@article {399, title = {Conformation-Dependent Hydrogen-Bonding Interactions in a Switchable Artificial Metalloprotein}, journal = {Biochemistry}, year = {2024}, abstract = {

Hydrogen-bonding (H-bonding) interactions in metalloprotein active sites can critically regulate enzyme function. Changes in the protein structure triggered by interplay with substrates, products, and partner proteins are often translated to the metallocofactor by way of specific changes in H-bond networks connected to the active site. However, the complexities of metalloprotein architecture and mechanism often preclude our ability to define the precise molecular interactions giving rise to these intricate regulatory pathways. To address this shortcoming, we have developed conformationally switchable artificial metalloproteins (swArMs) in which allosteric Gln-binding triggers protein conformational changes that impact the microenvironment surrounding an installed metallocofactor. Herein, we report a combined structural, spectroscopic, and computational approach to enhance the conformation-dependent changes in H-bond interactions surrounding the metallocofactor site of a swArM. Structure-informed molecular dynamics simulations were employed to predict point mutations that could enhance active site H-bond interactions preferentially in the Gln-bound\ holo-conformation of the swArM. Testing our predictions via the unique infrared spectral signals associated with the metallocofactor site, we have identified three key residues capable of imparting conformational control over the metallocofactor microenvironment. The resultant swArMs not only model biologically relevant structural regulation but also provide an enhanced Gln-responsive biological probe to be leveraged in future biosensing applications.

}, doi = {10.1021/acs.biochem.4c00209}, url = {https://doi.org/10.1021/acs.biochem.4c00209}, author = {Fatima, Saman and Mehrafrooz, Behzad and Boggs, David G. and Ali, Noor and Singh, Swapnil and Thielges, Megan C. and Bridwell-Rabb, Jennifer and Aksimentiev, Aleksei and Olshansky, Lisa} } @article {397, title = {Dehydrated Biomimetic Membranes with Skinlike Structure and Function}, journal = {ACS Applied Materials \& Interfaces}, volume = {16}, year = {2024}, pages = {20865-20877}, abstract = {

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

}, doi = {10.1021/acsami.3c19572}, url = {https://doi.org/10.1021/acsami.3c19572}, author = {Oh, Hyeonji and Tu, Yu-Ming and Samineni, Laximicharan and De Respino, Sophie and Mehrafrooz, Behzad and Joshi, Himanshu and Massenburg, Lynnicia and Lopez-Marques, Horacio and Elessawy, Nada and Song, Woochul and Behera, Harekrushna and Dhiman, Raman and Boorla, Veda Sheersh and Kher, Kartik and Lin, Yi-Chih and Maranas, Costas and Aksimentiev, Aleksei and D. Freeman, Benny and Kumar, Manish} } @article {392, title = {Sulfur-Containing Foldamer-Based Artificial Lithium Channels}, journal = {Angewandte Chemie International Edition}, volume = {62}, year = {2023}, pages = {e202305623}, abstract = {

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

}, keywords = {Foldamers, H-Bonds, Lithium Channels, Organic Nanotubes, Supramolecular Chemistry}, doi = {https://doi.org/10.1002/anie.202305623}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/anie.202305623}, author = {Shen, Jie and R, Deepa and Li, Zhongyan and Oh, Hyeonji and Behera, Harekrushna and Joshi, Himanshu and Kumar, Manish and Aksimentiev, Aleksei and Zeng, Huaqiang} } @article {371, title = {Resolving Isomeric Posttranslational Modifications Using a Biological Nanopore as a Sensor of Molecular Shape}, journal = {Journal of the American Chemical Society}, volume = {144}, year = {2022}, month = {08/2022}, pages = {16060--16068}, abstract = {

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

}, doi = {10.1021/jacs.2c06211}, url = {https://pubs.acs.org/doi/full/10.1021/jacs.2c06211}, author = {Tobias Ennslen and Kumar Sarthak and Aleksei Aksimentiev and Jan C. Behrends} } @article {364, title = {A nanoscale reciprocating rotary mechanism with coordinated mobility control.}, journal = {Nature Communications}, volume = {12}, year = {2021}, month = {12/2021}, pages = {7138}, chapter = {7138}, abstract = {

