@article {389, title = {A DNA turbine powered by a transmembrane potential across a nanopore}, journal = {Nature Nanotechnology}, volume = {19}, year = {2024}, month = {03/2024}, pages = {338--344}, chapter = {338}, abstract = {

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

}, issn = {1748-3395}, doi = {10.1038/s41565-023-01527-8}, url = {https://doi.org/10.1038/s41565-023-01527-8}, author = {Shi, Xin and Pumm, Anna-Katharina and Maffeo, Christopher and Kohler, Fabian and Feigl, Elija and Zhao, Wenxuan and Verschueren, Daniel and Golestanian, Ramin and Aksimentiev, Aleksei and Dietz, Hendrik and Dekker, Cees} } @article {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 {388, title = {Benchmarking Molecular Dynamics Force Fields for All-Atom Simulations of Biological Condensates}, journal = {Journal of Chemical Theory and Computation}, volume = {19}, year = {2023}, month = {05/2023}, pages = {3721--3740}, abstract = {

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

}, doi = {10.1021/acs.jctc.3c00148}, url = {https://pubs.acs.org/doi/10.1021/acs.jctc.3c00148}, author = {Kumar Sarthak and David Winogradoff and Yingda Ge and Sua Myong and Aleksei Aksimentiev} } @article {360, title = {Synthetic Macrocycle Nanopore for Potassium-Selective Transmembrane Transport}, journal = {Journal of the American Chemical Society}, volume = {143}, year = {2021}, month = {08/2021}, pages = {15975-15983}, chapter = {15975}, abstract = {

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

}, keywords = {Electrical conductivity, MD Simulations, Nanopores, Potassium Ions Selectivity}, doi = {10.1021/jacs.1c04910}, author = {Qiao, Dan and Joshi, Himanshu and Zhu, Huangtianzhi and Wang, Fushi and Xu, Yang and Gao, Jia and Huang, Feihe and Aleksei Aksimentiev and Feng, Jiandong} } @article {356, title = {The emerging landscape of single-molecule protein sequencing technologies}, journal = {Nature Methods}, volume = {18}, year = {2021}, month = {06/2021}, chapter = {604-617}, abstract = {

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

}, doi = {10.1038/s41592-021-01143-1}, url = {https://doi.org/10.1038/s41592-021-01143-1}, author = {Javier Antonio Alfaro and Peggy Bohl{\"a}nder and Mingjie Dai and Mike Filius and Cecil J. Howard and Xander F. van Kooten and Shilo Ohayon and Adam Pomorski and Sonja Schmid and Aleksei Aksimentiev and Eric V. Anslyn and Georges Bedran and Chan Cao and Mauro Chinappi and Etienne Coyaud and Cees Dekker and Gunnar Dittmar and Nicholas Drachman and Rienk Eelkema and David Goodlett and S{\'e}bastien Hentz and Umesh Kalathiya and Neil L. Kelleher and Ryan T. Kelly and Zvi Kelman and Sung Hyun Kim and Bernhard Kuster and David Rodriguez-Larrea and Stuart Lindsay and Giovanni Maglia and Edward M. Marcotte and John P. Marino and Christophe Masselon and Michael Mayer and Patroklos Samaras and Kumar Sarthak and Lusia Sepiashvili and Derek Stein and Meni Wanunu and Mathias Wilhelm and Peng Yin and Amit Meller and Chirlmin Joo} } @article {341, title = {Translocation of DNA through Ultrathin Nanoslits}, journal = {Advanced Materials}, volume = {33}, year = {2021}, month = {02/2021}, pages = {2007682}, chapter = {2007682}, abstract = {

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

}, keywords = {2D nanoslits, biopolymers, DNA translocation, graphene, Nanofluidics}, doi = {https://doi.org/10.1002/adma.202007682}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/adma.202007682}, author = {Yang, Wayne and Radha, Boya and Choudhary, Adnan and You, Yi and Mettela, Gangaiah and Geim, Andre K. and Aleksei Aksimentiev and Keerthi, Ashok and Dekker, Cees} } @article {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 {298, title = {Rapid and Accurate Determination of Nanopore Ionic Current Using a Steric Exclusion Model}, journal = {ACS sensors}, volume = {4}, year = {2019}, month = {03/2019}, pages = {634--644}, abstract = {

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

}, doi = {10.1021/acssensors.8b01375}, url = {https://pubs.acs.org/doi/full/10.1021/acssensors.8b01375}, author = {Wilson, James and Sarthak, Kumar and Si, Wei and Gao, Luyu and Aleksei Aksimentiev} } @article {290, title = {PoreDesigner for tuning solute selectivity in a robust and highly permeable outer membrane pore}, journal = {Nature Communications}, volume = {9}, year = {2018}, month = {09/2018}, pages = {3661}, abstract = {

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

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

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

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

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

}, keywords = {Computational biophysics, DNA nanostructures, Membrane biophysics, Nanobiotechnology}, doi = {10.1038/s41467-018-04821-5}, url = {http://www.nature.com/articles/s41467-018-04821-5}, author = {Ohmann, Alexander and Li, Chen-Yu and Maffeo, Christopher and Al Nahas, Kareem and Baumann, Kevin N. and G{\"o}pfrich, Kerstin and Yoo, Jejoong and Keyser, Ulrich F. and Aleksei Aksimentiev} } @article {279, title = {Porphyrin-Assisted Docking of a Thermophage Portal Protein into Lipid Bilayers: Nanopore Engineering and Characterization}, journal = {ACS Nano}, volume = {11}, year = {2017}, month = {12/2017}, pages = {11931-11945}, abstract = {

