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Ion channels: structural bioinformatics and modelling

C. E. Capener
2002 Human Molecular Genetics  
In combination with molecular dynamics simulations and associated calculations, modelling provides a powerful approach to understanding structure/function relationships in human ion channels.  ...  Here we review how a combination of structural bioinformatics, homology modelling and molecular simulations can be used to generate and evaluate models of homologues of bacterial ion channels.  ...  Comparison of Kir6.2 and KcsA simulations suggested a degree of flexibility in the filter, thus complicating models of ion selectivity based upon a rigid filter.  ... 
doi:10.1093/hmg/11.20.2425 pmid:12351578 fatcat:e33dpodnxnakle5lo5qmhqo2t4

Physics of Ion Channels

Serdar Kuyucak, Turgut Bastug
2003 Journal of biological physics (Print)  
We review the basic physics involved in transport of ions across membrane channels in cells.  ...  A case is made for use of Brownian dynamics as the minimal phenomenological model that provides a bridge between experiments and more fundamental theoretical approaches.  ...  Introduction Ion channels are water filled holes in cell membranes that are formed by proteins embedded in the lipid bilayer.  ... 
doi:10.1023/a:1027309113522 pmid:23345858 pmcid:PMC3456178 fatcat:py4u4e7wxrdulcmlplzfvkufie

Cholesterol binding to ion channels

Irena Levitan, Dev K. Singh, Avia Rosenhouse-Dantsker
2014 Frontiers in Physiology  
Clearly, however, these are only the first few steps in obtaining a general understanding of cholesterol-ion channels interactions and their roles in cellular and organ functions.  ...  Numerous studies demonstrated that membrane cholesterol is a major regulator of ion channel function.  ...  ACKNOWLEDGMENTS This work was supported by a Scientist Development Grant (11SDG5190025) from the American Heart Association (to Avia Rosenhouse-Dantsker), and by the US NIH grants HL-073965, HL-083298  ... 
doi:10.3389/fphys.2014.00065 pmid:24616704 pmcid:PMC3935357 fatcat:7xglgtrt65f2bob7tpesvenyky

Ion Channels in Microbes

Boris Martinac, Yoshiro Saimi, Ching Kung
2008 Physiological Reviews  
Unlike soluble proteins, ion channels reside in the membrane and function to ferry ions across the lipid bilayer, a special environment.  ...  It therefore seems clear that these channels are employed to handle environmental challenges, which we have yet to simulate in the laboratory.  ... 
doi:10.1152/physrev.00005.2008 pmid:18923187 pmcid:PMC2579964 fatcat:ef5xmfv5nvgzbafbkeslpkgrmm

Binding of general anesthetics to ion channels [article]

Letícia Stock, Juliana Hosoume, Leonardo Cirqueira, Werner Treptow
2018 bioRxiv   pre-print
The direct-site hypothesis assumes general anesthetics bind ion channels to impact protein equilibrium and function, inducing anesthesia.  ...  We focus on clinically used sevoflurane interaction to anesthetic-sensitive Kv1.2 mammalian channel to resolve if sevoflurane binds the protein's well-characterized open and closed structures in a conformation-dependent  ...  Acknowledgements The research was supported in part by the Brazilian Agencies CNPq, CAPES and FAPDF under Grants 305008/20153, 23038.010052/201395 and 193.001.202/2016.  ... 
doi:10.1101/266809 fatcat:nxfmhmxierhapjehbei76ilwyu

Recent advances in ion channel research

Shin-Ho Chung, Serdar Kuyucak
2002 Biochimica et Biophysica Acta - Biomembranes  
The field of ion channels has entered into a rapid phase of development in the last few years, partly due to the breakthroughs in determination of the crystal structures of membrane proteins and advances  ...  in computer simulations of biomolecules.  ...  We thank our collaborators Toby Allen, Ben Corry, Scott Edwards, Matthew Hoyles, Megan O'Mara and Siu-Cheung Li, who have contributed to the BD and MD studies of channels reported in this review.  ... 
doi:10.1016/s0005-2736(02)00574-6 pmid:12409200 fatcat:dpi6o6vuozgm3gtj3ddfp2n5p4

Models of permeation in ion channels

Serdar Kuyucak, Olaf Sparre Andersen, Shin-Ho Chung
2001 Reports on progress in physics (Print)  
Ion channels are formed by specific proteins embedded in the cell membrane and provide pathways for fast and controlled flow of selected ions down their electrochemical gradient.  ...  In this paper, we present a critical review of various approaches to modelling of ion transport in membrane channels, including continuum theories, Brownian dynamics, and classical and ab initio molecular  ...  We thank our collaborators Toby Allen, Ben Corry, Scott Edwards, Matthew Hoyles and Siu-Cheung Li, who have contributed to the BD and MD studies of channels reported in this review.  ... 
doi:10.1088/0034-4885/64/11/202 fatcat:rzwb2j3rlrfxdc6et5powbqpwe

Pentameric ligand-gated ion channels: insights from computation

Reza Salari, Sruthi Murlidaran, Grace Brannigan
2014 Molecular Simulation  
Here we review contributions from a variety of computational approaches, including normal mode analysis, automated docking, and fully atomistic molecular dynamics simulation.  ...  New insights into the complex mechanisms underlying pLGIC gating, ion selectivity, and modulation have recently been gained via a series of crystal structures in prokaryotes and C .elegans, as well as  ...  Flooding MD simulations are a more expensive alternative to docking with the advantage of being fully atomistic, including water molecules and lipids, and fully flexible.  ... 
doi:10.1080/08927022.2014.896462 pmid:25931676 pmcid:PMC4412168 fatcat:fbcxx6h6ynbazjkioy4ymorffa