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

}, keywords = {Cryoelectron Microscopy, DNA, Molecular Conformation, Molecular Dynamics Simulation, Nanostructures, Nanotechnology, Rotation}, issn = {2041-1723}, doi = {10.1038/s41467-021-27230-7}, author = {Bertosin, Eva and Maffeo, Christopher M and Drexler, Thomas and Honemann, Maximilian N and Aleksei Aksimentiev and Dietz, Hendrik} } @article {365, title = {Multiple rereads of single proteins at single{\textendash}amino acid resolution using nanopores}, journal = {Science}, volume = {374}, year = {2021}, month = {11/2021}, pages = {1509{\textendash}1513}, abstract = {

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

}, doi = {10.1021/acs.nanolett.1c04203}, author = {Brinkerhoff, Henry and Kang, Albert SW and Liu, Jingqian and Aleksei Aksimentiev and Dekker, Cees} } @article {362, title = {DNA Origami Voltage Sensors for Transmembrane Potentials with Single-Molecule Sensitivity}, journal = {Nano Letters}, volume = {21}, year = {2021}, month = {10/2021}, pages = {8634-8641}, chapter = {8634}, abstract = {

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

}, doi = {10.1021/acs.nanolett.1c02584}, url = {https://pubs.acs.org/doi/10.1021/acs.nanolett.1c02584?fig=tgr1\&ref=pdf}, author = {Ochmann, Sarah E and Joshi, Himanshu and Büber, Ece and Franquelim, Henri G and Stegemann, Pierre and Sacc{\`a}, Barbara and Keyser, Ulrich F and Aleksei Aksimentiev and Tinnefeld, Philip} } @article {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 {354, title = {Hydrophobic Interactions between DNA Duplexes and Synthetic and Biological Membranes.}, journal = {Journal of the American Chemical Society}, volume = {143}, year = {2021}, month = {05/2021}, pages = {8305-8313}, chapter = {8305}, abstract = {

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

}, issn = {1520-5126}, doi = {10.1021/jacs.0c13235}, author = {Jones, Sioned F and Joshi, Himanshu and Terry, Stephen J and Burns, Jonathan R and Aleksei Aksimentiev and Eggert, Ulrike S and Howorka, Stefan} } @article {346, title = {Electrical unfolding of cytochrome during translocation through a nanopore constriction.}, journal = {Proceedings of the National Academy of Sciences}, volume = {118}, year = {2021}, month = {04/2021}, 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 {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 {317, title = {Electrical recognition of the twenty proteinogenic amino acids using an aerolysin nanopore}, journal = {Nature Biotechnology}, volume = {38}, year = {2020}, month = {02/2020}, pages = {176-181}, chapter = {176}, abstract = {

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

Research Highlights

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

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

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

}, isbn = {1546-1696}, doi = {10.1038/s41587-019-0345-2}, url = {https://doi.org/10.1038/s41587-019-0345-2}, author = {Ouldali, Hadjer and Sarthak, Kumar and Ensslen, Tobias and Piguet, Fabien and Manivet, Philippe and Pelta, Juan and Behrends, Jan C. and Aleksei Aksimentiev and Oukhaled, Abdelghani} } @article {307, title = {Single molecule analysis of structural fluctuations in DNA nanostructures}, journal = {Nanoscale}, volume = {11}, year = {2019}, month = {10/2019}, pages = {18475 - 18482}, abstract = {

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

}, issn = {2040-3364}, doi = {10.1039/C9NR03826D}, url = {http://xlink.rsc.org/?DOI=C9NR03826Dhttp://pubs.rsc.org/en/content/articlepdf/2019/NR/C9NR03826Dhttp://pubs.rsc.org/en/content/articlepdf/2019/NR/C9NR03826D}, author = {Jepsen, Mette D. E. and S{\o}rensen, Rasmus Sch{\o}ler and Maffeo, Christopher and Aleksei Aksimentiev and Kjems, J{\o}rgen and Birkedal, Victoria} } @article {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 {286, title = {A synthetic enzyme built from DNA flips 10$^{7}$ lipids per second in biological membranes}, journal = {Nature Communications}, volume = {9}, year = {2018}, month = {07/2018}, pages = {2426}, abstract = {