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

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

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

}, doi = {10.1021/acs.jpcb.7b08045}, url = {http://pubs.acs.org/doi/abs/10.1021/acs.jpcb.7b08045}, author = {Wolfe, Aaron John and Si, Wei and Zhang, Zhengqi and Blanden, Adam R and Hsueh, Yi-Ching and Gugel, Jack Fredrick and Pham, Bach and Chen, Min and Loh, Stewart N and Rozovsky, Sharon and Aleksei Aksimentiev and Movileanu, Liviu} } @article {251, title = {Selective Permeability of Truncated Aquaporin 1 in Silico}, journal = {ACS Biomaterials Science \& Engineering}, volume = {3}, year = {2017}, month = {02/2017}, pages = {342-348}, chapter = {342}, abstract = {

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

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

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

}, doi = {10.1021/acsnano.6b07570}, author = {Kai Tian and Karl Decker and Aleksei Aksimentiev and Li-Qun Gu} } @article {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 {208, title = {Mapping fast protein folding with multiple-site fluorescent probes.}, journal = {Proc Natl Acad Sci U S A}, volume = {112}, year = {2015}, month = {06/2015}, pages = {7966-71}, abstract = {

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

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

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

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

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

}, issn = {1520-5207}, doi = {10.1021/jp412459z}, author = {Goodman, J S and Shu-Han Chao and Pogorelov, T V and Martin Gruebele} } @article {doi:10.1021/jp501492g, title = {Rectification of Ion Current in Nanopores Depends on the Type of Monovalent Cations: Experiments and Modeling}, journal = {The Journal of Physical Chemistry C}, volume = {118}, number = {18}, year = {2014}, pages = {9809-9819}, abstract = {Rectifying nanopores feature ion currents that are higher for voltages of one polarity compared to the currents recorded for corresponding voltages of the opposite polarity. Rectification of nanopores has been found to depend on the pore opening diameter and distribution of surface charges on the pore walls as well as pore geometry. Very little is known, however, on the dependence of ionic rectification on the type of transported ions of the same charge. We performed experiments with single conically shaped nanopores in a polymer film and recorded current-voltage curves in three electrolytes: LiCl, NaCl, and KCl. Rectification degrees of the pores, quantified as the ratio of currents recorded for voltages of opposite polarities, were the highest for KCl and the lowest for LiCl. The experimental observations could not be explained by a continuum modeling based on the Poisson-Nernst-Planck equations. All-atom molecular dynamics simulations revealed differential binding between Li+, Na+, and K+ ions and carboxyl groups on the pore walls, resulting in changes to both the effective surface charge of the nanopore and cation mobility within the pore.}, doi = {10.1021/jp501492g}, url = {http://dx.doi.org/10.1021/jp501492g}, author = {Gamble, Trevor and Karl Decker and Plett, Timothy S. and Pevarnik, Matthew and Pietschmann, Jan-Frederik and Vlassiouk, Ivan and Aleksei Aksimentiev and Siwy, Zuzanna S.} } @article {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 {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 {33, title = {Atoms-to-microns model for small solute transport through sticky nanochannels}, journal = {Lab Chip}, volume = {11}, year = {2011}, month = {2011 Nov 21}, pages = {3766-73}, abstract = {

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

}, keywords = {Microfluidic Analytical Techniques, Molecular Conformation, Molecular Dynamics Simulation, Motion, Nanotechnology, Reproducibility of Results, Surface Properties}, issn = {1473-0189}, doi = {10.1039/c1lc20697d}, author = {Carr, Rogan and Jeffrey Comer and Ginsberg, Mark D and Aleksei Aksimentiev} } @article {28, title = {Microscopic Perspective on the Adsorption Isotherm of a Heterogeneous Surface}, journal = {J Phys Chem Lett}, volume = {2}, year = {2011}, month = {2011 Jul 2}, pages = {1804-1807}, abstract = {

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

}, issn = {1948-7185}, doi = {10.1021/jz200749d}, author = {Carr, Rogan and Jeffrey Comer and Ginsberg, Mark D and Aleksei Aksimentiev} } @article {39, title = {Modeling Pressure-Driven Transport of Proteins through a Nanochannel}, journal = {IEEE Trans Nanotechnol}, volume = {10}, year = {2011}, month = {2011 Jan}, pages = {75-82}, abstract = {

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

}, issn = {1536-125X}, author = {Carr, Rogan and Jeffrey Comer and Ginsberg, Mark D and Aleksei Aksimentiev} } @article {68, title = {The electromechanics of DNA in a synthetic nanopore}, journal = {Biophys J}, volume = {90}, year = {2006}, month = {2006 Feb 1}, pages = {1098-106}, abstract = {

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

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

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

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

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

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

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

}, keywords = {DNA, Nanotechnology, Static Electricity, Stress, Mechanical}, issn = {1530-6984}, doi = {10.1021/nl0510816}, author = {Jiunn B Heng and Aleksei Aksimentiev and Chuen Ho and Patrick Marks and Yelena V Grinkova and S Sligar and Klaus Schulten and Gregory Timp} } @article {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 {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} }