-assembly. A homogeneous mixture of water, cationic detergent, and phospholipid was observed to spontaneously self-assemble around the nanocapsule into a layered, liposome-like structure, where the nanocapsule was enveloped by a layer of cationic detergent followed by a layer of phospholipid. Fusion of such a layered liposome with a lipid bilayer membrane was observed to embed the nanocapsule into the lipid bilayer. The resulting assembly was found to remain stable even after the surface of the capsule was exposed to electrolyte. In the latter conformation, water was observed to flow into and out of the capsule as Na(+) cations entered, suggesting that a polyoxometalate nanocapsule can form a functional synthetic ion channel in a lipid bilayer membrane.

}, keywords = {Ion Channels, Kinetics, Lipid Bilayers, Liposomes, Models, Molecular, Molecular Conformation, Nanocapsules, Porosity, Tungsten Compounds}, issn = {1530-6984}, doi = {10.1021/nl802366k}, author = {Carr, Rogan and Weinstock, Ira A and Sivaprasadarao, Asipu and M{\"u}ller, Achim and Aleksei Aksimentiev} } @article {60, title = {Stretching and unzipping nucleic acid hairpins using a synthetic nanopore}, journal = {Nucleic Acids Res}, volume = {36}, year = {2008}, month = {2008 Mar}, pages = {1532-41}, abstract = {

We have explored the electromechanical properties of DNA by using an electric field to force single hairpin molecules to translocate through a synthetic pore in a silicon nitride membrane. We observe a threshold voltage for translocation of the hairpin through the pore that depends sensitively on the diameter and the secondary structure of the DNA. The threshold for a diameter 1.5 < d < 2.3 nm is V > 1.5 V, which corresponds to the force required to stretch the stem of the hairpin, according to molecular dynamics simulations. On the other hand, for 1.0 < d < 1.5 nm, the threshold voltage collapses to V < 0.5 V because the stem unzips with a lower force than required for stretching. The data indicate that a synthetic nanopore can be used like a molecular gate to discriminate between the secondary structures in DNA.

}, keywords = {Biological Transport, DNA, Electric Conductivity, Membranes, Artificial, Models, Molecular, Nanostructures, Nucleic Acid Conformation, Silicon Compounds}, issn = {1362-4962}, doi = {10.1093/nar/gkm1017}, author = {Zhao, Q and Jeffrey Comer and Valentin Dimitrov and Yemenicioglu, S and Aleksei Aksimentiev and Gregory Timp} } @article {62, title = {Detection of DNA sequences using an alternating electric field in a nanopore capacitor}, journal = {Nano Lett}, volume = {8}, year = {2008}, month = {2008 Jan}, pages = {56-63}, abstract = {

Molecular dynamics simulations revealed that back-and-forth motion of DNA strands through a 1 nm diameter pore exhibits sequence-specific hysteresis that arises from the reorientation of the DNA bases in the nanopore constriction. Such hysteresis of the DNA motion results in detectable changes of the electrostatic potential at the electrodes of the nanopore capacitor and in a sequence-specific drift of the DNA strand under an oscillating transmembrane bias. A strategy is suggested for sequencing DNA in a nanopore using the electric field that alternates periodically in time.

}, keywords = {DNA, Electricity, Nanostructures, Sequence Analysis, DNA}, issn = {1530-6984}, doi = {10.1021/nl071890k}, author = {G Sigalov and Jeffrey Comer and Gregory Timp and Aleksei Aksimentiev} } @article {56, title = {Electro-osmotic screening of the DNA charge in a nanopore}, journal = {Phys Rev E Stat Nonlin Soft Matter Phys}, volume = {78}, year = {2008}, month = {2008 Aug}, pages = {021912}, abstract = {

Extensive all-atom molecular dynamics simulations were performed to characterize the microscopic origin of the force experienced by DNA in a bulk electrolyte and a solid-state nanopore when subject to an external electrostatic field E. The effective screening of the DNA charge was found to originate from the hydrodynamic drag of the electro-osmotic flow that is driven by the motion of counterions along the surface of DNA. We show that the effective driving force F in a nanopore obeys the same law as in a bulk electrolyte: F=ximuE , where xi and mu are the friction coefficient and electrophoretic mobility of DNA, respectively. Using this relationship, we suggest a method for determining the effective driving force on DNA in a nanopore that does not require a direct force measurement.

}, keywords = {DNA, Models, Theoretical, Nanostructures, Osmosis, Static Electricity, Water}, issn = {1539-3755}, author = {Luan, Binquan and Aleksei Aksimentiev} } @article {61, title = {In meso crystal structure and docking simulations suggest an alternative proteoglycan binding site in the OpcA outer membrane adhesin}, journal = {Proteins}, volume = {71}, year = {2008}, month = {2008 Apr}, pages = {24-34}, abstract = {

OpcA is an integral outer membrane adhesin protein from Neisseria meningitidis, the causative agent of meningococcal meningitis and septicemia. It binds to sialic acid (SA)-containing polysaccharides on the surface of epithelial cells. The crystal structure of OpcA showed that the protein adopts a 10-stranded beta-barrel structure, with five extensive loop regions on the extracellular side of the membrane. These form a crevice structure, lined with basic residues, which was hypothesized to act as the binding site for polysaccharide ligands. In the current study, a distinctly different OpcA structure has been obtained using crystals grown from a lipidic mesophase. Comparison of the two structures shows that the largest loop (L2), which closes over the end of the beta-barrel in the original crystal form, adopts a much more extended structure by reaching outward and away from the protein. The difference in conformation may be attributable to the absence of zinc ions from the crystallization conditions for the in meso crystal form: in the original structure, two zinc ions were bound to the external loops. Molecular dynamics (MD) simulations performed on the two OpcA models in a lipid bilayer environment demonstrated pronounced loop mobility. These observations support the view that the loop regions of OpcA are capable of a high degree of conformational flexibility. The original binding site for polysaccharide is not present in the in meso crystal form, and is disrupted during MD simulations. Docking analysis suggests a putative alternative location for the SA ligand in the new crystal form of OpcA.