Energetics of ion conduction through the gramicidin channel

T. W. Allen, O. S. Andersen, B. Roux
2003 Proceedings of the National Academy of Sciences of the United States of America  
Since the first MD simulations on a fully flexible atomic model of gA were carried out 20 yr ago (12), system sizes and simulation times have grown by orders of magnitude, yet quantitative agreement with  ...  Atomic structures have been reported for many ion channels, but none is structurally and functionally as well characterized (4), or as amenable to computer simulation, as the gramicidin A (gA) channel.  ...  We thank Guillaume Lamoureux for his help with polarizable water and Prof. David Chandler for insightful discussions on reaction coordinates for ion permeation.  ... 
doi:10.1073/pnas.2635314100 pmid:14691245 pmcid:PMC314148 fatcat:g25fvqvugfdo5furokkechn224

Binding of the general anesthetic sevoflurane to ion channels

Letícia Stock, Juliana Hosoume, Leonardo Cirqueira, Werner Treptow
2018 PLoS Computational Biology  
The direct-site hypothesis assumes general anesthetics bind ion channels to impact protein equilibrium and function, inducing anesthesia.  ...  We focus on the clinically used sevoflurane interaction to anesthetic-sensitive Kv1.2 mammalian channel to resolve if sevoflurane binds protein's well-characterized open and closed structures in a conformation-dependent  ...  Formal analysis: Letícia Stock, Juliana Hosoume, Leonardo Cirqueira. Funding acquisition: Werner Treptow. Writing -original draft: Werner Treptow.  ... 
doi:10.1371/journal.pcbi.1006605 pmid:30475796 pmcid:PMC6283617 fatcat:wekwziiofbfkdcayynqkdqphay

The Selectivity of K+ Ion Channels: Testing the Hypotheses

Philip W. Fowler, Kaihsu Tai, Mark S.P. Sansom
2008 Biophysical Journal  
We also find that the ions and waters in the NaK selectivity filter unexpectedly move to a new conformation in seven K 1 simulations: the two K 1 ions rapidly move from site S4 to S2 and from the cavity  ...  less selective channel NaK embedded in lipid bilayers.  ...  Rempe, Benoît Roux, and Sameer Varma for helpful discussions. David Bostick and Charles L. Brooks III also generously provided their data for our Fig. 6 .  ... 
doi:10.1529/biophysj.108.132035 pmid:18790851 pmcid:PMC2586581 fatcat:n2n6g4i26bbyhhph5brnjpjpgi

Transmembrane domains of viral ion channel proteins: A molecular dynamics simulation study

Wolfgang B. Fischer, Lucy R. Forrest, Graham R. Smith, Mark S. P. Sansom
2000 Biopolymers  
Nanosecond molecular dynamics simulations in a fully solvated phospholipid bilayer have been performed on single transmembrane ␣-helices from three putative ion channel proteins encoded by viruses: NB  ...  However, helix/bilayer mismatch such that a helix ends abruptly within the bilayer core destabilizes the end of the helix, especially in the presence of Gly and Ala residues.  ...  This work was supported by a European Union (TMR) fellowship to WBF. MSPS thanks The Wellcome Trust for financial support. Our thanks to Indira Shrivastava and Rong-I Hong for helpful discussions.  ... 
doi:10.1002/(sici)1097-0282(200006)53:7<529::aid-bip1>3.0.co;2-6 pmid:10766949 fatcat:qsrujjkxcja4njsebsbiwcgvvy

Non Markovian Noise mediated through Anamolous Diffusion within Ion Channels [article]

Sisir Roy, Indranil Mitra, Rodolfo Llinas
2008 arXiv   pre-print
It is quite clear from a wide range of experiments that gating phenomena of ion channels is inherently stochastic.  ...  It has been discussed using BD simulations in a recent paper that memory effects in ion transport is negligible, unless the barrier height is high.  ...  We have in our analysis have thereby relied on BD simulations with some assumptions overlaid. BD simulations were first proposed as a way to study ion channels by [39] .  ... 
arXiv:0801.3764v1 fatcat:y5gpxeslkzf6pm65glq5v3auoa

Cooperative transport in a potassium ion channel

Jean-Fang Gwan, Artur Baumgaertner
2007 Journal of Chemical Physics  
In particular, there is strong evidence for pairwise translocations where one ion and one water molecule form a bound state.  ...  Our current understanding of ion permeation through the selectivity filter of the KcsA potassium channel is based on the concept of a multi-ion transport mechanism.  ...  Jung-Hsing Lin for the help on the model construction and for many useful suggestions.  ... 
doi:10.1063/1.2756531 pmid:17672726 fatcat:xkyrxsemp5ghvegvz3plkaq3vm

Estimation of ion Channel Kinetics from Macroscopic Recordings

Luciano Moffatt
2011 Biophysical Journal  
Co-expression of a6(Q237R) with b2 and g2L subunits resulted in no significant reduction in total or surface expression of any subunit.  ...  On-cell a6(Q237R)b2g2 and a6b2g2 single channel currents had similar mean open durations, but opening and burst frequencies were significantly higher for mutant than for wt currents.  ...  The structure reveals an open pore and molecular dynamics simulations suggest that the protein is stable on a 20 ns timescale when embedded in a lipid bilayer [1] .  ... 
doi:10.1016/j.bpj.2010.12.1697 fatcat:a45mhhfyvvbqpehxhp2zhq6w2a
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