Document Detail


Automatic analysis of protein conformational changes by multiple linkage clustering.
MedLine Citation:
PMID:  7473739     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
An automatic algorithm is presented for analyzing protein conformational changes such as those occurring upon substrate binding or in different crystal forms of the same protein. Using, as sole information, the atomic coordinates of a pair of protein structures, the procedure first generates structure alignments, which optimize the root-mean-square deviation of the backbone atoms. To this end, equivalent secondary structures and/or loops from both proteins are combined by a multiple linkage hierarchic clustering algorithm, which generates several intertwined clustering trees. Automatic analysis of these clustering trees is used to dissect the mechanism of the conformational change. It allows the identification of the static core, representing the collection of secondary structures which undergo no structural changes, as well as other entities which move like rigid bodies. It also permits the description of the movement of secondary structures or loops relative to this core or entities. USing this information, it can be inferred whether a particular conformational change involves shear or hinge motion, or components of both. The algorithm is applied to the analysis of the conformational changes of citrate synthase, lactate dehydrogenase, lactoferrin and beta-glucosyltransferase, representing typical examples of shear- and hinge-type mechanisms, and a varied range in movement size. The results are shown to be in excellent agreement with previous analyses, and to provide additional information which gives a more complete and objective picture of the conformational change. Using our automatic algorithm, we find that any conformational change may be viewed as having components of both shear- and hinge-type motion. Determining which of these is most appropriate requires the combination of the information provided by our procedure with detailed knowledge of the protein tertiary structures.
Authors:
N S Boutonnet; M J Rooman; S J Wodak
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Publication Detail:
Type:  Journal Article; Research Support, Non-U.S. Gov't    
Journal Detail:
Title:  Journal of molecular biology     Volume:  253     ISSN:  0022-2836     ISO Abbreviation:  J. Mol. Biol.     Publication Date:  1995 Nov 
Date Detail:
Created Date:  1995-12-18     Completed Date:  1995-12-18     Revised Date:  2006-11-15    
Medline Journal Info:
Nlm Unique ID:  2985088R     Medline TA:  J Mol Biol     Country:  ENGLAND    
Other Details:
Languages:  eng     Pagination:  633-47     Citation Subset:  IM    
Affiliation:
Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Paris, France.
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MeSH Terms
Descriptor/Qualifier:
Algorithms*
Citrate (si)-Synthase / chemistry
Glucosyltransferases / chemistry
L-Lactate Dehydrogenase / chemistry
Lactoferrin / chemistry
Models, Molecular*
Protein Conformation
Proteins / chemistry*
Chemical
Reg. No./Substance:
0/Lactoferrin; 0/Proteins; EC 1.1.1.27/L-Lactate Dehydrogenase; EC 2.3.3.1/Citrate (si)-Synthase; EC 2.4.1.-/Glucosyltransferases

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