}, keywords = {Adhesins, Bacterial, Bacterial Outer Membrane Proteins, Binding Sites, Computer Simulation, Crystallography, X-Ray, Models, Molecular, Neisseria meningitidis, Protein Binding, Proteoglycans, Spectrum Analysis}, issn = {1097-0134}, doi = {10.1002/prot.21841}, author = {Cherezov, Vadim and Liu, Wei and Derrick, Jeremy P and Luan, Binquan and Aleksei Aksimentiev and Katritch, Vsevolod and Caffrey, Martin} } @article {54, title = {Computer modeling in biotechnology: a partner in development}, journal = {Methods Mol Biol}, volume = {474}, year = {2008}, month = {2008}, pages = {181-234}, abstract = {

Computational modeling can be a useful partner in biotechnology, in particular, in nanodevice engineering. Such modeling guides development through nanoscale views of biomolecules and devices not available through experimental imaging methods. We illustrate the role of computational modeling, mainly of molecular dynamics, through four case studies: development of silicon bionanodevices for single molecule electrical recording, development of carbon nano-tube-biomolecular systems as in vivo sensors, development of lipoprotein nanodiscs for assays of single membrane proteins, and engineering of oxygen tolerance into the enzyme hydrogenase for photosynthetic hydrogen gas production. The four case studies show how molecular dynamics approaches were adapted to the specific technical uses through (i) multi-scale extensions, (ii) fast quantum chemical force field evaluation, (iii) coarse graining, and (iv) novel sampling methods. The adapted molecular dynamics simulations provided key information on device behavior and revealed development opportunities, arguing that the "computational microscope" is an indispensable nanoengineering tool.

}, keywords = {Biosensing Techniques, Biotechnology, Computational Biology, Computer Simulation, Models, Molecular, Nanostructures}, issn = {1064-3745}, doi = {10.1007/978-1-59745-480-3_11}, author = {Aleksei Aksimentiev and Robert Brunner and Cohen, Jordi and Jeffrey Comer and Eduardo Cruz-Ch{\'u} and Hardy, David and Rajan, Aruna and Amy Y Shih and G Sigalov and Yin, Ying and Klaus Schulten} } @article {64, title = {Exploring transmembrane transport through alpha-hemolysin with grid-steered molecular dynamics}, journal = {J Chem Phys}, volume = {127}, year = {2007}, month = {2007 Sep 28}, pages = {125101}, abstract = {

The transport of biomolecules across cell boundaries is central to cellular function. While structures of many membrane channels are known, the permeation mechanism is known only for a select few. Molecular dynamics (MD) is a computational method that can provide an accurate description of permeation events at the atomic level, which is required for understanding the transport mechanism. However, due to the relatively short time scales accessible to this method, it is of limited utility. Here, we present a method for all-atom simulation of electric field-driven transport of large solutes through membrane channels, which in tens of nanoseconds can provide a realistic account of a permeation event that would require a millisecond simulation using conventional MD. In this method, the average distribution of the electrostatic potential in a membrane channel under a transmembrane bias of interest is determined first from an all-atom MD simulation. This electrostatic potential, defined on a grid, is subsequently applied to a charged solute to steer its permeation through the membrane channel. We apply this method to investigate permeation of DNA strands, DNA hairpins, and alpha-helical peptides through alpha-hemolysin. To test the accuracy of the method, we computed the relative permeation rates of DNA strands having different sequences and global orientations. The results of the G-SMD simulations were found to be in good agreement in experiment.

}, keywords = {Bacterial Toxins, Biological Transport, Computer Simulation, DNA, Single-Stranded, Electricity, Electrophysiology, Hemolysin Proteins, Hydrogen-Ion Concentration, Lipid Bilayers, Membranes, Models, Molecular, Molecular Conformation, Permeability, Protein Structure, Secondary, Protons, Static Electricity, Time Factors, Water}, issn = {0021-9606}, doi = {10.1063/1.2770738}, author = {David B Wells and Abramkina, Volha and Aleksei Aksimentiev} } @article {63, title = {Structure refinement of the OpcA adhesin using molecular dynamics}, journal = {Biophys J}, volume = {93}, year = {2007}, month = {2007 Nov 1}, pages = {3058-69}, abstract = {

OpcA from Neisseria meningitidis, the causative agent of meningococcal meningitis and septicemia, is an integral outer membrane protein that facilitates meningococcal adhesion through binding the proteoglycan receptors of susceptible cells. Two structures of OpcA have been determined by x-ray diffraction to 2 A resolution, revealing dramatically different conformations in the extracellular loops--the protein domain implicated in proteoglycan binding. In the first structure, a positively charged crevice formed by loops 1 and 2 was identified as the site for binding proteoglycans, whereas in the second structure the crevice was not evident as loops 1 and 2 adopted different conformations. To reconcile these results, molecular-dynamics simulations were carried out on both structures embedded in a solvated lipid bilayer membrane. Free of crystal contacts and crystallization agents, the loops were observed to undergo large structural transformations, suggesting that the conformation of the loops in either x-ray structure is affected by crystallization. Subsequent simulations of both structures in their crystal lattices confirmed this conclusion. Based on our molecular-dynamics trajectories, we propose a model for OpcA that combines stable structural features of the available x-ray structures. In this model, all five extracellular loops of OpcA have stable secondary structures. The loops form a funnel that leads to the base of the beta-barrel and that includes Tyr-169 on its exposed surface, which has been implicated in proteoglycan binding.

}, keywords = {Adhesins, Bacterial, Bacterial Outer Membrane Proteins, Computer Simulation, Crystallography, X-Ray, Models, Molecular, Neisseria meningitidis, Protein Structure, Tertiary, Thermodynamics}, issn = {0006-3495}, doi = {10.1529/biophysj.107.106724}, author = {Luan, Binquan and Caffrey, Martin and Aleksei Aksimentiev} } @article {65, title = {Detecting SNPs using a synthetic nanopore}, journal = {Nano Lett}, volume = {7}, year = {2007}, month = {2007 Jun}, pages = {1680-5}, abstract = {

We have discovered a voltage threshold for permeation through a synthetic nanopore of dsDNA bound to a restriction enzyme that depends on the sequence. Molecular dynamic simulations reveal that the threshold is associated with a nanonewton force required to rupture the DNA-protein complex. A single mutation in the recognition site for the restriction enzyme, i.e., a single nucleotide polymorphism (SNP), can easily be detected as a change in the threshold voltage. Consequently, by measuring the threshold voltage in a synthetic nanopore, it may be possible to discriminate between two variants of the same gene (alleles) that differ in one base.

