Document Detail


Calculation of the water-cyclohexane transfer free energies of neutral amino acid side-chain analogs using the OPLS all-atom force field.
MedLine Citation:
PMID:  14515375     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
We calculated the free energy of solvation of the neutral analogs of 18 amino acid side-chains (not including glycine and proline) using the OPLS all-atom force field in TIP4P water, SPC water, and cyclohexane by molecular dynamics simulation and thermodynamic integration. The average unsigned errors in the free energies of solvation in TIP4P, SPC, and cyclohexane are 4.4, 4.9, and 2.1 kJ/mol respectively. Most of the calculated hydration free energies are not favorable enough compared to experiment. The largest errors are found for tryptophan, histidine, glutamic acid, and glutamine. The average unsigned errors in the free energy of transfer from TIP4P to cyclohexane and from SPC to cyclohexane are 4.0 and 4.1 kJ/mol, respectively. The largest errors, of more than 7.5 kJ/mol, are found for histidine, glutamine, and glutamatic acid.
Authors:
Justin L MacCallum; D Peter Tieleman
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Publication Detail:
Type:  Comparative Study; Journal Article; Research Support, Non-U.S. Gov't    
Journal Detail:
Title:  Journal of computational chemistry     Volume:  24     ISSN:  0192-8651     ISO Abbreviation:  J Comput Chem     Publication Date:  2003 Nov 
Date Detail:
Created Date:  2003-09-29     Completed Date:  2004-03-24     Revised Date:  2008-11-21    
Medline Journal Info:
Nlm Unique ID:  9878362     Medline TA:  J Comput Chem     Country:  United States    
Other Details:
Languages:  eng     Pagination:  1930-5     Citation Subset:  IM    
Copyright Information:
Copyright 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1930-1935, 2003
Affiliation:
Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada.
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MeSH Terms
Descriptor/Qualifier:
Algorithms
Amino Acids / chemistry*
Chemistry, Physical
Computer Simulation
Cyclohexanes / chemistry*
Energy Transfer*
Mathematics
Models, Chemical
Physicochemical Phenomena
Proteins / chemistry
Thermodynamics
Water / chemistry*
Chemical
Reg. No./Substance:
0/Amino Acids; 0/Cyclohexanes; 0/Proteins; 7732-18-5/Water

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


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