Document Detail


Backbone-dependent rotamer library for proteins. Application to side-chain prediction.
MedLine Citation:
PMID:  8464064     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
A backbone-dependent rotamer library for amino acid side-chains is developed and used for constructing protein side-chain conformations from the main-chain co-ordinates. The rotamer library is obtained from 132 protein chains in the Brookhaven Protein Database. A grid of 20 degrees by 20 degrees blocks for the main-chain angles phi, psi is used in the rotamer library. Significant correlations are found between side-chain dihedral angle probabilities and backbone phi, psi values. These probabilities are used to place the side-chains on the known backbone in test applications for six proteins for which high-resolution crystal structures are available. A minimization scheme is used to reorient side-chains that conflict with the backbone or other side-chains after the initial placement. The initial placement yields 59% of both chi 1 and chi 2 values in the correct position (to within 40 degrees) for thermolysin to 81% for crambin. After refinement the values range from 61% (lysozyme) to 89% (crambin). It is evident from the results that a single protein does not adequately test a prediction scheme. The computation time required by the method scales linearly with the number of side-chains. An initial prediction from the library takes only a few seconds of computer time, while the iterative refinement takes on the order of hours. The method is automated and can easily be applied to aid experimental side-chain determinations and homology modeling. The high degree of correlation between backbone and side-chain conformations may introduce a simplification in the protein folding process by reducing the available conformational space.
Authors:
R L Dunbrack; M Karplus
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Publication Detail:
Type:  Comparative Study; Journal Article; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.    
Journal Detail:
Title:  Journal of molecular biology     Volume:  230     ISSN:  0022-2836     ISO Abbreviation:  J. Mol. Biol.     Publication Date:  1993 Mar 
Date Detail:
Created Date:  1993-04-30     Completed Date:  1993-04-30     Revised Date:  2006-11-15    
Medline Journal Info:
Nlm Unique ID:  2985088R     Medline TA:  J Mol Biol     Country:  ENGLAND    
Other Details:
Languages:  eng     Pagination:  543-74     Citation Subset:  IM    
Affiliation:
Department of Chemistry, Harvard University, Cambridge, MA 02138.
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MeSH Terms
Descriptor/Qualifier:
Amino Acid Sequence
Databases, Factual*
Enzymes / chemistry
Models, Molecular
Molecular Sequence Data
Probability
Protein Conformation*
Proteins / chemistry*
Software*
X-Ray Diffraction / methods
Chemical
Reg. No./Substance:
0/Enzymes; 0/Proteins

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


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