@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 {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 {386, title = {Super-Resolution Detection of DNA Nanostructures Using a Nanopore}, journal = {Advanced Materials}, year = {2023}, month = {01/2023}, pages = {2207434}, abstract = {

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

}, keywords = {biosensing, DNA nanostructures, Nanopores, single molecule, super resolution}, doi = {https://doi.org/10.1002/adma.202207434}, author = {Chen, Kaikai and Choudhary, Adnan and Sandler, Sarah E. and Maffeo, Christopher and Ducati, Caterina and Aksimentiev, Aleksei and Keyser, Ulrich F.} } @article {377, title = {Multi-resolution simulation of DNA transport through large synthetic nanostructures.}, journal = {Phys Chem Chem Phys}, volume = {24}, year = {2022}, month = {2022 Feb 02}, pages = {2706-2716}, abstract = {

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

}, keywords = {Biological Transport, DNA, Electricity, Molecular Dynamics Simulation, Nanopores}, issn = {1463-9084}, doi = {10.1039/d1cp04589j}, author = {Choudhary, Adnan and Maffeo, Christopher and Aleksei Aksimentiev} } @article {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 {373, title = {Single-molecule biophysics experiments in silico: Toward a physical model of a replisome}, journal = {iScience}, volume = {25}, year = {2022}, month = {05/2022}, pages = {104264}, abstract = {

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

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

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

}, doi = {10.1021/acs.nanolett.1c04203}, author = {Tabatabaei, S Kasra and Pham, Bach and Pan, Chao and Liu, Jingqian and Chandak, Shubham and Shorkey, Spencer A and Hernandez, Alvaro G and Aleksei Aksimentiev and Chen, Min and Schroeder, Charles M and Milenkovic, Olgica} } @article {351, title = {Foldamer-Based Ultrapermeable and Highly Selective Artificial Water Channels that Exclude Protons}, journal = {Nature Nanotechnology}, volume = {16}, year = {2021}, month = {08/2021}, pages = {911-917}, chapter = {911}, abstract = {

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

}, doi = {10.1038/s41565-021-00915-2}, author = {Roy, Arundhati and Shen, Jie and Joshi, Himanshu and Song, Woochul and Tu, Yu-Ming and Chowdhury, Ratul and Ruijuan, Ye and Li, Ning and Ren, Changliang and Kumar, Manish and Aleksei Aksimentiev and Zeng, Huaqiang} } @article {355, title = {The Manipulation of the Internal Hydrophobicity of FraC Nanopores Augments Peptide Capture and Recognition}, journal = {ACS Nano}, year = {2021}, month = {06/2021}, abstract = {

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

}, doi = {10.1021/acsnano.0c09958}, url = {https://doi.org/10.1021/acsnano.0c09958}, author = {Florian Leonardus Rudolfus Lucas and Kumar Sarthak and Erica Mariska Lenting and David Coltan and Nieck Jordy van der Heide and Roderick Corstiaan Abraham Versloot and Aleksei Aksimentiev and Giovanni Maglia} } @article {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 {341, title = {Translocation of DNA through Ultrathin Nanoslits}, journal = {Advanced Materials}, volume = {33}, year = {2021}, month = {02/2021}, pages = {2007682}, chapter = {2007682}, abstract = {

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

}, keywords = {2D nanoslits, biopolymers, DNA translocation, graphene, Nanofluidics}, doi = {https://doi.org/10.1002/adma.202007682}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/adma.202007682}, author = {Yang, Wayne and Radha, Boya and Choudhary, Adnan and You, Yi and Mettela, Gangaiah and Geim, Andre K. and Aleksei Aksimentiev and Keerthi, Ashok and Dekker, Cees} } @article {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 {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 {337, title = {Single-Protein Collapse Determines Phase Equilibria of a Biological Condensate}, journal = {J. Phys. Chem. Lett. }, volume = {11}, year = {2020}, month = {05/2020}, pages = {4923 - 4929}, chapter = {4923}, abstract = {