}, keywords = {Deoxyribonuclease EcoRI, DNA, DNA Mutational Analysis, Electromagnetic Fields, Macromolecular Substances, Materials Testing, Molecular Conformation, Nanostructures, Nanotechnology, Particle Size, Polymorphism, Single Nucleotide, Porosity, Sequence Analysis, DNA, Surface Properties}, issn = {1530-6984}, doi = {10.1021/nl070668c}, author = {Zhao, Q and G Sigalov and Valentin Dimitrov and Dorvel, B and Mirsaidov, U and S Sligar and Aleksei Aksimentiev and Gregory Timp} } @article {66, title = {Water-silica force field for simulating nanodevices}, journal = {J Phys Chem B}, volume = {110}, year = {2006}, month = {2006 Nov 2}, pages = {21497-508}, abstract = {

Amorphous silica is an inorganic material that is central for many nanotechnology applications, such as nanoelectronics, microfluidics, and nanopore sensors. To use molecular dynamics (MD) simulations to study the behavior of biomolecules interacting with silica, we developed a force field for amorphous silica surfaces based on their macroscopic wetting properties that is compatible with the CHARMM force field and TIP3P water model. The contact angle of a water droplet on a silica surface served as a criterion to tune the intermolecular interactions. The resulting force field was used to study the permeation of water through silica nanopores, illustrating the influence of the surface topography and the intermolecular parameters on permeation kinetics. We find that minute modeling of the amorphous surface is critical for MD studies, since the particular arrangement of surface atoms controls sensitively electrostatic interactions between silica and water.

}, keywords = {Nanostructures, Silicon Dioxide, Water}, issn = {1520-6106}, doi = {10.1021/jp063896o}, author = {Eduardo Cruz-Ch{\'u} and Aleksei Aksimentiev and Klaus Schulten} } @article {67, title = {The role of molecular modeling in bionanotechnology}, journal = {Phys Biol}, volume = {3}, year = {2006}, month = {2006 Mar}, pages = {S40-53}, abstract = {

Molecular modeling is advocated here as a key methodology for research and development in bionanotechnology. Molecular modeling provides nanoscale images at atomic and even electronic resolution, predicts the nanoscale interaction of unfamiliar combinations of biological and inorganic materials, and evaluates strategies for redesigning biopolymers for nanotechnological uses. The methodology is illustrated in this paper through reviewing three case studies. The first one involves the use of single-walled carbon nanotubes as biomedical sensors where a computationally efficient, yet accurate, description of the influence of biomolecules on nanotube electronic properties through nanotube-biomolecule interactions was developed; this development furnishes the ability to test nanotube electronic properties in realistic biological environments. The second case study involves the use of nanopores manufactured into electronic nanodevices based on silicon compounds for single molecule electrical recording, in particular, for DNA sequencing. Here, modeling combining classical molecular dynamics, material science and device physics, described the interaction of biopolymers, e.g., DNA, with silicon nitrate and silicon oxide pores, furnished accurate dynamic images of pore translocation processes, and predicted signals. The third case study involves the development of nanoscale lipid bilayers for the study of embedded membrane proteins and cholesterol. Molecular modeling tested scaffold proteins, redesigned apolipoproteins found in mammalian plasma that hold the discoidal membranes in the proper shape, and predicted the assembly as well as final structure of the nanodiscs. In entirely new technological areas such as bionanotechnology, qualitative concepts, pictures and suggestions are sorely needed; these three case studies document that molecular modeling can serve a critical role in this respect, even though it may still fall short on quantitative precision.

}, keywords = {Biosensing Techniques, Chemical Engineering, DNA, Lipid Bilayers, Membrane Potentials, Models, Molecular, Nanotechnology, Nanotubes, Carbon, Sequence Analysis, Silicon}, issn = {1478-3975}, doi = {10.1088/1478-3975/3/1/S05}, author = {Lu, Deyu and Aleksei Aksimentiev and Amy Y Shih and Eduardo Cruz-Ch{\'u} and Freddolino, Peter L and Arkhipov, Anton and Klaus Schulten} } @article {68, title = {The electromechanics of DNA in a synthetic nanopore}, journal = {Biophys J}, volume = {90}, year = {2006}, month = {2006 Feb 1}, pages = {1098-106}, abstract = {

We have explored the electromechanical properties of DNA on a nanometer-length scale using an electric field to force single molecules through synthetic nanopores in ultrathin silicon nitride membranes. At low electric fields, E < 200 mV/10 nm, we observed that single-stranded DNA can permeate pores with a diameter >/=1.0 nm, whereas double-stranded DNA only permeates pores with a diameter >/=3 nm. For pores <3.0 nm diameter, we find a threshold for permeation of double-stranded DNA that depends on the electric field and pH. For a 2 nm diameter pore, the electric field threshold is approximately 3.1 V/10 nm at pH = 8.5; the threshold decreases as pH becomes more acidic or the diameter increases. Molecular dynamics indicates that the field threshold originates from a stretching transition in DNA that occurs under the force gradient in a nanopore. Lowering pH destabilizes the double helix, facilitating DNA translocation at lower fields.

}, keywords = {Biophysics, Computer Simulation, DNA, Electrochemistry, Electromagnetic Fields, Electrophoresis, Electrophoresis, Agar Gel, Hydrogen-Ion Concentration, Ions, Membrane Potentials, Microscopy, Electron, Transmission, Models, Molecular, Nanostructures, Nanotechnology, Nucleic Acid Conformation, Polymerase Chain Reaction, Porosity, Silicon Compounds, Time Factors}, issn = {0006-3495}, doi = {10.1529/biophysj.105.070672}, author = {Jiunn B Heng and Aleksei Aksimentiev and Ho, C and Patrick Marks and Yelena V Grinkova and S Sligar and Klaus Schulten and Gregory Timp} } @article {191, title = {Simulation of the electric response of DNA translocation through a semiconductor nanopore-capacitor}, journal = {Nanotechnology}, volume = {17}, year = {2006}, pages = {622{\textendash}633}, abstract = {

A multi-scale/multi-material computational model for simulation of the electric signal detected on the electrodes of a metal{\textendash}oxide{\textendash}semiconductor (MOS) capacitor forming a nanoscale artificial membrane, and containing a nanopore with translocating DNA, is presented. The multi-scale approach is based on the incorporation of a molecular dynamics description of a translocating DNA molecule in the nanopore within a three-dimensional Poisson equation self-consistent scheme involving electrolytic and semiconductor charges for the electrostatic potential calculation. The voltage signal obtained from the simulation supports the possibility for single nucleotide resolution with a nanopore device. The electric signal predicted on the capacitor electrodes complements ongoing experiments exploring the use of nanopores in a MOS capacitor membrane for DNA sequencing.

