Normal mode analysis of biomolecular structures: functional mechanisms of membrane proteins

I Bahar, TR Lezon, A Bakan, IH Shrivastava - Chemical reviews, 2010 - ACS Publications
A polymer chain of N atoms enjoys 3N-6 internal degrees of freedom, which gives rise to
infinitely many conformations. Even a simple model of N) 100 atoms where bond lengths …

Voltage-gated potassium channels: a structural examination of selectivity and gating

DM Kim, CM Nimigean - Cold Spring Harbor …, 2016 - cshperspectives.cshlp.org
Voltage-gated potassium channels play a fundamental role in the generation and
propagation of the action potential. The discovery of these channels began with predictions …

The crystal structure of a voltage-gated sodium channel

J Payandeh, T Scheuer, N Zheng, WA Catterall - Nature, 2011 - nature.com
Voltage-gated sodium (NaV) channels initiate electrical signalling in excitable cells and are
the molecular targets for drugs and disease mutations, but the structural basis for their …

Structural basis for Ca2+ selectivity of a voltage-gated calcium channel

L Tang, TMG El-Din, J Payandeh, GQ Martinez… - Biophysical …, 2014 - cell.com
Nuclear factor kappa B (NFkB) transcription factors are responsible for the regulation of
more than 150 target genes, their expression is induced by many classes of stimuli, and …

Direct knock-on of desolvated ions governs strict ion selectivity in K+ channels

W Kopec, DA Köpfer, ON Vickery, AS Bondarenko… - Nature …, 2018 - nature.com
The seeming contradiction that K+ channels conduct K+ ions at maximal throughput rates
while not permeating slightly smaller Na+ ions has perplexed scientists for decades …

[HTML][HTML] The persistent question of potassium channel permeation mechanisms

A Mironenko, U Zachariae, BL de Groot… - Journal of Molecular …, 2021 - Elsevier
Potassium channels play critical roles in many physiological processes, providing a
selective permeation route for K+ ions in and out of a cell, by employing a carefully designed …

A practical guide to reliable first principles computational thermochemistry predictions across the periodic table

DA Dixon, D Feller, KA Peterson - Annual reports in computational …, 2012 - Elsevier
Abstract The Feller–Peterson–Dixon approach to the reliable prediction of thermochemical
properties to chemical accuracy is described. The method calculates the total atomization …

Mechanism of potassium-channel selectivity revealed by Na+ and Li+ binding sites within the KcsA pore

AN Thompson, I Kim, TD Panosian… - Nature structural & …, 2009 - nature.com
Potassium channels allow K+ ions to diffuse through their pores while preventing smaller
Na+ ions from permeating. Discrimination between these similar, abundant ions enables …

Solving a new R2lox protein structure by microcrystal electron diffraction

H Xu, H Lebrette, MTB Clabbers, J Zhao, JJ Griese… - Science …, 2019 - science.org
Microcrystal electron diffraction (MicroED) has recently shown potential for structural biology.
It enables the study of biomolecules from micrometer-sized 3D crystals that are too small to …

A single NaK channel conformation is not enough for non-selective ion conduction

C Shi, Y He, K Hendriks, BL de Groot, X Cai… - Nature …, 2018 - nature.com
NaK and other non-selective channels are able to conduct both sodium (Na+) and
potassium (K+) with equally high efficiency. In contrast to previous crystallographic results …