Document Detail


Using molecular dynamics simulations on crambin to evaluate the suitability of different continuum dielectric and hydrogen atom models for protein simulations.
MedLine Citation:
PMID:  2360995     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
Molecular dynamics simulations of enzymes with enough explicit waters of solvation to realistically account for solute-solvent interactions can burden the computational resources required to perform the simulation by more than two orders of magnitude. Since enzyme simulations even with an implicit solvation model can be imposing for a supercomputer, it is important to assess the suitability of different continuum dielectric models for protein simulations. A series of 100-picosecond molecular dynamics simulations were performed on the X-ray crystal structure of the protein crambin to examine how well computed structures, obtained using seven continuum dielectric and two hydrogen atom models, agreed with the X-ray structure. The best level of agreement between computed and experimental structures was obtained using a constant dielectric of 2 and the all-hydrogen model. Continuum dielectric models of 1, 1r, and 2r also led to computed structures in reasonably good agreement with the X-ray structure. In all cases, the all-hydrogen model gave better agreement than the united atom model, although, in one case, the difference was not significant. Dielectric models of 4, 80, and 4r with either hydrogen model yielded significantly poorer fits. It is especially noteworthy that the observed trends did not semiquantitatively converge until about 50 picoseconds into the simulations, suggesting that validation studies for protein calculations based on energy minimizations or short simulations should be viewed with caution.
Authors:
R L Ornstein
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Publication Detail:
Type:  Journal Article; Research Support, U.S. Gov't, Non-P.H.S.    
Journal Detail:
Title:  Journal of biomolecular structure & dynamics     Volume:  7     ISSN:  0739-1102     ISO Abbreviation:  J. Biomol. Struct. Dyn.     Publication Date:  1990 Apr 
Date Detail:
Created Date:  1990-08-06     Completed Date:  1990-08-06     Revised Date:  2006-11-15    
Medline Journal Info:
Nlm Unique ID:  8404176     Medline TA:  J Biomol Struct Dyn     Country:  UNITED STATES    
Other Details:
Languages:  eng     Pagination:  1019-41     Citation Subset:  IM    
Affiliation:
Pacific Northwest Laboratory, Molecular Science Research Center, Richland, Washington 99352.
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MeSH Terms
Descriptor/Qualifier:
Computer Simulation
Hydrogen Bonding
Models, Molecular
Plant Proteins*
Protein Conformation
Chemical
Reg. No./Substance:
0/Plant Proteins; 78783-34-3/crambin protein, Crambe abyssinica

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


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