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

}, keywords = {Computational biophysics, DNA nanostructures, Membrane biophysics, Nanobiotechnology}, doi = {10.1038/s41467-018-04821-5}, url = {http://www.nature.com/articles/s41467-018-04821-5}, author = {Ohmann, Alexander and Li, Chen-Yu and Maffeo, Christopher and Al Nahas, Kareem and Baumann, Kevin N. and G{\"o}pfrich, Kerstin and Yoo, Jejoong and Keyser, Ulrich F. and Aleksei Aksimentiev} } @article {285, title = {Inchworm movement of two rings switching onto a thread by biased Brownian diffusion represent a three-body problem}, journal = {Proceedings of the National Academy of Sciences}, year = {2018}, month = {05/2018}, abstract = {

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

}, issn = {0027-8424}, doi = {10.1073/pnas.1719539115}, url = {http://www.pnas.org/content/early/2018/05/03/1719539115}, author = {Benson, Christopher R. and Maffeo, Christopher and Fatila, Elisabeth M. and Liu, Yun and Sheetz, Edward G. and Aleksei Aksimentiev and Singharoy, Abhishek and Flood, Amar H.} } @article {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 {251, title = {Selective Permeability of Truncated Aquaporin 1 in Silico}, journal = {ACS Biomaterials Science \& Engineering}, volume = {3}, year = {2017}, month = {02/2017}, pages = {342-348}, chapter = {342}, abstract = {

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

}, doi = {10.1021/acsbiomaterials.6b00583 }, author = {Karl Decker and Martin Page and Ashley Boyd and Irene MacAllister and Mark Ginsberg and Aleksei Aksimentiev} } @article {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 {316, title = {Promiscuous Histone Mis-Assembly Is Actively Prevented by Chaperones.}, journal = {J Am Chem Soc}, volume = {138}, year = {2016}, month = {10/2016}, pages = {13207-13218}, abstract = {

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

}, keywords = {Centromere Protein A, DNA-Binding Proteins, HeLa Cells, Histones, Humans, Molecular Dynamics Simulation, Protein Folding, Protein Multimerization, Protein Structure, Quaternary, Substrate Specificity}, doi = {10.1021/jacs.6b05355}, author = {Zhao*, Haiqing and Winogradoff*, David and Bui, Minh and Dalal, Yamini and Papoian, Garegin A} } @article {237, title = {Large-Conductance Transmembrane Porin Made from DNA Origami}, journal = {ACS Nano}, volume = {10}, year = {2016}, month = {08/2016}, pages = {8207--8214}, abstract = {

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

}, doi = {10.1021/acsnano.6b03759}, author = {Kerstin G{\"o}pfrich* and Chen-Yu Li* and Maria Ricci and Satya Prathyusha Bhamidimarri and Jejoong Yoo and Bertalan Gyenes and Alexander Ohmann and Mathias Winterhalter and Aleksei Aksimentiev and Ulrich F Keyser} } @article {236, title = {Ion Channels Made from a Single Membrane-Spanning DNA Duplex}, journal = {Nano Letters}, volume = {16}, year = {2016}, month = {06/2016}, pages = {4665--4669}, abstract = {

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

}, doi = {10.1021/acs.nanolett.6b02039}, author = {Kerstin G{\"o}pfrich and Chen-Yu Li and Iwona Mames and Satya Prathyusha Bhamidimarri and Maria Ricci and Jejoong Yoo and Adam Mames and Alexander Ohmann and Mathias Winterhalter and Eugen Stulz and Aleksei Aksimentiev and Ulrich F Keyser} } @article {BELK2016, title = {Molecular Dynamics Simulation of DNA Capture and Transport in Heated Nanopores}, journal = {ACS Applied Materials and Interfaces}, volume = {8}, year = {2016}, note = {PMID: 26963065}, month = {05/2016}, pages = {12599{\textendash}12608}, type = {Research}, abstract = {