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

}, author = {Han-Yi Chou and Aleksei Aksimentiev} } @article {320, title = {Polyhydrazide-based organic nanotubes as extremely efficient and highly selective artificial iodide channels}, journal = {Angewandte Chemie International Edition}, volume = {12}, year = {2020}, month = {02/2020}, pages = {4806-4813}, chapter = {4806}, abstract = {

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

}, doi = { https://doi.org/10.1002/anie.201916287}, author = {Roy, Arundhati and Joshi, Himanshu and Ye, Ruijuan and Shen, Jie and Chen, Feng and Aleksei Aksimentiev and Zeng, Huaqiang} } @article {318, title = {Artificial Water Channels Enable Fast and Selective Water Permeation Through Water-wire Networks}, journal = {Nature Nanotechnology.}, volume = {15,}, year = {2020}, month = {01/2020}, pages = {73-79}, chapter = {73}, abstract = {

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

}, doi = {https://doi.org/10.1038/s41565-019-0586-8}, author = {Woochul Song and Himanshu Joshi and Ratul Chowdhury and Joseph S. Najem and Yue-xiao Shen and Chao Lang and Codey B. Henderson and Yu-Ming Tu and Megan Farell and Megan E. Pitz and Costas D. Maranas and Paul S. Cremer and Robert J. Hickey and Stephen A. Sarles and Jun-li Hou and Aleksei Aksimentiev and Manish Kumar} } @article {308, title = {Atoms to Phenotypes: Molecular Design Principles of Cellular Energy Metabolism}, journal = {Cell}, volume = {179}, year = {2019}, month = {11/2019}, pages = {1098 - 1111.e23}, abstract = {

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

}, keywords = {bioenergetics, biological membranes, charge transport, chromatophore, integrative model, MD, mitochondria, Molecular Dynamics Simulation, optical spectroscopy, photosynthesis}, issn = {0092-8674}, doi = {10.1016/j.cell.2019.10.021}, url = {http://www.sciencedirect.com/science/article/pii/S0092867419311717}, author = {Abhishek Singharoy and Christopher Maffeo and Karelia H. Delgado-Magnero and David J.K. Swainsbury and Melih Sener and Ulrich Kleinekath{\"o}fer and John W. Vant and Jonathan Nguyen and Andrew Hitchcock and Barry Isralewitz and Ivan Teo and Danielle E. Chandler and John E. Stone and James C. Phillips and Taras V. Pogorelov and M. Ilaria Mallus and Christophe Chipot and Zaida Luthey-Schulten and D. Peter Tieleman and C. Neil Hunter and Emad Tajkhorshid and Aleksei Aksimentiev and Klaus Schulten} } @article {297, title = {Effect of temperature and hydrophilic ratio on the structure of poly(N-vinylcaprolactam)-block-poly(dimethylsiloxane)-block-poly(N-vinylcaprolactam) polymersomes}, journal = {ACS Applied Polymer Materials}, volume = {1}, year = {2019}, month = {04/2019}, pages = {722--736}, chapter = {722}, abstract = {

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

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

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

}, doi = {10.1021/acs.langmuir.9b00164}, url = {https://doi.org/10.1021/acs.langmuir.9b00164}, author = {Farell, Megan and Wetherington, Maxwell and Shankla, Manish and Chae, Inseok and Subramanian, Shruti and Kim, Seong H. and Aleksei Aksimentiev and Robinson, Joshua and Kumar, Manish} } @article {296, title = {Molecular Mechanisms of DNA Replication and Repair Machinery: Insights from Microscopic Simulations}, journal = {Advanced Theory and Simulations}, volume = {2}, year = {2019}, month = {02/2019}, pages = {1800191}, abstract = {

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

}, keywords = {coarse-grained simulation, DNA damage, DNA repair, homologous recombination, Molecular dynamics, nucleic acids, QM/MM, replisome}, doi = {10.1002/adts.201800191}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/adts.201800191}, author = {Maffeo, Christopher and Chou, Han-Yi and Aleksei Aksimentiev} } @article {290, title = {PoreDesigner for tuning solute selectivity in a robust and highly permeable outer membrane pore}, journal = {Nature Communications}, volume = {9}, year = {2018}, month = {09/2018}, pages = {3661}, abstract = {