}, doi = {10.1088/0957-4484/17/3/002}, author = {Maria E. Gracheva and A. Xiong and Aleksei Aksimentiev and Klaus Schulten and Gregory Timp and Jean-Pierre Leburton} } @article {190, title = {Electrical signatures of single-stranded DNA with single base mutations in a nanopore capacitor}, volume = {17}, year = {2006}, pages = {3160{\textendash}3165}, abstract = {

In this paper, we evaluate the magnitude of the electrical signals produced by DNA translocation through a 1\ nm diameter nanopore in a capacitor membrane with a numerical multi-scale approach, and assess the possibility of resolving individual nucleotides as well as their types in the absence of conformational disorder. We show that the maximum recorded voltage caused by the DNA translocation is about 35\ mV, while the maximum voltage signal due to the DNA backbone is about 30\ mV, and the maximum voltage of a DNA base is about 8\ mV. Signals from individual nucleotides can be identified in the recorded voltage traces, suggesting a 1\ nm diameter pore in a capacitor can be used to accurately count the number of nucleotides in a DNA strand. Furthermore, we study the effect of a single base substitution on the voltage trace, and calculate the differences among the voltage traces due to a single base mutation for the sequences C3AC7, C3CC7, C3GC7 and C3TC7. The calculated voltage differences are in the 5{\textendash}10\ mV range. The calculated maximum voltage caused by the translocation of individual bases varies from 2 to 9\ mV, which is experimentally detectable.

}, doi = {10.1088/0957-4484/17/13/014}, author = {Maria E. Gracheva and Aleksei Aksimentiev and Jean-Pierre Leburton} } @article {69, title = {Stretching DNA using the electric field in a synthetic nanopore}, journal = {Nano Lett}, volume = {5}, year = {2005}, month = {2005 Oct}, pages = {1883-8}, abstract = {

The mechanical properties of DNA over segments comparable to the size of a protein-binding site (3-10 nm) are examined using an electric-field-induced translocation of single molecules through a nanometer diameter pore. DNA, immersed in an electrolyte, is forced through synthetic pores ranging from 0.5 to 1.5 nm in radius in a 10 nm thick Si(3)N(4) membrane using an electric field. To account for the stretching and bending, we use molecular dynamics to simulate the translocation. We have found a threshold for translocation that depends on both the dimensions of the pore and the applied transmembrane bias. The voltage threshold coincides with the stretching transition that occurs in double-stranded DNA near 60 pN.

}, keywords = {DNA, Nanotechnology, Static Electricity, Stress, Mechanical}, issn = {1530-6984}, doi = {10.1021/nl0510816}, author = {Jiunn B Heng and Aleksei Aksimentiev and Chuen Ho and Patrick Marks and Yelena V Grinkova and S Sligar and Klaus Schulten and Gregory Timp} } @article {72, title = {Imaging alpha-hemolysin with molecular dynamics: ionic conductance, osmotic permeability, and the electrostatic potential map}, journal = {Biophys J}, volume = {88}, year = {2005}, month = {2005 Jun}, pages = {3745-61}, abstract = {

alpha-Hemolysin of Staphylococcus aureus is a self-assembling toxin that forms a water-filled transmembrane channel upon oligomerization in a lipid membrane. Apart from being one of the best-studied toxins of bacterial origin, alpha-hemolysin is the principal component in several biotechnological applications, including systems for controlled delivery of small solutes across lipid membranes, stochastic sensors for small solutes, and an alternative to conventional technology for DNA sequencing. Through large-scale molecular dynamics simulations, we studied the permeability of the alpha-hemolysin/lipid bilayer complex for water and ions. The studied system, composed of approximately 300,000 atoms, included one copy of the protein, a patch of a DPPC lipid bilayer, and a 1 M water solution of KCl. Monitoring the fluctuations of the pore structure revealed an asymmetric, on average, cross section of the alpha-hemolysin stem. Applying external electrostatic fields produced a transmembrane ionic current; repeating simulations at several voltage biases yielded a current/voltage curve of alpha-hemolysin and a set of electrostatic potential maps. The selectivity of alpha-hemolysin to Cl(-) was found to depend on the direction and the magnitude of the applied voltage bias. The results of our simulations are in excellent quantitative agreement with available experimental data. Analyzing trajectories of all water molecule, we computed the alpha-hemolysin{\textquoteright}s osmotic permeability for water as well as its electroosmotic effect, and characterized the permeability of its seven side channels. The side channels were found to connect seven His-144 residues surrounding the stem of the protein to the bulk solution; the protonation of these residues was observed to affect the ion conductance, suggesting the seven His-144 to comprise the pH sensor that gates conductance of the alpha-hemolysin channel.

}, keywords = {Bacterial Toxins, Biophysical Phenomena, Biophysics, Computer Simulation, Electric Conductivity, Hemolysin Proteins, Hydrogen-Ion Concentration, Ion Channels, Lipid Bilayers, Models, Biological, Models, Molecular, Osmosis, Permeability, Static Electricity, Thermodynamics, Water}, issn = {0006-3495}, doi = {10.1529/biophysj.104.058727}, author = {Aleksei Aksimentiev and Klaus Schulten} } @article {70, title = {Orientation discrimination of single-stranded DNA inside the alpha-hemolysin membrane channel}, journal = {Proc Natl Acad Sci U S A}, volume = {102}, year = {2005}, month = {2005 Aug 30}, pages = {12377-82}, abstract = {

We characterize the voltage-driven motion and the free motion of single-stranded DNA (ssDNA) molecules captured inside the approximately 1.5-nm alpha-hemolysin pore, and show that the DNA-channel interactions depend strongly on the orientation of the ssDNA molecules with respect to the pore. Remarkably, the voltage-free diffusion of the 3{\textquoteright}-threaded DNA (in the trans to cis direction) is two times slower than the corresponding 5{\textquoteright}-threaded DNA having the same poly(dA) sequence. Moreover, the ion currents flowing through the blocked pore with either a 3{\textquoteright}-threaded DNA or 5{\textquoteright} DNA differ by approximately 30\%. All-atom molecular dynamics simulations of our system reveal a microscopic mechanism for the asymmetric behavior. In a confining pore, the ssDNA straightens and its bases tilt toward the 5{\textquoteright} end, assuming an asymmetric conformation. As a result, the bases of a 5{\textquoteright}-threaded DNA experience larger effective friction and forced reorientation that favors co-passing of ions. Our results imply that the translocation process through a narrow pore is more complicated than previously believed and involves base tilting and stretching of ssDNA molecules inside the confining pore.

