Document Detail


Atomic solvation parameters applied to molecular dynamics of proteins in solution.
MedLine Citation:
PMID:  1304905     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
A solvation energy function for use in the molecular simulation of proteins is proposed. It is based on the accessible surface areas of atoms in the protein and on atomic solvation parameters derived from empirical vapor-to-water free energies of transfer of amino acid side-chain analogs. The energy function and its derivatives were added to the CHARMM molecular simulation program (Brooks, B.R., Bruccoleri, R.E., Olafson, B.D., States, D.J., Swaminathan, S., & Karplus, M., 1983, J. Comput. Chem. 4(2), 187-217). The effect of the added energy term was evaluated by 110 ps of molecular dynamics on the 26-residue protein melittin. The melittin monomer and tetramer were studied both with and without the added term. With the added energy term the monomer partially unfolded, while the secondary structure of the tetramer was preserved, in agreement with reported experiments (Brown, L.R., Lauterwein, J., & Wuethrich, K., 1980, Biochim. Biophys. Acta 622(2), 231-244; Lauterwein, J., Brown, L.R., & Wuethrich, K., 1980, Biochim. Biophys. Acta 622(2), 219-230).
Authors:
L Wesson; D Eisenberg
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Publication Detail:
Type:  Comparative Study; Journal Article; Research Support, U.S. Gov't, Non-P.H.S.; Research Support, U.S. Gov't, P.H.S.    
Journal Detail:
Title:  Protein science : a publication of the Protein Society     Volume:  1     ISSN:  0961-8368     ISO Abbreviation:  Protein Sci.     Publication Date:  1992 Feb 
Date Detail:
Created Date:  1993-07-09     Completed Date:  1993-07-09     Revised Date:  2010-09-07    
Medline Journal Info:
Nlm Unique ID:  9211750     Medline TA:  Protein Sci     Country:  UNITED STATES    
Other Details:
Languages:  eng     Pagination:  227-35     Citation Subset:  IM    
Affiliation:
Molecular Biology Institute, University of California, Los Angeles 90024-1570.
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MeSH Terms
Descriptor/Qualifier:
Amino Acid Sequence
Amino Acids / chemistry
Chemistry, Physical
Computer Simulation
Melitten / chemistry*
Models, Chemical*
Models, Molecular
Molecular Sequence Data
Physicochemical Phenomena
Protein Conformation
Proteins / chemistry*
Reference Values
Solutions / chemistry*
Water / chemistry
Chemical
Reg. No./Substance:
0/Amino Acids; 0/Proteins; 0/Solutions; 20449-79-0/Melitten; 7732-18-5/Water
Comments/Corrections

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