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

}, issn = {2041-1723}, doi = {10.1038/s41467-018-06097-1}, url = {https://doi.org/10.1038/s41467-018-06097-1}, author = {Chowdhury, Ratul and Ren, Tingwei and Shankla, Manish and Decker, Karl and Grisewood, Matthew and Prabhakar, Jeevan and Baker, Carol and Golbeck, John H and Aleksei Aksimentiev and Kumar, Manish and Maranas, Costas D} } @article {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 {250, title = {Mechanical Trapping of DNA in a Double-Nanopore System}, journal = {Nano Letters}, volume = {16}, year = {2016}, month = {11/2016}, pages = {8021-8028 }, abstract = {

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

}, doi = {10.1021/acs.nanolett.6b04642}, author = {Sergii Pud and Shu-Han Chao and Maxim Belkin and Daniel Verschueren and Teun Huijben and Casper van Engelenburg and Cees Dekker and Aleksei Aksimentiev} } @article {246, title = {DNA sequence-dependent ionic currents in ultra-small solid-state nanopores}, journal = {Nanoscale}, volume = {18}, year = {2016}, month = {04/2016}, pages = {9600-9613}, abstract = {

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

}, doi = {10.1039/C6NR01061J}, url = {http://pubs.rsc.org/en/content/articlehtml/2016/nr/c6nr01061j}, author = {Jeffrey Comer and Aleksei Aksimentiev} } @article {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 {204, title = {Plasmonic Nanopores for Trapping, Controlling Displacement, and Sequencing of DNA}, journal = {ACS Nano}, volume = {9}, year = {2015}, month = {09/2015}, pages = {10598--10611}, type = {Article}, abstract = {

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

}, doi = {10.1021/acsnano.5b04173}, url = {http://pubs.acs.org/doi/10.1021/acsnano.5b04173}, author = {Maxim Belkin and Shu-Han Chao and Magnus P. Jonsson and Cees Dekker and Aleksei Aksimentiev} } @article {208, title = {Mapping fast protein folding with multiple-site fluorescent probes.}, journal = {Proc Natl Acad Sci U S A}, volume = {112}, year = {2015}, month = {06/2015}, pages = {7966-71}, abstract = {

Fast protein folding involves complex dynamics in many degrees of freedom, yet microsecond folding experiments provide only low-resolution structural information. We enhance the structural resolution of the five-helix bundle protein λ6-85 by engineering into it three fluorescent tryptophan-tyrosine contact probes. The probes report on distances between three different helix pairs: 1-2, 1-3, and 3-2. Temperature jump relaxation experiments on these three mutants reveal two different kinetic timescales: a slower timescale for 1-3 and a faster one for the two contacts involving helix 2. We hypothesize that these differences arise from a single folding mechanism that forms contacts on different timescales, and not from changes of mechanism due to adding the probes. To test this hypothesis, we analyzed the corresponding three distances in one published single-trajectory all-atom molecular-dynamics simulation of a similar mutant. Autocorrelation analysis of the trajectory reveals the same "slow" and "fast" distance change as does experiment, but on a faster timescale; smoothing the trajectory in time shows that this ordering is robust and persists into the microsecond folding timescale. Structural investigation of the all-atom computational data suggests that helix 2 misfolds to produce a short-lived off-pathway trap, in agreement with the experimental finding that the 1-2 and 3-2 distances involving helix 2 contacts form a kinetic grouping distinct from 1 to 3. Our work demonstrates that comparison between experiment and simulation can be extended to several order parameters, providing a stronger mechanistic test.