}, keywords = {Bacterial Toxins, Base Sequence, Biophysical Phenomena, Biophysics, DNA, Single-Stranded, Hemolysin Proteins, Ion Channels, Models, Molecular, Motion, Nucleic Acid Conformation, Poly A, Thermodynamics}, issn = {0027-8424}, doi = {10.1073/pnas.0502947102}, author = {Math{\'e}, J{\'e}r{\^o}me and Aleksei Aksimentiev and Nelson, David R and Klaus Schulten and Meller, Amit} } @article {71, title = {Molecular dynamics simulations of proteins in lipid bilayers}, journal = {Curr Opin Struct Biol}, volume = {15}, year = {2005}, month = {2005 Aug}, pages = {423-31}, abstract = {

With recent advances in X-ray crystallography of membrane proteins promising many new high-resolution structures, molecular dynamics simulations will become increasingly valuable for understanding membrane protein function, as they can reveal the dynamic behavior concealed in the static structures. Dramatic increases in computational power, in synergy with more efficient computational methodologies, now allow us to carry out molecular dynamics simulations of any structurally known membrane protein in its native environment, covering timescales of up to 0.1 micros. At the frontiers of membrane protein simulations are ion channels, aquaporins, passive and active transporters, and bioenergetic proteins.

}, keywords = {Computer Simulation, Ion Channels, Lipid Bilayers, Membrane Proteins, Models, Molecular, Protein Conformation}, issn = {0959-440X}, doi = {10.1016/j.sbi.2005.07.007}, author = {Gumbart, James and Wang, Yi and Aleksei Aksimentiev and Tajkhorshid, Emad and Klaus Schulten} } @article {59, title = {Beyond the Gene Chip}, journal = {Bell Labs Tech J}, volume = {10}, year = {2005}, month = {2005}, pages = {5-22}, abstract = {

We describe a prospective strategy for reading the encyclopedic information encoded in the genome: using a nanopore in a membrane formed from an MOS-capacitor to sense the charge in DNA. In principle, as DNA permeates the capacitor-membrane through the pore, the electrostatic charge distribution characteristic of the molecule should polarize the capacitor and induce a voltage on the electrodes that can be measured. Silicon nanofabrication and molecular dynamic simulations with atomic detail are technological linchpins in the development of this detector. The sub-nanometer precision available through silicon nanotechnology facilitates the fabrication of the detector, and molecular dynamics provides us with a means to design it and analyze the experimental outcomes.

}, issn = {1089-7089}, doi = {10.1002/bltj.20102}, author = {Jiunn B Heng and Aleksei Aksimentiev and Ho, C and Valentin Dimitrov and Sorsch, T and Miner, J and Mansfield, W and Klaus Schulten and Gregory Timp} } @inbook {189, title = {Toward understanding membrane channels}, booktitle = { Bacterial ion channels and their eukaryotic homologues}, year = {2005}, pages = {153{\textendash}190}, publisher = {ASM Press}, organization = {ASM Press}, address = {Washington, DC}, abstract = {

Membrane channels play key roles in all living cells. Owing to recent advances in protein crystallography, atomic-resolution structures for a representative set of membrane channels have become available. Transport of materials through these channels, however, is a dynamic process and cannot be fully understood from static structural information alone. Molecular dynamics simulations are in a unique position to describe the dynamics of channel transport in the cases in which the structures of channel proteins are known. However, simulation of channel permeability and gating in the native environment of lipid bilayer and water involves large systems with 100,000 - 300,000 atoms.

This review article focuses on four case studies that demonstrate the power of molecular dynamics simulations in unraveling the mechanisms underlying the function of membrane channels. Simulations of AQP water channels present a prime example of the effectiveness and usefulness of molecular dynamics in simulating conduction and explaining selectivity. A detailed energetic analysis of ion permeation through chloride channels proposes a two- ion permeation mechanism that reconciles naturally structural and physiological data. The study of ion and water permeation through hemolysin exemplifies how accurately one can simulate today even very large membrane channel systems. Finally, the study of mechanical gating of MscS shows that molecular dynamics can account even for complex gating motions of channels.

}, author = {Tajkhorshid, Emad and Cohen, Jordi and Aleksei Aksimentiev and Marcos Sotomayor and Klaus Schulten}, editor = {Boris Martinac and Andrzej Kubalski} } @article {73, title = {Microscopic Kinetics of DNA Translocation through synthetic nanopores}, journal = {Biophys J}, volume = {87}, year = {2004}, month = {2004 Sep}, pages = {2086-97}, abstract = {

We have previously demonstrated that a nanometer-diameter pore in a nanometer-thick metal-oxide-semiconductor-compatible membrane can be used as a molecular sensor for detecting DNA. The prospects for using this type of device for sequencing DNA are avidly being pursued. The key attribute of the sensor is the electric field-induced (voltage-driven) translocation of the DNA molecule in an electrolytic solution across the membrane through the nanopore. To complement ongoing experimental studies developing such pores and measuring signals in response to the presence of DNA, we conducted molecular dynamics simulations of DNA translocation through the nanopore. A typical simulated system included a patch of a silicon nitride membrane dividing water solution of potassium chloride into two compartments connected by the nanopore. External electrical fields induced capturing of the DNA molecules by the pore from the solution and subsequent translocation. Molecular dynamics simulations suggest that 20-basepair segments of double-stranded DNA can transit a nanopore of 2.2 x 2.6 nm(2) cross section in a few microseconds at typical electrical fields. Hydrophobic interactions between DNA bases and the pore surface can slow down translocation of single-stranded DNA and might favor unzipping of double-stranded DNA inside the pore. DNA occluding the pore mouth blocks the electrolytic current through the pore; these current blockades were found to have the same magnitude as the blockade observed when DNA transits the pore. The feasibility of using molecular dynamics simulations to relate the level of the blocked ionic current to the sequence of DNA was investigated.

