Document Detail


Toward an accurate theoretical framework for describing ensembles for proteins under strongly denaturing conditions.
MedLine Citation:
PMID:  16766618     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
Our focus is on an appropriate theoretical framework for describing highly denatured proteins. In high concentrations of denaturants, proteins behave like polymers in a good solvent and ensembles for denatured proteins can be modeled by ignoring all interactions except excluded volume (EV) effects. To assay conformational preferences of highly denatured proteins, we quantify a variety of properties for EV-limit ensembles of 23 two-state proteins. We find that modeled denatured proteins can be best described as follows. Average shapes are consistent with prolate ellipsoids. Ensembles are characterized by large correlated fluctuations. Sequence-specific conformational preferences are restricted to local length scales that span five to nine residues. Beyond local length scales, chain properties follow well-defined power laws that are expected for generic polymers in the EV limit. The average available volume is filled inefficiently, and cavities of all sizes are found within the interiors of denatured proteins. All properties characterized from simulated ensembles match predictions from rigorous field theories. We use our results to resolve between conflicting proposals for structure in ensembles for highly denatured states.
Authors:
Hoang T Tran; Rohit V Pappu
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Publication Detail:
Type:  Journal Article; Research Support, U.S. Gov't, Non-P.H.S.     Date:  2006-06-09
Journal Detail:
Title:  Biophysical journal     Volume:  91     ISSN:  0006-3495     ISO Abbreviation:  Biophys. J.     Publication Date:  2006 Sep 
Date Detail:
Created Date:  2006-08-16     Completed Date:  2006-10-05     Revised Date:  2010-09-15    
Medline Journal Info:
Nlm Unique ID:  0370626     Medline TA:  Biophys J     Country:  United States    
Other Details:
Languages:  eng     Pagination:  1868-86     Citation Subset:  IM    
Affiliation:
Department of Biomedical Engineering and Center for Computational Biology, Washington University in St. Louis, St. Louis, Missouri 63130-4899, USA.
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MeSH Terms
Descriptor/Qualifier:
Algorithms*
Computer Simulation
Models, Chemical*
Models, Molecular*
Multiprotein Complexes / chemistry*,  ultrastructure*
Protein Conformation
Protein Denaturation*
Protein Folding
Sensitivity and Specificity
Solvents / chemistry*
Chemical
Reg. No./Substance:
0/Multiprotein Complexes; 0/Solvents
Comments/Corrections

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