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

}, doi = {10.1021/acsami.6b00463}, url = {http://dx.doi.org/10.1021/acsami.6b00463}, author = {Maxim Belkin and Aleksei Aksimentiev} } @article {247, title = {Water Mediates Recognition of DNA Sequence via Ionic Current Blockade in a Biological Nanopore}, journal = {ACS Nano}, volume = {10}, year = {2016}, month = {04/2016}, pages = {4644{\textendash}4651}, abstract = {

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

}, doi = {10.1021/acsnano.6b00940}, author = {Swati Bhattacharya and Jejoong Yoo and Aleksei Aksimentiev} } @article {216, title = {The Hinge Region Strengthens the Nonspecific Interaction between Lac-Repressor and DNA: A Computer Simulation Study}, journal = {PLoS ONE}, volume = {11}, year = {2016}, month = {02/2016}, pages = {e0152002}, abstract = {

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

}, doi = {10.1371/journal.pone.0152002}, url = {http://journals.plos.org/plosone/article?id=10.1371\%2Fjournal.pone.0152002}, author = {Lili Sun and Marcin Tabaka and Sen Hou and Lin Li and Krzysztof Burdzy and Aleksei Aksimentiev and Christopher Maffeo and Xuzhu Zhang and Robert Holyst} } @article {313, title = {Promiscuous histone mis-assembly is actively prevented by chaperones.}, journal = {Journal of the American Chemical Society}, volume = {138}, year = {2016}, pages = {13207--13218}, doi = {10.1021/jacs.6b05355}, author = {Zhao*, Haiqing and Winogradoff*, David and Minh Bui and Yamini Dalal and Garegin Papoian} } @article {204, title = {Plasmonic Nanopores for Trapping, Controlling Displacement, and Sequencing of DNA}, journal = {ACS Nano}, volume = {9}, year = {2015}, month = {09/2015}, pages = {10598--10611}, type = {Article}, abstract = {

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

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

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

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

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

}, keywords = {graphene, graphene{\textendash}DNA interactions, Molecular dynamics, Nanopores, stacked membranes}, issn = {1616-3028}, doi = {10.1002/adfm.201403719}, url = {http://dx.doi.org/10.1002/adfm.201403719}, author = {Banerjee, Shouvik and James Wilson and Shim, Jiwook and Shankla, Manish and Corbin, Elise A. and Aleksei Aksimentiev and Rashid Bashir} } @article {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 {20, title = {Stretching and controlled motion of single-stranded DNA in locally heated solid-state nanopores}, journal = {ACS Nano}, volume = {7}, year = {2013}, month = {08/2013}, pages = {6816-24}, abstract = {

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

}, issn = {1936-086X}, doi = {10.1021/nn403575n}, author = {Maxim Belkin and Christopher Maffeo and David B Wells and Aleksei Aksimentiev} } @article {18, title = {Modeling and simulation of ion channels}, journal = {Chem Rev}, volume = {112}, year = {2012}, month = {2012 Dec 12}, pages = {6250-6284}, abstract = {

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

}, keywords = {Review}, issn = {1520-6890}, doi = {10.1021/cr3002609}, author = {Christopher Maffeo and Bhattacharya, Swati and Yoo, Jejoong and David B Wells and Aleksei Aksimentiev} } @article {13, title = {Assessing graphene nanopores for sequencing DNA.}, journal = {Nano Letters}, volume = {12}, year = {2012}, month = {2012 Aug 8}, pages = {4117-4123}, abstract = {

