Structure-based method for analyzing protein–protein interfaces
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 | https://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 | Article | 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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