Enhanced-sampling simulations for the estimation of ligand binding kinetics: current status and perspective

K Ahmad, A Rizzi, R Capelli, D Mandelli… - Frontiers in molecular …, 2022 - frontiersin.org
The dissociation rate (k off) associated with ligand unbinding events from proteins is a
parameter of fundamental importance in drug design. Here we review recent major …

Constant ph molecular dynamics simulations: Current status and recent applications

VM de Oliveira, R Liu, J Shen - Current opinion in structural biology, 2022 - Elsevier
Many important protein functions are carried out through proton-coupled conformational
dynamics. Thus, the ability to accurately model protonation states dynamically has wide …

Fluoride permeation mechanism of the Fluc channel in liposomes revealed by solid-state NMR

J Zhang, D Song, FK Schackert, J Li, S Xiang… - Science …, 2023 - science.org
Solid-state nuclear magnetic resonance (ssNMR) methods can probe the motions of
membrane proteins in liposomes at the atomic level and propel the understanding of …

The development of nucleic acids force fields: From an unchallenged past to a competitive future

K Liebl, M Zacharias - Biophysical Journal, 2023 - cell.com
Molecular dynamics simulations have strongly matured as a method to study biomolecular
processes. Their validity, however, is determined by the accuracy of the underlying force …

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 …

Structural insights into anion selectivity and activation mechanism of LRRC8 volume-regulated anion channels

H Liu, MM Polovitskaya, L Yang, M Li, H Li, Z Han… - Cell reports, 2023 - cell.com
Volume-regulated anion channels (VRACs) are hexamers of LRRC8 proteins that are
crucial for cell volume regulation. N termini (NTs) of the obligatory LRRC8A subunit …

Evaluating polarizable biomembrane simulations against experiments

HS Antila, S Dixit, B Kav, JJ Madsen… - Journal of Chemical …, 2024 - ACS Publications
Owing to the increase of available computational capabilities and the potential for providing
a more accurate description, polarizable molecular dynamics force fields are gaining …

Uncovering the Mechanism of the Proton-Coupled Fluoride Transport in the CLCF Antiporter

KR Mills, H Torabifard - Journal of Chemical Information and …, 2023 - ACS Publications
Fluoride is a natural antibiotic abundantly present in the environment and, in micromolar
concentrations, is able to inhibit enzymes necessary for bacteria to survive. However, as is …

Fluorinated Protein–Ligand Complexes: A Computational Perspective

L Wehrhan, BG Keller - The Journal of Physical Chemistry B, 2024 - ACS Publications
Fluorine is an element renowned for its unique properties. Its powerful capability to modulate
molecular properties makes it an attractive substituent for protein binding ligands; however …

[HTML][HTML] When is a hydrophobic gate not a hydrophobic gate?

D Seiferth, PC Biggin, SJ Tucker - Journal of General Physiology, 2022 - rupress.org
The flux of ions through a channel is most commonly regulated by changes that result in
steric occlusion of its pore. However, ion permeation can also be prevented by formation of a …