@article {371, title = {Resolving Isomeric Posttranslational Modifications Using a Biological Nanopore as a Sensor of Molecular Shape}, journal = {Journal of the American Chemical Society}, volume = {144}, year = {2022}, month = {08/2022}, pages = {16060--16068}, abstract = {

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

}, doi = {10.1021/jacs.2c06211}, url = {https://pubs.acs.org/doi/full/10.1021/jacs.2c06211}, author = {Tobias Ennslen and Kumar Sarthak and Aleksei Aksimentiev and Jan C. Behrends} } @article {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 {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 {239, title = {Refined Parameterization of Nonbonded Interactions Improves Conformational Sampling and Kinetics of Protein Folding Simulations}, journal = {Journal of Physical Chemistry Letters}, volume = {7}, year = {2016}, month = {09/2016}, pages = {3812{\textendash}3818}, chapter = {3812}, abstract = {

Recent advances in computational technology have enabled brute-force molecular dynamics (MD) simulations of protein folding using physics-based molecular force fields. The extensive sampling of protein conformations afforded by such simulations revealed, however, considerable compaction of the protein conformations in the unfolded state, which is inconsistent with experiment. Here, we show that a set of surgical corrections to nonbonded interactions between amine nitrogen{\textendash}carboxylate oxygen and aliphatic carbon{\textendash}carbon atom pairs can considerably improve the realism of protein folding simulations. Specifically, we show that employing our corrections in \~{}500 μs all-atom replica-exchange MD simulations of the WW domain and villin head piece proteins increases the size of the denatured proteins{\textquoteright} conformations and does not destabilize the native conformations of the proteins. In addition to making the folded conformations a global minimum of the respective free energy landscapes at room temperature, our corrections also make the free energy landscape smoother, considerably accelerating the folding kinetics and, hence, reducing the computational expense of a protein folding simulation.

}, doi = {10.1021/acs.jpclett.6b01747}, author = {Jejoong Yoo and Aleksei Aksimentiev} } @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 {195, title = {Rectification of the current in alpha-hemolysin pore depends on the cation type: the alkali series probed by MD simulations and experiments}, journal = {The Journal of Physical Chemistry C}, volume = {115}, year = {2011}, month = {2011 Feb 21}, pages = {4255-4264}, abstract = {

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

}, issn = {1932-7447}, doi = {10.1021/jp111441p}, author = {Bhattacharya, Swati and Muzard, L and Payet, Linda and Math{\'e}, J{\'e}r{\^o}me and Bockelmann, Ulrich and Aleksei Aksimentiev and Viasnoff, Virgile} } @article {67, title = {The role of molecular modeling in bionanotechnology}, journal = {Phys Biol}, volume = {3}, year = {2006}, month = {2006 Mar}, pages = {S40-53}, abstract = {

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

}, keywords = {Biosensing Techniques, Chemical Engineering, DNA, Lipid Bilayers, Membrane Potentials, Models, Molecular, Nanotechnology, Nanotubes, Carbon, Sequence Analysis, Silicon}, issn = {1478-3975}, doi = {10.1088/1478-3975/3/1/S05}, author = {Lu, Deyu and Aleksei Aksimentiev and Amy Y Shih and Eduardo Cruz-Ch{\'u} and Freddolino, Peter L and Arkhipov, Anton and Klaus Schulten} }