Structure-based method for analyzing protein–protein interfaces

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dc.contributor.author Wang, Renxiao en_US
dc.contributor.author Gao, Ying en_US
dc.contributor.author Lai, Luhua en_US
dc.date.accessioned 2006-09-11T19:29:41Z
dc.date.available 2006-09-11T19:29:41Z
dc.date.issued 2004-02 en_US
dc.identifier.citation Gao, Ying; Wang, Renxiao; Lai, Luhua; (2004). "Structure-based method for analyzing protein–protein interfaces." Journal of Molecular Modeling 10(1): 44-54. <http://hdl.handle.net/2027.42/47876> en_US
dc.identifier.issn 1610-2940 en_US
dc.identifier.issn 0948-5023 en_US
dc.identifier.uri http://hdl.handle.net/2027.42/47876
dc.identifier.uri http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=retrieve&db=pubmed&list_uids=14634848&dopt=citation en_US
dc.description.abstract Hydrogen bond, hydrophobic and vdW interactions are the three major non-covalent interactions at protein–protein interfaces. We have developed a method that uses only these properties to describe interactions between proteins, which can qualitatively estimate the individual contribution of each interfacial residue to the binding and gives the results in a graphic display way. This method has been applied to analyze alanine mutation data at protein–protein interfaces. A dataset containing 13 protein–protein complexes with 250 alanine mutations of interfacial residues has been tested. For the 75 hot-spot residues (ΔΔ G ≥1.5 kcal mol -1 ), 66 can be predicted correctly with a success rate of 88%. In order to test the tolerance of this method to conformational changes upon binding, we utilize a set of 26 complexes with one or both of their components available in the unbound form. The difference of key residues exported by the program is 11% between the results using complexed proteins and those from unbound ones. As this method gives the characteristics of the binding partner for a particular protein, in-depth studies on protein–protein recognition can be carried out. Furthermore, this method can be used to compare the difference between protein–protein interactions and look for correlated mutation. en_US
dc.format.extent 421642 bytes
dc.format.extent 3115 bytes
dc.format.mimetype application/pdf
dc.format.mimetype text/plain
dc.language.iso en_US
dc.publisher Springer-Verlag en_US
dc.subject.other Chemistry en_US
dc.subject.other Correlated Mutation en_US
dc.subject.other PP_SITE en_US
dc.subject.other Interface Analysis en_US
dc.subject.other Hot Spot en_US
dc.subject.other Protein–Protein Interaction en_US
dc.title Structure-based method for analyzing protein–protein interfaces en_US
dc.type Original Paper en_US
dc.subject.hlbsecondlevel "Molecular, Cellular, and Developmental Biology" en_US
dc.subject.hlbtoplevel Science en_US
dc.description.peerreviewed Peer Reviewed en_US
dc.contributor.affiliationum State Key Laboratory of Structural Chemistry for Stable and Unstable Species, College of Chemistry and Molecular Engineering, Peking University, 100871, Beijing, China; Medical Chemistry and Comprehensive Cancer Center, University of Michigan, 1500 E. Medical Center Drive Ann Arbor, MI 48109-0934, USA en_US
dc.contributor.affiliationother State Key Laboratory of Structural Chemistry for Stable and Unstable Species, College of Chemistry and Molecular Engineering, Peking University, 100871, Beijing, China; Center for Theoretical Biology, Peking University, 100871, Beijing, China en_US
dc.contributor.affiliationother State Key Laboratory of Structural Chemistry for Stable and Unstable Species, College of Chemistry and Molecular Engineering, Peking University, 100871, Beijing, China en_US
dc.contributor.affiliationumcampus Ann Arbor en_US
dc.identifier.pmid 14634848 en_US
dc.description.bitstreamurl http://deepblue.lib.umich.edu/bitstream/2027.42/47876/1/894_2003_Article_168.pdf en_US
dc.identifier.doi http://dx.doi.org/10.1007/s00894-003-0168-3 en_US
dc.identifier.source Journal of Molecular Modeling en_US
dc.owningcollname Interdisciplinary and Peer-Reviewed
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