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

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

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

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

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

}, keywords = {Biological Transport, DNA, Electric Conductivity, Electroosmosis, Hemolysin Proteins, Ions, Lipid Bilayers, Molecular Dynamics Simulation, Nanopores, Porins, Solvents, Thermodynamics}, issn = {1940-6029}, doi = {10.1007/978-1-61779-773-6_10}, author = {David B Wells and Bhattacharya, Swati and Carr, Rogan and Christopher Maffeo and Anthony H. Ho and Jeffrey Comer and Aleksei Aksimentiev} } @article {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 {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 {195, title = {Rectification of the current in alpha-hemolysin pore depends on the cation type: the alkali series probed by MD simulations and experiments}, journal = {The Journal of Physical Chemistry C}, volume = {115}, year = {2011}, month = {2011 Feb 21}, pages = {4255-4264}, abstract = {

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

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

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

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

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

}, keywords = {Aluminum Oxide, Biosensing Techniques, DNA, Fluorescence Recovery After Photobleaching, Ion Channels, Lipid Bilayers, Models, Biological, Molecular Dynamics Simulation, Nanopores, Nanotechnology, Phosphatidylcholines, Sequence Analysis, DNA, Silicon Dioxide, Staining and Labeling, Titanium}, issn = {1572-8781}, doi = {10.1007/s10544-011-9537-3}, author = {Venkatesan, Bala Murali and Polans, James and Jeffrey Comer and Sridhar, Supriya and Wendell, David and Aleksei Aksimentiev and Rashid Bashir} } @inbook {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 {17, title = {DNA-DNA interactions in tight supercoils are described by a small effective charge density}, journal = {Phys Rev Lett}, volume = {105}, year = {2010}, month = {2010 Oct 8}, pages = {158101}, abstract = {

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

}, keywords = {Biomechanical Phenomena, DNA, Superhelical, Molecular Dynamics Simulation, Monte Carlo Method, Salts, Static Electricity}, issn = {1079-7114}, doi = {10.1103/PhysRevLett.105.158101 }, url = {http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.105.158101}, author = {Christopher Maffeo and Sch{\"o}pflin, Robert and Brutzer, Hergen and Stehr, Ren{\'e} and Aleksei Aksimentiev and Wedemann, Gero and Seidel, Ralf} } @article {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 {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 {76, title = {Insights into the molecular mechanism of rotation in the Fo sector of ATP synthase}, journal = {Biophys J}, volume = {86}, year = {2004}, month = {2004 Mar}, pages = {1332-44}, abstract = {

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

}, keywords = {Binding Sites, Cell Membrane, Computer Simulation, Dimerization, Models, Chemical, Models, Molecular, Models, Statistical, Molecular Motor Proteins, Protein Binding, Protein Conformation, Protein Subunits, Proton-Translocating ATPases, Rotation, Stochastic Processes}, issn = {0006-3495}, doi = {10.1016/S0006-3495(04)74205-8}, author = {Aleksei Aksimentiev and Ilya A Balabin and Fillingame, Robert H and Klaus Schulten} } @article {77, title = {Large scale simulation of protein mechanics and function}, journal = {Adv Protein Chem}, volume = {66}, year = {2003}, month = {2003}, pages = {195-247}, keywords = {Amino Acid Motifs, Aquaporins, Catalysis, Cell Membrane, Computer Simulation, Fibronectins, Hydrogen Bonding, Models, Molecular, Protein Conformation, Protein Denaturation, Protein Folding, Protein Structure, Secondary, Proteins, Proton-Translocating ATPases, Substrate Specificity, Time Factors, Water}, issn = {0065-3233}, author = {Tajkhorshid, Emad and Aleksei Aksimentiev and Ilya A Balabin and Gao, Mu and Isralewitz, Barry and Phillips, James C and Zhu, Fangqiang and Klaus Schulten} } @article {78, title = {Diffusion on curved, periodic surfaces}, journal = {Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics}, volume = {60}, year = {1999}, month = {1999 Jul}, pages = {302-7}, abstract = {

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

}, issn = {1063-651X}, author = {Robert Ho{\l}yst and Plewczy{\'n}ski, D and Aleksei Aksimentiev and Burdzy, K} }