Document Detail

A computer simulation study of the hydrated proton in a synthetic proton channel.
MedLine Citation:
PMID:  12885634     Owner:  NLM     Status:  MEDLINE    
Classical molecular dynamics simulations using the multistate empirical valence bond model for aqueous proton transport were performed to characterize the hydration structure of an excess proton inside a leucine-serine synthetic ion channel, LS2. For such a nonuniform pore size ion channel, it is found that the Zundel ion (H(5)O(2)(+)) solvation structure is generally more stable in narrow channel regions than in wider channel regions, which is in agreement with a recent study on idealized hydrophobic proton channels. However, considerable diversity in the relative stability of the Zundel to Eigen cation (H(9)O(4)(+)) was observed. Three of the five wide channel regions, one located at the channel's center and the other two located near the channel mouths, are found to show extraordinary preference for the Eigen solvation structure. This implies that proton hopping is inhibited in these regions and therefore suggests that these regions may behave as barriers in the proton conducting pathway inside the channel. The proton solvation is also greatly influenced by the local molecular environment of the protein. In particular, the polar side chains of the Ser residues, which are intimately involved in the solvation structure, can greatly influence proton solvation. However, no preference of the influence by the various Ser side chains was found; they can either promote or prevent the formation of certain solvation structures.
Yujie Wu; Gregory A Voth
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Publication Detail:
Type:  Comparative Study; Evaluation Studies; Journal Article; Research Support, U.S. Gov't, P.H.S.; Validation Studies    
Journal Detail:
Title:  Biophysical journal     Volume:  85     ISSN:  0006-3495     ISO Abbreviation:  Biophys. J.     Publication Date:  2003 Aug 
Date Detail:
Created Date:  2003-07-29     Completed Date:  2004-05-24     Revised Date:  2013-06-09    
Medline Journal Info:
Nlm Unique ID:  0370626     Medline TA:  Biophys J     Country:  United States    
Other Details:
Languages:  eng     Pagination:  864-75     Citation Subset:  IM    
Department of Chemistry, University of Utah, Salt Lake City, Utah, USA.
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MeSH Terms
Computer Simulation
Ion Channel Gating
Ion Channels / chemistry*
Leucine / chemistry*
Membrane Lipids / chemistry*
Models, Molecular*
Protein Conformation
Proton Pumps / chemistry*
Serine / chemistry*
Water / chemistry*
Grant Support
Reg. No./Substance:
0/Ion Channels; 0/Membrane Lipids; 0/Proton Pumps; 0/Protons; 56-45-1/Serine; 61-90-5/Leucine; 7732-18-5/Water
Erratum In:
Biophys J. 2004 Jan;86(1 Pt 1):662

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

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