}, keywords = {Biological Transport, Biophysics, DNA, Electrophoresis, Electrophysiology, Hemolysin Proteins, Ions, Kinetics, Metals, Models, Molecular, Models, Statistical, Nanotechnology, Nucleic Acid Conformation, Oxides, Semiconductors, Stress, Mechanical, Time Factors}, issn = {0006-3495}, doi = {10.1529/biophysj.104.042960}, author = {Aleksei Aksimentiev and Jiunn B Heng and Gregory Timp and Klaus Schulten} } @article {74, title = {Sizing DNA using a nanometer-diameter pore}, journal = {Biophys J}, volume = {87}, year = {2004}, month = {2004 Oct}, pages = {2905-11}, abstract = {

Each species from bacteria to human has a distinct genetic fingerprint. Therefore, a mechanism that detects a single molecule of DNA represents the ultimate analytical tool. As a first step in the development of such a tool, we have explored using a nanometer-diameter pore, sputtered in a nanometer-thick inorganic membrane with a tightly focused electron beam, as a transducer that detects single molecules of DNA and produces an electrical signature of the structure. When an electric field is applied across the membrane, a DNA molecule immersed in electrolyte is attracted to the pore, blocks the current through it, and eventually translocates across the membrane as verified unequivocally by gel electrophoresis. The relationship between DNA translocation and blocking current has been established through molecular dynamics simulations. By measuring the duration and magnitude of the blocking current transient, we can discriminate single-stranded from double-stranded DNA and resolve the length of the polymer.

}, keywords = {DNA, Electrochemistry, Nanotechnology, Particle Size, Porosity, Reproducibility of Results, Sensitivity and Specificity, Ultrafiltration}, issn = {0006-3495}, doi = {10.1529/biophysj.104.041814}, author = {Jiunn B Heng and Chuen Ho and Kim, Taekyung and Timp, Rolf and Aleksei Aksimentiev and Yelena V Grinkova and S Sligar and Klaus Schulten and Gregory Timp} } @article {75, title = {Extending molecular modeling methodology to study insertion of membrane nanopores}, journal = {Proc Natl Acad Sci U S A}, volume = {101}, year = {2004}, month = {2004 Mar 30}, pages = {4337-8}, keywords = {Biosensing Techniques, Computer Simulation, DNA, Lipid Bilayers, Membrane Proteins, Models, Molecular, Protein Conformation}, issn = {0027-8424}, doi = {10.1073/pnas.0400739101}, author = {Aleksei Aksimentiev and Klaus Schulten} } @article {76, title = {Insights into the molecular mechanism of rotation in the Fo sector of ATP synthase}, journal = {Biophys J}, volume = {86}, year = {2004}, month = {2004 Mar}, pages = {1332-44}, abstract = {

F(1)F(o)-ATP synthase is a ubiquitous membrane protein complex that efficiently converts a cell{\textquoteright}s transmembrane proton gradient into chemical energy stored as ATP. The protein is made of two molecular motors, F(o) and F(1), which are coupled by a central stalk. The membrane unit, F(o), converts the transmembrane electrochemical potential into mechanical rotation of a rotor in F(o) and the physically connected central stalk. Based on available data of individual components, we have built an all-atom model of F(o) and investigated through molecular dynamics simulations and mathematical modeling the mechanism of torque generation in F(o). The mechanism that emerged generates the torque at the interface of the a- and c-subunits of F(o) through side groups aSer-206, aArg-210, and aAsn-214 of the a-subunit and side groups cAsp-61 of the c-subunits. The mechanism couples protonation/deprotonation of two cAsp-61 side groups, juxtaposed to the a-subunit at any moment in time, to rotations of individual c-subunit helices as well as rotation of the entire c-subunit. The aArg-210 side group orients the cAsp-61 side groups and, thereby, establishes proton transfer via aSer-206 and aAsn-214 to proton half-channels, while preventing direct proton transfer between the half-channels. A mathematical model proves the feasibility of torque generation by the stated mechanism against loads typical during ATP synthesis; the essential model characteristics, e.g., helix and subunit rotation and associated friction constants, have been tested and furnished by steered molecular dynamics simulations.

}, keywords = {Binding Sites, Cell Membrane, Computer Simulation, Dimerization, Models, Chemical, Models, Molecular, Models, Statistical, Molecular Motor Proteins, Protein Binding, Protein Conformation, Protein Subunits, Proton-Translocating ATPases, Rotation, Stochastic Processes}, issn = {0006-3495}, doi = {10.1016/S0006-3495(04)74205-8}, author = {Aleksei Aksimentiev and Ilya A Balabin and Fillingame, Robert H and Klaus Schulten} } @article {77, title = {Large scale simulation of protein mechanics and function}, journal = {Adv Protein Chem}, volume = {66}, year = {2003}, month = {2003}, pages = {195-247}, keywords = {Amino Acid Motifs, Aquaporins, Catalysis, Cell Membrane, Computer Simulation, Fibronectins, Hydrogen Bonding, Models, Molecular, Protein Conformation, Protein Denaturation, Protein Folding, Protein Structure, Secondary, Proteins, Proton-Translocating ATPases, Substrate Specificity, Time Factors, Water}, issn = {0065-3233}, author = {Tajkhorshid, Emad and Aleksei Aksimentiev and Ilya A Balabin and Gao, Mu and Isralewitz, Barry and Phillips, James C and Zhu, Fangqiang and Klaus Schulten} } @article {183, title = {Morphology of surfaces in mesoscopic polymers, surfactants, electrons, or reaction-diffusion systems: Methods, simulation and measurements}, journal = {Advances in Chemical Physics}, volume = {121}, year = {2002}, pages = {141{\textendash}239}, abstract = {

In this chapter the authors discuss systems with internal surfaces, ordered surfaces, topological transformations, and dynamical scaling. In Section II the authors show specific examples of mesoscopic systems with special attention devoted to the surfaces in the system{\textemdash}that is, periodic surfaces in surfactant systems, periodic surfaces in diblock copolymers, bicontinuous disordered interfaces in spinodally decomposing blends, ordered charge density wave patterns in electron liquids, and dissipative structures in reaction{\textendash}diffusion systems. Section III covers the theory of morphological measures, including the Euler characteristic and the Gaussian and mean curvatures.

