Hydrated anions: From clusters to bulk solution with quasi-chemical theory

DT Gomez, LR Pratt, DN Asthagiri… - Accounts of Chemical …, 2022 - ACS Publications
Conspectus The interactions of hydrated ions with molecular and macromolecular solution
and interface partners are strong on a chemical energy scale. Here, we recount the foremost …

All-Atom Biomolecular Simulation in the Exascale Era

TL Beck, P Carloni, DN Asthagiri - Journal of Chemical Theory and …, 2024 - ACS Publications
Exascale supercomputers have opened the door to dynamic simulations, facilitated by AI/ML
techniques, that model biomolecular motions over unprecedented length and time scales …

A physical derivation of high-flux ion transport in biological channel via quantum ion coherence

Y Wang, Y Hu, JP Guo, J Gao, B Song… - Nature …, 2024 - nature.com
Biological ion channels usually conduct the high-flux transport of 107~ 108 ions· s− 1;
however, the underlying mechanism is still lacking. Here, by applying the KcsA potassium …

Direct visualization of electric-field-stimulated ion conduction in a potassium channel

BR Lee, KI White, M Socolich, MA Klureza, R Henning… - Cell, 2025 - cell.com
Understanding protein function would be facilitated by direct, real-time observation of
chemical kinetics in the atomic structure. The selectivity filter (SF) of the K+ channel provides …

Computationally driven discovery of SARS-CoV-2 M pro inhibitors: from design to experimental validation

L El Khoury, Z Jing, A Cuzzolin, A Deplano, D Loco… - Chemical …, 2022 - pubs.rsc.org
We report a fast-track computationally driven discovery of new SARS-CoV-2 main protease
(Mpro) inhibitors whose potency ranges from mM for the initial non-covalent ligands to sub …

Water nanoconfined in a hydrophobic pore: Molecular dynamics simulations of transmembrane protein 175 and the influence of water models

CI Lynch, G Klesse, S Rao, SJ Tucker, MSP Sansom - ACS nano, 2021 - ACS Publications
Water molecules within biological ion channels are in a nanoconfined environment and
therefore exhibit behaviors which differ from that of bulk water. Here, we investigate the …

Simulation and machine learning methods for ion-channel structure determination, mechanistic studies and drug design

Z Zhu, Z Deng, Q Wang, Y Wang, D Zhang… - Frontiers in …, 2022 - frontiersin.org
Ion channels are expressed in almost all living cells, controlling the in-and-out
communications, making them ideal drug targets, especially for central nervous system …

Electronic polarization is essential for the stabilization and dynamics of buried ion pairs in staphylococcal nuclease mutants

J Deng, Q Cui - Journal of the American Chemical Society, 2022 - ACS Publications
Buried charged residues play important roles in the modulation of protein stabilities and
conformational dynamics and make crucial contributions to protein functions. Considering …

Ion conduction mechanisms in potassium channels revealed by permeation cycles

CK Lam, BL de Groot - Journal of Chemical Theory and …, 2023 - ACS Publications
Potassium channels are responsible for the selective yet efficient permeation of potassium
ions across cell membranes. Despite many available high-resolution structures of potassium …

Classical exchange polarization: An anisotropic variable polarizability model

MKJ Chung, Z Wang, JA Rackers… - The Journal of Physical …, 2022 - ACS Publications
Polarizability, or the tendency of the electron distribution to distort under an electric field,
often depends on the local chemical environment. For example, the polarizability of a …