Literature DB >> 35874965

Computational methods and theory for ion channel research.

C Guardiani1, F Cecconi2, L Chiodo3, G Cottone4, P Malgaretti5, L Maragliano6, M L Barabash7, G Camisasca1,8, M Ceccarelli9, B Corry10, R Roth11, A Giacomello1, B Roux12.   

Abstract

Ion channels are fundamental biological devices that act as gates in order to ensure selective ion transport across cellular membranes; their operation constitutes the molecular mechanism through which basic biological functions, such as nerve signal transmission and muscle contraction, are carried out. Here, we review recent results in the field of computational research on ion channels, covering theoretical advances, state-of-the-art simulation approaches, and frontline modeling techniques. We also report on few selected applications of continuum and atomistic methods to characterize the mechanisms of permeation, selectivity, and gating in biological and model channels.

Entities:  

Keywords:  Ion channels; biomimetic nanopores; conductance; continuum models; gating; machine learning; molecular dynamics; rare events; selectivity

Year:  2022        PMID: 35874965      PMCID: PMC9302924          DOI: 10.1080/23746149.2022.2080587

Source DB:  PubMed          Journal:  Adv Phys X        ISSN: 2374-6149


  296 in total

1.  Conduction properties of KcsA measured using brownian dynamics with flexible carbonyl groups in the selectivity filter.

Authors:  Shin-Ho Chung; Ben Corry
Journal:  Biophys J       Date:  2007-04-13       Impact factor: 4.033

Review 2.  Molecular properties of voltage-sensitive sodium channels.

Authors:  W A Catterall
Journal:  Annu Rev Biochem       Date:  1986       Impact factor: 23.643

3.  Definition and testing of the GROMOS force-field versions 54A7 and 54B7.

Authors:  Nathan Schmid; Andreas P Eichenberger; Alexandra Choutko; Sereina Riniker; Moritz Winger; Alan E Mark; Wilfred F van Gunsteren
Journal:  Eur Biophys J       Date:  2011-04-30       Impact factor: 1.733

4.  Ion permeation in K⁺ channels occurs by direct Coulomb knock-on.

Authors:  David A Köpfer; Chen Song; Tim Gruene; George M Sheldrick; Ulrich Zachariae; Bert L de Groot
Journal:  Science       Date:  2014-10-17       Impact factor: 47.728

5.  Electroosmotic Trap Against the Electrophoretic Force Near a Protein Nanopore Reveals Peptide Dynamics During Capture and Translocation.

Authors:  Alina Asandei; Irina Schiopu; Mauro Chinappi; Chang Ho Seo; Yoonkyung Park; Tudor Luchian
Journal:  ACS Appl Mater Interfaces       Date:  2016-05-16       Impact factor: 9.229

6.  The Free Energy Landscape of GABA Binding to a Pentameric Ligand-Gated Ion Channel and Its Disruption by Mutations.

Authors:  Federico Comitani; Vittorio Limongelli; Carla Molteni
Journal:  J Chem Theory Comput       Date:  2016-06-09       Impact factor: 6.006

7.  A heuristic derived from analysis of the ion channel structural proteome permits the rapid identification of hydrophobic gates.

Authors:  Shanlin Rao; Gianni Klesse; Phillip J Stansfeld; Stephen J Tucker; Mark S P Sansom
Journal:  Proc Natl Acad Sci U S A       Date:  2019-06-24       Impact factor: 11.205

Review 8.  Hydrophobic gating in ion channels.

Authors:  Prafulla Aryal; Mark S P Sansom; Stephen J Tucker
Journal:  J Mol Biol       Date:  2014-08-12       Impact factor: 6.151

Review 9.  Controlling DNA Translocation Through Solid-state Nanopores.

Authors:  Zhishan Yuan; Youming Liu; Min Dai; Xin Yi; Chengyong Wang
Journal:  Nanoscale Res Lett       Date:  2020-04-15       Impact factor: 4.703

Review 10.  Molecular dynamics simulations of membrane proteins and their interactions: from nanoscale to mesoscale.

Authors:  Matthieu Chavent; Anna L Duncan; Mark Sp Sansom
Journal:  Curr Opin Struct Biol       Date:  2016-06-21       Impact factor: 7.786

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