Document Detail


Web interface for Brownian dynamics simulation of ion transport and its applications to beta-barrel pores.
MedLine Citation:
PMID:  22102176     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
Brownian dynamics (BD) based on accurate potential of mean force is an efficient and accurate method for simulating ion transport through wide ion channels. Here, a web-based graphical user interface (GUI) is presented for carrying out grand canonical Monte Carlo (GCMC) BD simulations of channel proteins: http://www.charmm-gui.org/input/gcmcbd. The webserver is designed to help users avoid most of the technical difficulties and issues encountered in setting up and simulating complex pore systems. GCMC/BD simulation results for three proteins, the voltage dependent anion channel (VDAC), α-Hemolysin (α-HL), and the protective antigen pore of the anthrax toxin (PA), are presented to illustrate the system setup, input preparation, and typical output (conductance, ion density profile, ion selectivity, and ion asymmetry). Two models for the input diffusion constants for potassium and chloride ions in the pore are compared: scaling of the bulk diffusion constants by 0.5, as deduced from previous all-atom molecular dynamics simulations of VDAC, and a hydrodynamics based model (HD) of diffusion through a tube. The HD model yields excellent agreement with experimental conductances for VDAC and α-HL, while scaling bulk diffusion constants by 0.5 leads to underestimates of 10-20%. For PA, simulated ion conduction values overestimate experimental values by a factor of 1.5-7 (depending on His protonation state and the transmembrane potential), implying that the currently available computational model of this protein requires further structural refinement.
Authors:
Kyu Il Lee; Sunhwan Jo; Huan Rui; Bernhard Egwolf; Benoît Roux; Richard W Pastor; Wonpil Im
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Publication Detail:
Type:  Journal Article; Research Support, N.I.H., Extramural; Research Support, N.I.H., Intramural; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.     Date:  2011-11-21
Journal Detail:
Title:  Journal of computational chemistry     Volume:  33     ISSN:  1096-987X     ISO Abbreviation:  J Comput Chem     Publication Date:  2012 Jan 
Date Detail:
Created Date:  2011-12-15     Completed Date:  2012-04-03     Revised Date:  2014-09-14    
Medline Journal Info:
Nlm Unique ID:  9878362     Medline TA:  J Comput Chem     Country:  United States    
Other Details:
Languages:  eng     Pagination:  331-9     Citation Subset:  IM    
Copyright Information:
Copyright © 2011 Wiley Periodicals, Inc.
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MeSH Terms
Descriptor/Qualifier:
Antigens, Bacterial / chemistry,  immunology
Bacterial Toxins / immunology
Hemolysin Proteins / chemistry
Internet*
Ion Transport
User-Computer Interface*
Grant Support
ID/Acronym/Agency:
GM062342/GM/NIGMS NIH HHS; P20 RR-17708/RR/NCRR NIH HHS; P20 RR017708/RR/NCRR NIH HHS; P20 RR017708-10/RR/NCRR NIH HHS; R01 GM062342/GM/NIGMS NIH HHS; R01 GM070855/GM/NIGMS NIH HHS; R01 GM070855-07/GM/NIGMS NIH HHS; R01 RR026061/RR/NCRR NIH HHS; R01 RR026061-04/RR/NCRR NIH HHS
Chemical
Reg. No./Substance:
0/Antigens, Bacterial; 0/Bacterial Toxins; 0/Hemolysin Proteins; 0/anthrax toxin
Comments/Corrections

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


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