}, doi = {10.1002/0471264318.ch3}, author = {Aleksei Aksimentiev and Robert Ho{\l}yst and Marcin Fialkowski} } @article {79, title = {Scaling of the Euler characteristic, surface area, and curvatures in the phase separating or ordering systems}, journal = {Phys Rev Lett}, volume = {86}, year = {2001}, month = {2001 Jan 8}, pages = {240-3}, abstract = {

We present robust scaling laws for the Euler characteristic and curvatures applicable to any symmetric system undergoing phase separating or ordering kinetics. We apply it to the phase ordering in a system of the nonconserved scalar order parameter and find three scaling regimes. The appearance of the preferred nonzero curvature of an interface separating +/- domains marks the crossover to the late stage regime characterized by the Lifshitz-Cahn-Allen scaling.

}, issn = {0031-9007}, author = {Marcin Fialkowski and Aleksei Aksimentiev and Robert Ho{\l}yst} } @article {182, title = {Application of the Euler characteristic to the study of homopolymer blends and copolymer melts}, journal = {Polimery}, volume = {46}, year = {2001}, pages = {309{\textendash}322}, abstract = {

The Euler characteristic is applied to study the phase separation/ordering phenomena occurring in polymer mixtures. Several methods used to compute Euler characteristics are described and discussed in terms of accuracy and efficiency. A novel, robust and exact algorithm based on simplex decomposition is presented. The simulated morphology of spinodal decomposition and the phase equilibrium diagram of gradient copolymers are analyzed in terms of Euler characteristics. Again, the Euler characteristics are applied to specify the connectivity of bicontinuous patterns, to distinguish the disperse and the bicontinuous morphologies, and to detect the percolarion transition. During the spinodal decomposition, the dynamic transformation between the bicontinuous and the droplet patterns is shown to involve the formation of a transient "cylindrical" morphology.

}, url = {http://en.www.ichp.pl/Application-of-the-Euler-characteristic}, author = {Aleksei Aksimentiev and Robert Ho{\l}yst} } @article {80, title = {Influence of the free-energy functional form on simulated morphology of spinodally decomposing blends}, journal = {Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics}, volume = {62}, year = {2000}, month = {2000 Nov}, pages = {6821-30}, abstract = {

The spinodal decomposition of a binary mixture has been studied within several mesoscopic models. It has been found that the form of the equilibrium free energy has a crucial effect on the morphological development in asymmetric blends. We have shown that the principal quantity that determines the topology of the interface (and type of morphology) is the equilibrium minority phase volume fraction, while the transition from bicontinuous to droplet morphology can be treated as a percolation. The concentration dependence of the square gradient coefficient attributed for the Flory-Huggins-de Gennes free energy has no significant influences on the average domain growth, but can be distinguished experimentally from its constant-coefficient alternative by measuring the maximum wave vector of the scattering intensity as a function of the minority phase volume fraction for spinodally decomposing asymmetric blends. The concentration dependence of the Onsager coefficient has the weak, systematic effect of slowing down the morphological development. The local shape of the interface is not affected considerably by the concentration dependence of the square gradient and Onsager coefficient.

}, issn = {1063-651X}, author = {Aleksei Aksimentiev and Robert Ho{\l}yst} } @article {181, title = {Scaling properties of the morphological measures at the early and intermediate stages of the spinodal decomposition in homopolymer blends}, journal = {The Journal of Chemical Physics}, volume = {112}, year = {2000}, pages = {6049{\textendash}6062}, abstract = {

The spinodal decomposition of the homopolymer blends has been studied by the numerical integration of the Cahn{\textendash}Hilliard{\textendash}Cook equation. We have investigated the time evolution of the morphological measures that characterize quantitatively the interface in the system. For symmetric blends we have found that the Euler characteristic of the interface is negative and increases with time as τ0.75 (connectivity of the domains decreases) regardless of the final quench temperature. The homogeneity index of the interface is constant in this case. This suggests that at the level of the integral geometry quantities (Minkowski functionals), the dynamic scaling hypothesis holds for the evolution of the interface morphology in quenched critical systems. The nonuniversal morphological evolution of the asymmetric blends have been studied. Also, we have shown that the thermal fluctuations can modify significantly the curvature distribution.

}, doi = {10.1063/1.481178}, author = {Aleksei Aksimentiev and Krzysztof Moorthi and Robert Ho{\l}yst} } @article {180, title = {Kinetics of the droplet formation at the early and intermediate stages of the spinodal decomposition in homopolymer blends}, journal = {Macromolecular Theory and Simulations}, volume = {9}, year = {2000}, pages = {661{\textendash}674}, abstract = {

The kinetics of the droplet formation during the spinodal decomposition (SD) of the homopolymer blends has been studied by numerical integration of the Cahn-Hilliard-Cook equation. We have found that the droplet formation and growth occurs when the minority phase volume fraction, fm , approaches the percolation threshold value, fthr = 0.3 {\textpm} 0.01. The time for the formation of the disperse droplet morphology (coarsening time) depends only on the equilibrium minority phase volume fraction, fm . fm approaches its equilibrium value logarithmically at the late SD stages, and, therefore, the coarsening time decreases exponentially as the average volume fraction or the quench depth decrease. Since the temporal evolution of the total interfacial area does not depend on the quench conditions and blend morphology, the average droplet size and the droplet number density is determined by the coarsening time. Within the time scale studied, the droplet number density decreases with time as t{\textendash}0.63{\textpm}0.03; the average mean curvature decreases as t{\textendash}0.35{\textpm}0.05; the average Gaussian curvature decreases as t{\textendash}0.42{\textpm}0.03, and the average droplet compactness \~{}V/S3/2 where S is the surface area and V is the volume) approaches a spherical limit logarithmically with time. The droplets with larger area have lower compactness and in the low compactness limit their area is a parabolic function of compactness. The size and shape distribution functions have been also investigated.

