Document Detail


Molecular dynamics simulations of the gramicidin A-dimyristoylphosphatidylcholine system with an ion in the channel pore region.
MedLine Citation:
PMID:  11156294     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
To investigate the process of ion permeation in an ion channel systematically, we performed molecular dynamics (MD) simulations on a gramicidin A (GA)-phospholipid model system with an ion in the channel pore region. Each of the three types of ions (Ca2+, Na+ Cl-) was placed at five different positions along the channel axis by replacing a water molecule. MD simulations were performed on each system at constant pressure and constant temperature. The MD trajectories showed that the Ca2+ and Na+ ions could stably fluctuate in the pore region, but the Cl- ion was pushed out because of the unfavorable interaction with the channel. This result is consistent with experimental data. It was also found that the conformation of the GA channel underwent a significant change due to the presence of the ion, and the two ends of the GA monomer were more flexible than its middle region. In particular, the dramatic change of local pore radius near the ion indicated this kind of deformation. The strong interaction between the ion and carbonyl oxygen atoms of GA was the major contributor to this change. Furthermore, it was found that the ethanolamine group of the GA molecule was the most flexible group in the GA channel and often observed to block the entrance of GA. These results imply that the deformation of channel structure plays a very important factor in ion permeation, and the ethanolamine group may play a key role in regulating ion entry into the pore. In conclusion, our results indicate that the ion has a dominant influence on the structure of the GA channel and that the flexibility of the ion channel is a crucial factor in the ion permeation process.
Authors:
Y Z Tang; W Z Chen; C X Wang
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Publication Detail:
Type:  Journal Article; Research Support, Non-U.S. Gov't    
Journal Detail:
Title:  European biophysics journal : EBJ     Volume:  29     ISSN:  0175-7571     ISO Abbreviation:  Eur. Biophys. J.     Publication Date:  2000  
Date Detail:
Created Date:  2001-01-11     Completed Date:  2001-03-15     Revised Date:  2006-11-15    
Medline Journal Info:
Nlm Unique ID:  8409413     Medline TA:  Eur Biophys J     Country:  Germany    
Other Details:
Languages:  eng     Pagination:  523-34     Citation Subset:  IM    
Affiliation:
Center for Biomedical Engineering, Beijing Polytechnic University, PR China. cxwang@bjpu.edu.cn
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MeSH Terms
Descriptor/Qualifier:
Calcium
Chlorides
Computer Simulation
Dimerization
Dimyristoylphosphatidylcholine / chemistry*
Gramicidin / chemistry*
Ion Channels*
Kinetics
Models, Biological
Molecular Conformation
Protein Conformation
Sodium
Software
Time Factors
Chemical
Reg. No./Substance:
0/Chlorides; 0/Ion Channels; 13699-48-4/Dimyristoylphosphatidylcholine; 1405-97-6/Gramicidin; 7440-23-5/Sodium; 7440-70-2/Calcium

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


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