@article {396, title = {The structure and physical properties of a packaged bacteriophage particle}, journal = {Nature}, volume = {627}, year = {2024}, month = {03/2024}, pages = {905-914}, chapter = {905}, 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 = {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 {398, title = {Electro-Osmotic Flow Generation via a Sticky Ion Action}, journal = {ACS nano}, volume = {18}, year = {2024}, pages = {17521-17533}, chapter = {17521-17533}, abstract = {

Selective transport of ions through nanometer-sized pores is fundamental to cell biology and central to many technological processes such as water desalination and electrical energy storage. Conventional methods for generating ion selectivity include placement of fixed electrical charges at the inner surface of a nanopore through either point mutations in a protein pore or chemical treatment of a solid-state nanopore surface, with each nanopore type requiring a custom approach. Here, we describe a general method for transforming a nanoscale pore into a highly selective, anion-conducting channel capable of generating a giant electro-osmotic effect. Our molecular dynamics simulations and reverse potential measurements show that exposure of a biological nanopore to high concentrations of guanidinium chloride renders the nanopore surface positively charged due to transient binding of guanidinium cations to the protein surface. A comparison of four biological nanopores reveals the relationship between ion selectivity, nanopore shape, composition of the nanopore surface, and electro-osmotic flow. Guanidinium ions are also found to produce anion selectivity and a giant electro-osmotic flow in solid-state nanopores via the same mechanism. Our sticky-ion approach to generate electro-osmotic flow can have numerous applications in controlling molecular transport at the nanoscale and for detection, identification, and sequencing of individual proteins.

}, doi = {10.1021/acsnano.4c00829}, author = {Mehrafrooz, Behzad and Yu, Luning and Pandey, Laxmi and Siwy, Zuzanna S and Wanunu, Meni and Aksimentiev, Aleksei} } @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}, volume = {14}, 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 {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 {388, title = {Benchmarking Molecular Dynamics Force Fields for All-Atom Simulations of Biological Condensates}, journal = {Journal of Chemical Theory and Computation}, volume = {19}, year = {2023}, month = {05/2023}, pages = {3721--3740}, 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 {384, title = {Unidirectional single-file transport of full-length proteins through a nanopore}, journal = {Nature Biotechnology}, volume = {41}, year = {2023}, month = {01/2023}, pages = {1130--1139}, 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 {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 {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 {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 {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 {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}, pages = {e2016262118}, 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 {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 {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 {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 {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 {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 {301, title = {The Oligomerization Landscape of Histones}, journal = {Biophysical Journal}, volume = {116}, year = {2019}, month = {05/2019}, pages = {1845--1855}, doi = {doi.org/10.1016/j.bpj.2019.03.021}, url = {https://www.sciencedirect.com/science/article/pii/S0006349519302784}, author = {Zhao, Haiqing and Winogradoff, David and Dalal, Yamini and Papoian, Garegin A} } @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 {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 {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 {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 {316, title = {Promiscuous Histone Mis-Assembly Is Actively Prevented by Chaperones.}, journal = {J Am Chem Soc}, volume = {138}, year = {2016}, month = {10/2016}, pages = {13207-13218}, abstract = {

Histone proteins are essential for the organization, expression, and inheritance of genetic material for eukaryotic cells. A centromere-specific H3 histone variant, centromere protein A (CENP-A), shares about 50\% amino acid sequence identity with H3. CENP-A is required for packaging the centromere and for the proper separation of chromosomes during mitosis. Despite their distinct biological functions, previously reported crystal structures of the CENP-A/H4 and H3/H4 dimers reveal a high degree of similarity. In this work, we characterize the structural dynamics of CENP-A/H4 and H3/H4 dimers based on a dual-resolution approach, using both microsecond-scale explicit-solvent all-atom and coarse-grained (CG) molecular dynamics (MD) simulations. Our data show that the H4 histone is significantly more rigid compared with the H3 histone and its variant CENP-A, hence, serving as a reinforcing structural element within the histone core. We report that the CENP-A/H4 dimer is significantly more dynamic than its canonical counterpart H3/H4, and our results provide a physical explanation for this flexibility. Further, we observe that the centromere-specific chaperone Holliday Junction Recognition Protein (HJURP) stabilizes the CENP-A/H4 dimer by forming a specific electrostatic interaction network. Finally, replacing CENP-A S68 with E68 disrupts the binding interface between CENP-A and HJURP in all-atom MD simulation, and consistently, in vivo experiments demonstrate that replacing CENP-A S68 with E68 disrupts CENP-A{\textquoteright}s localization to the centromere. Based on all our results, we propose that, during the CENP-A/H4 deposition process, the chaperone HJURP protects various substructures of the dimer, serving both as a folding and binding chaperone.

