Document Detail

Ion transport in the gramicidin channel: molecular dynamics study of single and double occupancy.
MedLine Citation:
PMID:  7538804     Owner:  NLM     Status:  MEDLINE    
The structural and thermodynamic factors responsible for the singly and doubly occupied saturation states of the gramicidin channel are investigated with molecular dynamics simulations and free energy perturbation methods. The relative free energy of binding of all of the five common cations Li+, Na+, K+, Rb+, and Cs+ is calculated in the singly and doubly occupied channel and in bulk water. The atomic system, which includes the gramicidin channel, a model membrane made of neutral Lennard-Jones particles and 190 explicit water molecules to form the bulk region, is similar to the one used in previous work to calculate the free energy profile of a Na+ ion along the axis of the channel. In all of the calculations, the ions are positioned in the main binding sites located near the entrances of the channel. The calculations reveal that the doubly occupied state is relatively more favorable for the larger ions. Thermodynamic decomposition is used to show that the origin of the trend observed in the calculations is due to the loss of favorable interactions between the ion and the single file water molecules inside the channel. Small ions are better solvated by the internal water molecules in the singly occupied state than in the doubly occupied state; bigger ions are solvated almost as well in both occupation states. Water-channel interactions play a role in the channel response. The observed trends are related to general thermodynamical properties of electrolyte solutions.
B Roux; B Prod'hom; M Karplus
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Publication Detail:
Type:  In Vitro; Journal Article; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.    
Journal Detail:
Title:  Biophysical journal     Volume:  68     ISSN:  0006-3495     ISO Abbreviation:  Biophys. J.     Publication Date:  1995 Mar 
Date Detail:
Created Date:  1995-06-26     Completed Date:  1995-06-26     Revised Date:  2010-09-13    
Medline Journal Info:
Nlm Unique ID:  0370626     Medline TA:  Biophys J     Country:  UNITED STATES    
Other Details:
Languages:  eng     Pagination:  876-92     Citation Subset:  IM    
Département de physique, Université de Montréal, Canada.
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MeSH Terms
Binding Sites
Biophysical Phenomena
Computer Simulation
Gramicidin / chemistry,  metabolism*
Ion Channels / chemistry,  metabolism*
Ion Transport
Models, Biological
Molecular Structure
Sodium / metabolism
Water / chemistry
Reg. No./Substance:
0/Ion Channels; 1405-97-6/Gramicidin; 7440-23-5/Sodium; 7732-18-5/Water

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

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