Source:http://linkedlifedata.com/resource/pubmed/id/15495260
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| Predicate | Object |
|---|---|
| rdf:type | |
| lifeskim:mentions | |
| pubmed:issue |
1
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| pubmed:dateCreated |
2004-12-13
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| pubmed:abstractText |
Understanding energetics and mechanism of protein-protein association remains one of the biggest theoretical problems in structural biology. It is assumed that desolvation must play an essential role during the association process, and indeed protein-protein interfaces in obligate complexes have been found to be highly hydrophobic. However, the identification of protein interaction sites from surface analysis of proteins involved in non-obligate protein-protein complexes is more challenging. Here we present Optimal Docking Area (ODA), a new fast and accurate method of analyzing a protein surface in search of areas with favorable energy change when buried upon protein-protein association. The method identifies continuous surface patches with optimal docking desolvation energy based on atomic solvation parameters adjusted for protein-protein docking. The procedure has been validated on the unbound structures of a total of 66 non-homologous proteins involved in non-obligate protein-protein hetero-complexes of known structure. Optimal docking areas with significant low-docking surface energy were found in around half of the proteins. The 'ODA hot spots' detected in X-ray unbound structures were correctly located in the known protein-protein binding sites in 80% of the cases. The role of these low-surface-energy areas during complex formation is discussed. Burial of these regions during protein-protein association may favor the complexed configurations with near-native interfaces but otherwise arbitrary orientations, thus driving the formation of an encounter complex. The patch prediction procedure is freely accessible at http://www.molsoft.com/oda and can be easily scaled up for predictions in structural proteomics.
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| pubmed:language |
eng
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| pubmed:journal | |
| pubmed:citationSubset |
IM
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| pubmed:status |
MEDLINE
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| pubmed:month |
Jan
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| pubmed:issn |
1097-0134
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| pubmed:author | |
| pubmed:issnType |
Electronic
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| pubmed:day |
1
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| pubmed:volume |
58
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| pubmed:owner |
NLM
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| pubmed:authorsComplete |
Y
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| pubmed:pagination |
134-43
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| pubmed:meshHeading |
pubmed-meshheading:15495260-Binding Sites,
pubmed-meshheading:15495260-Computer Simulation,
pubmed-meshheading:15495260-Databases, Protein,
pubmed-meshheading:15495260-Models, Molecular,
pubmed-meshheading:15495260-Predictive Value of Tests,
pubmed-meshheading:15495260-Protein Interaction Mapping,
pubmed-meshheading:15495260-Protein Structure, Tertiary,
pubmed-meshheading:15495260-Surface Properties
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| pubmed:year |
2005
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| pubmed:articleTitle |
Optimal docking area: a new method for predicting protein-protein interaction sites.
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| pubmed:affiliation |
Department of Molecular Biology, Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.
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| pubmed:publicationType |
Journal Article
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