| Computational design, construction and characterization of a set of specificity determining residues in protein-protein interactions. | |
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MedLine Citation:
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PMID: 22674858 Owner: NLM Status: Publisher |
Abstract/OtherAbstract:
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Proteins interact with different partners to perform different functions and it is important to elucidate the determinants of partner specificity in protein complex formation. Although methods for detecting specificity determining positions have been developed previously, direct experimental evidence for these amino acid residues is scarce, and the lack of information has prevented further computational studies. In this paper, we constructed a dataset that is likely to exhibit specificity in protein complex formation, based on available crystal structures and several intuitive ideas about interaction profiles and functional subclasses. We then defined a "structure-based specificity determining position (sbSDP)" as a set of equivalent residues in a protein family showing a large variation in their interaction energy with different partners. We investigated sequence and structural features of sbSDPs and demonstrated that their amino acid propensities significantly differed from those of other interacting residues and that the importance of many of these residues for determining specificity had been verified experimentally. Proteins 2012. © 2012 Wiley Periodicals, Inc. |
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Authors:
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Chioko Nagao; Nozomi Izako; Shinji Soga; Samia Haseeb Khan; Shigeki Kawabata; Hiroki Shirai; Kenji Mizuguchi |
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Publication Detail:
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Type: JOURNAL ARTICLE Date: 2012-6-6 |
Journal Detail:
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Title: Proteins Volume: - ISSN: 1097-0134 ISO Abbreviation: - Publication Date: 2012 Jun |
Date Detail:
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Created Date: 2012-6-7 Completed Date: - Revised Date: - |
Medline Journal Info:
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Nlm Unique ID: 8700181 Medline TA: Proteins Country: - |
Other Details:
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Languages: ENG Pagination: - Citation Subset: - |
Copyright Information:
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Copyright © 2012 Wiley Periodicals, Inc. |
Affiliation:
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National Institute of Biomedical Innovation, 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan. chio@nibio.go.jp. |
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
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