}, keywords = {Fluorescent Dyes, Kinetics, Molecular Dynamics Simulation, Mutation, Protein Folding, Tryptophan, Tyrosine}, issn = {1091-6490}, doi = {10.1073/pnas.1422683112}, url = {http://www.pnas.org/content/112/26/7966.full?sid=da9112c1-35df-4a1b-83b8-cfe4c0c56f7b}, author = {Prigozhin*, Maxim B and Chao*, Shu-Han and Sukenik, Shahar and Pogorelov, Taras V and Gruebele, Martin} } @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 {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 {119, title = {Two Structural Scenarios for Protein Stabilization by PEG.}, journal = {J Phys Chem B}, volume = {118}, year = {2014}, month = {05/2014}, pages = {8388{\textendash}8395}, abstract = {

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

}, issn = {1520-5207}, doi = {10.1021/jp502234s}, author = {Shu-Han Chao and Matthews, Sam S and Paxman, Ryan and Aleksei Aksimentiev and Martin Gruebele and Price, Joshua L} } @article {121, title = {Filling Up the Heme Pocket Stabilizes Apomyoglobin and Speeds Up Its Folding.}, journal = {J Phys Chem B}, year = {2014}, month = {02/2014}, abstract = {

Wild type apomyoglobin folds in at least two steps: the ABGH core rapidly, followed much later by the heme-binding CDEF core. We hypothesize that the evolved heme-binding function of the CDEF core frustrates its folding: it has a smaller contact order and is no more complex topologically than ABGH, and thus, it should be able to fold faster. Therefore, filling up the empty heme cavity of apomyoglobin with larger, hydrophobic side chains should significantly stabilize the protein and increase its folding rate. Molecular dynamics simulations allowed us to design four different mutants with bulkier side chains that increase the native bias of the CDEF region. In vitro thermal denaturation shows that the mutations increase folding stability and bring the protein closer to two-state behavior, as judged by the difference of fluorescence- and circular dichroism-detected protein stability. Millisecond stopped flow measurements of the mutants exhibit refolding kinetics that are over 4 times faster than the wild type{\textquoteright}s. We propose that myoglobin-like proteins not evolved to bind heme are equally stable, and find an example. Our results illustrate how evolution for function can force proteins to adapt frustrated folding mechanisms, despite having simple topologies.

}, issn = {1520-5207}, doi = {10.1021/jp412459z}, author = {Goodman, J S and Shu-Han Chao and Pogorelov, T V and Martin Gruebele} } @article {14, title = {A Stabilized Finite Element Method for Modified Poisson-Nernst-Planck Equations to Determine Ion Flow Through a Nanopore}, journal = {Commun Comput Phys}, volume = {15}, year = {2014}, month = {01/2014}, pages = {93-125}, abstract = {

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

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

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

}, keywords = {Boundary-driven MD, Molecular dynamics, Nanofluidics, Non-equilibrium MD, Plasmonic heating, Soret coefficient, Thermodiffusion, Thermophoresis}, issn = {1569-8025}, doi = {10.1007/s10825-014-0594-8}, url = {http://dx.doi.org/10.1007/s10825-014-0594-8}, author = {Maxim Belkin and Shu-Han Chao and Giannetti, Gino and Aleksei Aksimentiev} } @article {27, title = {DNA base-calling from a nanopore using a Viterbi algorithm}, journal = {Biophys J}, volume = {102}, year = {2012}, month = {2012 May 16}, pages = {L37-9}, abstract = {

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

}, keywords = {Algorithms, Base Sequence, DNA, Electricity, Genome, Human, Humans, Markov Chains, Nanopores, Sequence Analysis, DNA, Signal-To-Noise Ratio}, issn = {1542-0086}, doi = {10.1016/j.bpj.2012.04.009}, author = {Timp, Winston and Jeffrey Comer and Aleksei Aksimentiev} } @article {29, title = {Predicting the DNA sequence dependence of nanopore ion current using atomic-resolution Brownian dynamics}, journal = {J Phys Chem C Nanomater Interfaces}, volume = {116}, year = {2012}, month = {2012 Feb 9}, pages = {3376-3393}, abstract = {

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

}, issn = {1932-7447}, doi = {10.1021/jp210641j}, author = {Jeffrey Comer and Aleksei Aksimentiev} } @article {24, title = {Toward detection of DNA-bound proteins using solid-state nanopores: insights from computer simulations}, journal = {Electrophoresis}, volume = {33}, year = {2012}, month = {2012 Dec}, pages = {3466-79}, abstract = {

