@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 {395, title = {A Marcus-Type Inverted Region in the Translocation Kinetics of a Knotted Protein}, journal = {The Journal of Physical Chemistry Letters}, volume = {14}, year = {2023}, month = {11/2023}, pages = {10719-10726}, abstract = {

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

}, doi = {10.1021/acs.jpclett.3c02183}, url = {https://doi.org/10.1021/acs.jpclett.3c02183}, author = {Tripathi, Prabhat and Mehrafrooz, Behzad and Aksimentiev, Aleksei and Jackson, Sophie E. and Gruebele, Martin and Wanunu, Meni} } @article {370, title = {Fluorofoldamer-Based Salt- and Proton-Rejecting Artificial Water Channels for Ultrafast Water Transport.}, journal = {Nano Lett}, volume = {22}, year = {2022}, month = {2022 06 22}, pages = {4831-4838}, abstract = {

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

}, keywords = {Aquaporins, Biological Transport, Protons, Sodium Chloride, Water}, issn = {1530-6992}, doi = {10.1021/acs.nanolett.2c01137}, author = {Shen, Jie and Roy, Arundhati and Joshi, Himanshu and Samineni, Laxmicharan and Ye, Ruijuan and Tu, Yu-Ming and Song, Woochul and Skiles, Matthew and Kumar, Manish and Aleksei Aksimentiev and Zeng, Huaqiang} } @article {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 {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 {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 {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 {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 {343, title = {Determining the In-Plane Orientation and Binding Mode of Single Fluorescent Dyes in DNA Origami Structures}, journal = {ACS Nano}, volume = {15}, year = {2021}, month = {03/2021}, pages = {5109-5117}, chapter = {5109}, abstract = {

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

}, keywords = {DNA Nanotechnology, DNA-PAINT, Single-molecule fluorescence polarization-resolved microscopy, Super-resolution microscopy}, doi = {https://doi.org/10.1021/acsnano.0c10259}, url = {https://pubs.acs.org/doi/10.1021/acsnano.0c10259}, author = {Hübner, Kristina and Joshi, Himanshu and Aleksei Aksimentiev and Stefani, Fernando D and Tinnefeld, Philip and Acuna, Guillermo P} } @article {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 {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 {319, title = {Rosette Nanotube Porins as Ion Selective Transporters and Single-Molecule Sensors}, journal = {Journal of the American Chemical Society}, volume = {142}, year = {2020}, month = {01/2020}, pages = {1680-1685}, chapter = {1680}, abstract = {

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

}, doi = {https://doi.org/10.1021/jacs.9b10993}, author = {Tripathi, Prabhat and Shuai, Liang and Joshi, Himanshu and Yamazaki, Hirohito and Fowle, William H and Aleksei Aksimentiev and Fenniri, Hicham and Wanunu, Meni} } @article {308, title = {Atoms to Phenotypes: Molecular Design Principles of Cellular Energy Metabolism}, journal = {Cell}, volume = {179}, year = {2019}, month = {11/2019}, pages = {1098 - 1111.e23}, abstract = {

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

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

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

}, keywords = {cholesterol-modified DNA nanostructures,, DNA Nanotechnology}, doi = {https://doi.org/10.1093/nar/gkz914}, url = {https://doi.org/10.1093/nar/gkz914}, author = {Ohmann, Alexander and G{\"o}pfrich, Kerstin and Joshi, Himanshu and Thompson, Rebecca F and Sobota, Diana and Ranson, Neil A and Aleksei Aksimentiev and Keyser, Ulrich F} } @article {281, title = {Optical voltage sensing using DNA origami}, journal = {Nano Letters}, volume = {18}, year = {2018}, pages = {1962-1971}, abstract = {

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

}, doi = {10.1021/acs.nanolett.7b05354}, url = {https://doi.org/10.1021/acs.nanolett.7b05354}, author = {Hemmig, Elisa Alina and Fitzgerald, Clare and Maffeo, Christopher and Hecker, Lisa and Ochmann, Sarah Elisabeth and Aleksei Aksimentiev and Tinnefeld, Philip and Keyser, Ulrich F} } @article {253, title = {Interference-free detection of genetic biomarkers using synthetic dipole-facilitated nanopore dielectophoresis.}, journal = {ACS Nano}, volume = {11}, year = {2017}, month = {01/2017}, pages = {1204-1213}, chapter = {1204}, abstract = {

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

}, doi = {10.1021/acsnano.6b07570}, author = {Kai Tian and Karl Decker and Aleksei Aksimentiev and Li-Qun Gu} } @article {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 {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 {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} } @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 {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 {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 {65, title = {Detecting SNPs using a synthetic nanopore}, journal = {Nano Lett}, volume = {7}, year = {2007}, month = {2007 Jun}, pages = {1680-5}, abstract = {

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

}, keywords = {Deoxyribonuclease EcoRI, DNA, DNA Mutational Analysis, Electromagnetic Fields, Macromolecular Substances, Materials Testing, Molecular Conformation, Nanostructures, Nanotechnology, Particle Size, Polymorphism, Single Nucleotide, Porosity, Sequence Analysis, DNA, Surface Properties}, issn = {1530-6984}, doi = {10.1021/nl070668c}, author = {Zhao, Q and G Sigalov and Valentin Dimitrov and Dorvel, B and Mirsaidov, U and S Sligar and Aleksei Aksimentiev and Gregory Timp} } @article {68, title = {The electromechanics of DNA in a synthetic nanopore}, journal = {Biophys J}, volume = {90}, year = {2006}, month = {2006 Feb 1}, pages = {1098-106}, abstract = {

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

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

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

}, doi = {10.1088/0957-4484/17/3/002}, author = {Maria E. Gracheva and A. Xiong and Aleksei Aksimentiev and Klaus Schulten and Gregory Timp and Jean-Pierre Leburton} } @article {69, title = {Stretching DNA using the electric field in a synthetic nanopore}, journal = {Nano Lett}, volume = {5}, year = {2005}, month = {2005 Oct}, pages = {1883-8}, abstract = {

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

}, keywords = {DNA, Nanotechnology, Static Electricity, Stress, Mechanical}, issn = {1530-6984}, doi = {10.1021/nl0510816}, author = {Jiunn B Heng and Aleksei Aksimentiev and Chuen Ho and Patrick Marks and Yelena V Grinkova and S Sligar and Klaus Schulten and Gregory Timp} } @article {71, title = {Molecular dynamics simulations of proteins in lipid bilayers}, journal = {Curr Opin Struct Biol}, volume = {15}, year = {2005}, month = {2005 Aug}, pages = {423-31}, abstract = {

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

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

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

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

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

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

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

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

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

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

}, keywords = {DNA, Electrochemistry, Nanotechnology, Particle Size, Porosity, Reproducibility of Results, Sensitivity and Specificity, Ultrafiltration}, issn = {0006-3495}, doi = {10.1529/biophysj.104.041814}, author = {Jiunn B Heng and Chuen Ho and Kim, Taekyung and Timp, Rolf and Aleksei Aksimentiev and Yelena V Grinkova and S Sligar and Klaus Schulten and Gregory Timp} } @article {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} }