Document Detail


Influence of protein flexibility on the electrostatic energy landscape in gramicidin A.
MedLine Citation:
PMID:  15536565     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
We describe an electrostatic model of the gramicidin A channel that allows protein atoms to move in response to the presence of a permeating ion. To do this, molecular dynamics simulations are carried out with a permeating ion at various positions within the channel. Then an ensemble of atomic coordinates taken from the simulations are used to construct energy profiles using macroscopic electrostatic calculations. The energy profiles constructed are compared to experimentally-determined conductance data by inserting them into Brownian dynamics simulations. We find that the energy landscape seen by a permeating ion changes significantly when we allow the protein atoms to move rather than using a rigid protein structure. However, the model developed cannot satisfactorily reproduce all of the experimental data. Thus, even when protein atoms are allowed to move, the dielectric model used in our electrostatic calculations breaks down when modeling the gramicidin channel.
Authors:
Ben Corry; Shin-Ho Chung
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Publication Detail:
Type:  Journal Article; Research Support, Non-U.S. Gov't     Date:  2004-11-05
Journal Detail:
Title:  European biophysics journal : EBJ     Volume:  34     ISSN:  0175-7571     ISO Abbreviation:  Eur. Biophys. J.     Publication Date:  2005 May 
Date Detail:
Created Date:  2005-05-02     Completed Date:  2005-08-01     Revised Date:  2008-11-21    
Medline Journal Info:
Nlm Unique ID:  8409413     Medline TA:  Eur Biophys J     Country:  Germany    
Other Details:
Languages:  eng     Pagination:  208-16     Citation Subset:  IM    
Affiliation:
Chemistry, School of Biomedical and Chemical Sciences, The University of Western Australia Crawley, WA 6009, Australia. ben@theochem.uwa.edu.au
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MeSH Terms
Descriptor/Qualifier:
Computer Simulation
Diffusion
Elasticity
Energy Transfer*
Gramicidin / analysis,  chemistry*
Ion Channel Gating*
Ion Channels / chemistry*
Ions
Lipid Bilayers / chemistry*
Models, Chemical*
Models, Molecular*
Motion
Protein Conformation
Protein Transport*
Static Electricity
Chemical
Reg. No./Substance:
0/Ion Channels; 0/Ions; 0/Lipid Bilayers; 1405-97-6/Gramicidin

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


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