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

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

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

}, keywords = {DNA, Graphite, Nanopores, Sequence Analysis, DNA}, issn = {1530-6992}, doi = {10.1021/nl301655d}, author = {David B Wells and Maxim Belkin and Jeffrey Comer and Aleksei Aksimentiev} } @article {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 {33, title = {Atoms-to-microns model for small solute transport through sticky nanochannels}, journal = {Lab Chip}, volume = {11}, year = {2011}, month = {2011 Nov 21}, pages = {3766-73}, abstract = {

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

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

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

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

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

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

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

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

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

}, issn = {1536-125X}, author = {Carr, Rogan and Jeffrey Comer and Ginsberg, Mark D and Aleksei Aksimentiev} } @article {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 {145, title = {Modeling the Interface between Biological and Synthetic Components in Hybrid Nanosystems}, booktitle = {Simulations in Nanobiotechnology}, year = {2011}, pages = {43-60}, publisher = {CRC Press}, organization = {CRC Press}, chapter = {2}, abstract = {Hybrid structures that combine biological and inorganic materials are ubiquitous in the biosphere, from the carbonated hydroxyapatite that makes up the inorganic structure of bones to the calcium carbonate created by coral polyps and coralline algae that form the structure of coral reefs. The ability to design materials that are bio-compatible, or able to be incorporated into organisms without provoking an immune response, is important for medicine and therapeutics, for example, in prosthetics and implanted medical devices such as pacemakers. However, designing synthetic materials to interact favorably with biological components is made difficult by the fact that many biological processes, including immune response, are dictated by interactions betweeen biomolecules and their environment on the nanometer scale. Therefore, our ability to fabricate materials with nanometer precision would provide hope for a future in which man-made devices can easily interface with the biological world.}, issn = {9781439835043}, url = {http://www.crcpress.com/product/isbn/9781439835043}, author = {Carr, Rogan and Jeffrey Comer and Aleksei Aksimentiev}, editor = {Eom, Kilho} } @inbook {193, title = {Nanopore Force Spectroscopy: Insights from Molecular Dynamics Simulations}, booktitle = {Nanopores: Sensing and Fundamental Biological Interactions}, year = {2011}, pages = {335{\textendash}356}, publisher = {Springer Science and Business Media, LLC}, organization = {Springer Science and Business Media, LLC}, chapter = {14}, address = {New York}, abstract = {

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

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

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

}, keywords = {Comparison between biological and synthetic nanopores, Hydrodynamic focusing, Molecular dynamics simulations, Sequencing DNA, Trapping DNA, λ-DNA}, isbn = {978-1-4419-8251-3}, doi = {10.1007/978-1-4419-8252-0_12}, url = {http://dx.doi.org/10.1007/978-1-4419-8252-0_12}, author = {Gregory Timp and Mirsaidov, Utkur and Timp, Winston and Shim, Jiwook and Wang, Deqiang and Valentin Dimitrov and Scrimgeour, Jan and Lin, Chunchen and Jeffrey Comer and Anthony H. Ho and Zou, Xueqing and Aleksei Aksimentiev and Klaus Schulten}, editor = {Iqbal, Samir M. and Rashid Bashir} } @article {41, title = {Slowing the translocation of double-stranded DNA using a nanopore smaller than the double helix}, journal = {Nanotechnology}, volume = {21}, year = {2010}, month = {2010 Oct 1}, pages = {395501}, abstract = {

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

}, keywords = {Bacteriophage lambda, DNA, DNA, Viral, Electrochemical Techniques, Microscopy, Electron, Transmission, Molecular Dynamics Simulation, Nanopores, Nanotechnology, Nucleic Acid Conformation, Particle Size}, issn = {1361-6528}, doi = {10.1088/0957-4484/21/39/395501}, author = {Mirsaidov, Utkur and Jeffrey Comer and Valentin Dimitrov and Aleksei Aksimentiev and Gregory Timp} } @article {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 {46, title = {The effect of calcium on the conformation of cobalamin transporter BtuB}, journal = {Proteins}, volume = {78}, year = {2010}, month = {2010 Apr}, pages = {1153-62}, abstract = {