}, keywords = {Centromere Protein A, DNA-Binding Proteins, HeLa Cells, Histones, Humans, Molecular Dynamics Simulation, Protein Folding, Protein Multimerization, Protein Structure, Quaternary, Substrate Specificity}, doi = {10.1021/jacs.6b05355}, author = {Zhao*, Haiqing and Winogradoff*, David and Bui, Minh and Dalal, Yamini and Papoian, Garegin A} } @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 {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 {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 {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 {313, title = {Promiscuous histone mis-assembly is actively prevented by chaperones.}, journal = {Journal of the American Chemical Society}, volume = {138}, year = {2016}, pages = {13207--13218}, doi = {10.1021/jacs.6b05355}, author = {Zhao*, Haiqing and Winogradoff*, David and Minh Bui and Yamini Dalal and Garegin Papoian} } @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 {220, title = {Shearing of the CENP-A dimerization interface mediates plasticity in the octameric centromeric nucleosome}, journal = {Scientific reports}, volume = {5}, year = {2015}, doi = {10.1038/srep17038}, author = {Winogradoff, David and Zhao, Haiqing and Dalal, Yamini and Papoian, Garegin A} } @article {219, title = {The acetylation landscape of the H4 histone tail: disentangling the interplay between the specific and cumulative effects}, journal = {J Am Chem Soc}, volume = {137}, year = {2015}, pages = {6245{\textendash}6253}, doi = {10.1021/jacs.5b00235}, author = {Winogradoff, David and Echeverria, Ignacia and Potoyan, Davit A and Papoian, Garegin A} } @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 {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 {135, title = {Single-base DNA discrimination via transverse ionic transport.}, journal = {Nanotechnology}, volume = {24}, year = {2013}, month = {10/2013}, pages = {415101}, abstract = {

We suggest the discrimination of single DNA bases via transverse ionic transport, namely by detecting the ionic current that flows in a channel while a single-stranded DNA is driven through an intersecting nanochannel. Our all-atom molecular dynamics simulations indeed show that the ionic currents of the four bases are statistically distinct, thus offering another possible approach to sequencing DNA.

}, keywords = {Base Sequence, DNA, Single-Stranded, Ion Transport, Ions, Molecular Dynamics Simulation, Nucleic Acid Conformation}, issn = {1361-6528}, doi = {10.1088/0957-4484/24/41/415101}, author = {James Wilson and Massimiliano Di Ventra} } @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 {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 {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 {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 {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 {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} } @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 {105, title = {Dehydration and ionic conductance quantization in nanopores}, journal = {J Phys Condens Matter}, volume = {22}, year = {2010}, month = {2010 Nov 17}, pages = {454126}, abstract = {

There has been tremendous experimental progress in the last decade in identifying the structure and function of biological pores (ion channels) and fabricating synthetic pores. Despite this progress, many questions still remain about the mechanisms and universal features of ionic transport in these systems. In this paper, we examine the use of nanopores to probe ion transport and to construct functional nanoscale devices. Specifically, we focus on the newly predicted phenomenon of quantized ionic conductance in nanopores as a function of the effective pore radius--a prediction that yields a particularly transparent way to probe the contribution of dehydration to ionic transport. We study the role of ionic species in the formation of hydration layers inside and outside of pores. We find that the ion type plays only a minor role in the radial positions of the predicted steps in the ion conductance. However, ions with higher valency form stronger hydration shells, and thus, provide even more pronounced, and therefore, more easily detected, drops in the ionic current. Measuring this phenomenon directly, or from the resulting noise, with synthetic nanopores would provide evidence of the deviation from macroscopic (continuum) dielectric behavior due to microscopic features at the nanoscale and may shed light on the behavior of ions in more complex biological channels.

}, keywords = {Computer Simulation, Ions, Models, Chemical, Models, Molecular, Nanostructures, Particle Size, Porosity, Water}, issn = {1361-648X}, doi = {10.1088/0953-8984/22/45/454126}, author = {Zwolak, Michael and James Wilson and Massimiliano Di Ventra} } @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 {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 {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 {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} }