Document Detail


Critical importance of length-scale dependence in implicit modeling of hydrophobic interactions.
MedLine Citation:
PMID:  17288425     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
The existence of length-scale dependence of hydrophobic solvation has important implications in the equilibrium of disordered, partially folded, and folded protein conformations. Neglecting this dependence, such as in popular solute surface-area based implicit solvent models with fixed surface tension coefficients, severely limits the ability to accurately model protein conformational equilibrium. We illustrate such fundamental limitations by examining the potentials of mean force of forming dimeric and trimeric nonpolar clusters and propose a new empirical model that effectively captures the context dependence of the local effective surface tension. Further optimization of the new model with other components of the implicit solvent force fields provides promise to significantly improve one's ability to simulate protein folding and conformational transitions. The existence of length-scale dependence of hydrophobic solvation has important implications in the equilibrium of disordered, partially folded, and folded protein conformations. Neglecting this dependence, such as in popular solute surface-area based implicit solvent models with fixed surface tension coefficients, severely limits the ability to accurately model protein conformational equilibrium. We illustrate such fundamental limitations by examining the potentials of mean force of forming dimeric and trimeric nonpolar clusters and propose a new empirical model that effectively captures the context dependence of the local effective surface tension. Further optimization of the new model with other components of the implicit solvent force fields provides promise to significantly improve one's ability to simulate protein folding and conformational transitions.
Authors:
Jianhan Chen; Charles L Brooks
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Publication Detail:
Type:  Journal Article; Research Support, N.I.H., Extramural     Date:  2007-02-09
Journal Detail:
Title:  Journal of the American Chemical Society     Volume:  129     ISSN:  0002-7863     ISO Abbreviation:  J. Am. Chem. Soc.     Publication Date:  2007 Mar 
Date Detail:
Created Date:  2007-02-28     Completed Date:  2007-06-01     Revised Date:  2013-06-06    
Medline Journal Info:
Nlm Unique ID:  7503056     Medline TA:  J Am Chem Soc     Country:  United States    
Other Details:
Languages:  eng     Pagination:  2444-5     Citation Subset:  IM    
Affiliation:
Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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MeSH Terms
Descriptor/Qualifier:
Algorithms*
Dimerization
Hydrogen Bonding
Hydrophobic and Hydrophilic Interactions*
Models, Molecular
Peptides / chemistry
Protein Folding*
Proteins / chemistry*
Static Electricity
Thermodynamics
Grant Support
ID/Acronym/Agency:
GM 48807/GM/NIGMS NIH HHS; P41 RR012255-118307/RR/NCRR NIH HHS; R01 GM048807-13/GM/NIGMS NIH HHS; RR 12255/RR/NCRR NIH HHS
Chemical
Reg. No./Substance:
0/Peptides; 0/Proteins
Comments/Corrections

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


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