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

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

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

}, issn = {1932-4510}, doi = {10.1109/MNANO.2008.931112}, author = {Aleksei Aksimentiev and Robert Brunner and Eduardo Cruz-Ch{\'u} and Jeffrey Comer and Klaus Schulten} } @article {49, title = {Analyzing the forces binding a restriction endonuclease to DNA using a synthetic nanopore}, journal = {Nucleic Acids Res}, volume = {37}, year = {2009}, month = {2009 Jul}, pages = {4170-9}, abstract = {

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

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

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

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

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

}, issn = {1932-7447}, doi = {10.1021/jp804724p}, author = {Eduardo Cruz-Ch{\'u} and Aleksei Aksimentiev and Klaus Schulten} } @article {58, title = {Synthetic ion channels via self-assembly: a route for embedding porous polyoxometalate nanocapsules in lipid bilayer membranes}, journal = {Nano Lett}, volume = {8}, year = {2008}, month = {2008 Nov}, pages = {3916-21}, abstract = {

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

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

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

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

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

}, keywords = {DNA, Electricity, Nanostructures, Sequence Analysis, DNA}, issn = {1530-6984}, doi = {10.1021/nl071890k}, author = {G Sigalov and Jeffrey Comer and Gregory Timp and Aleksei Aksimentiev} } @article {61, title = {In meso crystal structure and docking simulations suggest an alternative proteoglycan binding site in the OpcA outer membrane adhesin}, journal = {Proteins}, volume = {71}, year = {2008}, month = {2008 Apr}, pages = {24-34}, abstract = {

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

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

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

}, keywords = {Biosensing Techniques, Biotechnology, Computational Biology, Computer Simulation, Models, Molecular, Nanostructures}, issn = {1064-3745}, doi = {10.1007/978-1-59745-480-3_11}, author = {Aleksei Aksimentiev and Robert Brunner and Cohen, Jordi and Jeffrey Comer and Eduardo Cruz-Ch{\'u} and Hardy, David and Rajan, Aruna and Amy Y Shih and G Sigalov and Yin, Ying and Klaus Schulten} } @article {63, title = {Structure refinement of the OpcA adhesin using molecular dynamics}, journal = {Biophys J}, volume = {93}, year = {2007}, month = {2007 Nov 1}, pages = {3058-69}, abstract = {

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

}, keywords = {Adhesins, Bacterial, Bacterial Outer Membrane Proteins, Computer Simulation, Crystallography, X-Ray, Models, Molecular, Neisseria meningitidis, Protein Structure, Tertiary, Thermodynamics}, issn = {0006-3495}, doi = {10.1529/biophysj.107.106724}, author = {Luan, Binquan and Caffrey, Martin and Aleksei Aksimentiev} } @article {66, title = {Water-silica force field for simulating nanodevices}, journal = {J Phys Chem B}, volume = {110}, year = {2006}, month = {2006 Nov 2}, pages = {21497-508}, abstract = {

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

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

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

}, keywords = {Biosensing Techniques, Chemical Engineering, DNA, Lipid Bilayers, Membrane Potentials, Models, Molecular, Nanotechnology, Nanotubes, Carbon, Sequence Analysis, Silicon}, issn = {1478-3975}, doi = {10.1088/1478-3975/3/1/S05}, author = {Lu, Deyu and Aleksei Aksimentiev and Amy Y Shih and Eduardo Cruz-Ch{\'u} and Freddolino, Peter L and Arkhipov, Anton and Klaus Schulten} } @inbook {189, title = {Toward understanding membrane channels}, booktitle = { Bacterial ion channels and their eukaryotic homologues}, year = {2005}, pages = {153{\textendash}190}, publisher = {ASM Press}, organization = {ASM Press}, address = {Washington, DC}, abstract = {

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

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

}, author = {Tajkhorshid, Emad and Cohen, Jordi and Aleksei Aksimentiev and Marcos Sotomayor and Klaus Schulten}, editor = {Boris Martinac and Andrzej Kubalski} }