}, doi = {10.1002/1521-3919(20001101)9:8<661::AID-MATS661>3.0.CO;2-6}, author = {Aleksei Aksimentiev and Robert Ho{\l}yst and Krzysztof Moorthi} } @article {78, title = {Diffusion on curved, periodic surfaces}, journal = {Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics}, volume = {60}, year = {1999}, month = {1999 Jul}, pages = {302-7}, abstract = {

We present a simulation algorithm for a diffusion on a curved surface given by the equation phi(r)=0. The algorithm is tested against analytical results known for diffusion on a cylinder and a sphere, and applied to the diffusion on the P, D, and G periodic nodal surfaces. It should find application in an interpretation of two-dimensional exchange NMR spectroscopy data of diffusion on biological membranes.

}, issn = {1063-651X}, author = {Robert Ho{\l}yst and Plewczy{\'n}ski, D and Aleksei Aksimentiev and Burdzy, K} } @article {179, title = {Single-chain statistics in polymer systems}, journal = {Progress in Polymer Science}, volume = {24}, year = {1999}, pages = {1045{\textendash}1093}, abstract = {

In this review we study the behavior of a single labelled polymer chain in various polymer systems: polymer blends, diblock copolymers, gradient copolymers, ring copolymers, polyelectrolytes, grafted homopolymers, rigid nematogenic polymers, polymers in bad and good solvents, fractal polymers and polymers in fractal environments. We discuss many phenomena related to the single chain behavior, such as: collapse of polymers in bad solvents, protein folding, stretching of polymer brushes, coil{\textendash}rod transition in nematogenic main-chain polymers, knot formation in homopolymer melts, and shrinking and swelling of polymers at temperatures close to the bulk transition temperatures. Our description is mesoscopic, based on two models of polymer systems: the Edwards model with Fixman delta interactions, and the Landau{\textendash}Ginzburg model of phase transitions applied to polymers. In particular, we show the derivation of the Landau{\textendash}Ginzburg model from the Edwards model in the case of homopolymer blends and diblock copolymer melts. In both models, we calculate the radius of gyration and relate them to the correlation function for a single polymer chain. We discuss theoretical results as well as computer simulations and experiments.

}, doi = {10.1016/S0079-6700(99)00023-4}, author = {Aleksei Aksimentiev and Robert Ho{\l}yst} } @article {177, title = {Single chain conformations in the system of symmetric and asymmetric diblock copolymers}, journal = {Macromolecular Theory and Simulations}, volume = {8}, year = {1999}, pages = {328{\textendash}342}, abstract = {

A theory which describes a local structure and global properties of a diblock copolymer melt has been developed in the framework of the one-loop self-consistent approximation. We have derived expressions for the sizes of a single diblock macromolecule and its parts. Two different behaviors of single macromolecule conformations in the disordered melt have been obtained depending on the asymmetry of chains and morphologies occurring in ordered states after the order-disorder transition (ODT). In the nearly symmetric melt, 0.35 \< f ⪇ 0.5 (f is a composition), the blocks of both types shrink a little initially as the temperature decreases and then, at some temperature, they begin to swell. In strongly asymmetric melts, f \< 0.35, the block of a macromolecule which consists of the monomers of minority type shrinks monotonically, while the other block monotonically swells. We have found nearly Gaussian behavior of the individual blocks and stretching near the chemical bond joining the blocks. Near the ODT the chains are stretched with a magnitude which is of the order of a few percent of their Gaussian sizes. We have calculated the peak position in the scattering curve as a function of the Flory-Huggins interaction parameter, composition and degree of polymerization. Less then 5\% change in the size of copolymer molecules lead to a 25\% shift of the scattering peak in comparison to the Gaussian limit. We have found a good quantitative agreement of our theoretical results with the experimental neutron scattering data.

}, doi = {10.1002/(SICI)1521-3919(19990701)8:4<328::AID-MATS328>3.0.CO;2-3}, author = {Aleksei Aksimentiev and Robert Ho{\l}yst} } @article {178, title = {Phase behavior of gradient copolymers}, journal = {The Journal of Chemical Physics}, volume = {111}, year = {1999}, pages = {2329{\textendash}2339}, abstract = {

Phase properties of gradient ABcopolymer melts which consist of chains with the specified chemical distribution of A and B monomers have been studied within the Landau{\textendash}Ginzburg model. All the melts with the linear distribution of the monomers exhibit only a direct continuous phase transition from disordered to the lamellar phase. The hexagonal, body-centered-cubic, double-gyroid (G), and lamellar-ordered structures have been found in the melts with the monotonic but nonlinear distribution of the monomers. The G structure has been also found in the gradient copolymer melts with the distribution function of monomers similar to the A{\textendash}B{\textendash}A triblock copolymers.

}, doi = {10.1063/1.479504}, author = {Aleksei Aksimentiev and Robert Ho{\l}yst} } @article {176, title = {Swelling and shrinking of polymer chains in homopolymer blends}, journal = {Macromolecular Theory and Simulations}, volume = {7}, year = {1998}, pages = {447{\textendash}456}, abstract = {

The radius of gyration, R, of polymer chains in homopolymer blends is studied in the framework of a self-consistent one-loop approximation. We show that the polymer chains can shrink or swell in comparison to the Gaussian chain. Swelling of the polymer chains in a region far away from the critical point is caused by the steric repulsive forces that were included in the model as the constraint of incompressibility. The chains shrink progressively, as we approach the critical region passing through the Gaussian limit, R0 = sqrt(N/6) l, far away from the critical point (N - degree of polymerization, l - length of monomer). The correction responsible for the swelling and the shrinking is small when the concentrations of components ϕ are comparable (N = 1000, \<ϕ\> = 0.5, (R02-R2)/R02 =\ {\textpm}0.02\%). This effect, although small, leads to a local demixing, a sharp shrinking of chains in both components accompanied by a strong change of the global inter-monomer distance, which should be observable experimentally. When the local demixing occurs there is a sudden increase in the scattering intensity (of the order of 30\% for N = 1000, and ϕA = 0.2). The increase of the degree of polymerization of the same type of chains leads to an increase of the swelling-shrinking effects. In addition, the critical concentration of the shorter chains component is smaller in comparison to the value obtained in the Flory-Huggins theory. The self-consistent determination of the radius of gyration and the upper wave-vector cutoff make our model free from any divergences. In the limit of N\ {\textrightarrow} $\infty$ this theory reduces to the random phase approximation (RPA) of de Gennes.

}, doi = {10.1002/(SICI)1521-3919(19990701)8:4<328::AID-MATS328>3.0.CO;2-3}, author = {Aleksei Aksimentiev and Robert Ho{\l}yst} }