Investigation of protein quaternary structure via stoichiometry and symmetry information

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dc.authoridPrli?, Andreas/0000-0001-6346-6391
dc.authoridKorkmaz, Selçuk/0000-0003-4632-6850
dc.authoridZARARSIZ, GOKMEN/0000-0001-5801-1835
dc.authoridDuarte, Jose M/0000-0002-9544-5621
dc.authoridGOKSULUK, DINCER/0000-0002-2752-7668
dc.authoridZararsız, Gökmen/0000-0001-5801-1835
dc.authoridRose, Peter/0000-0001-9981-9750
dc.authorwosidPrli?, Andreas/A-6134-2012
dc.authorwosidKorkmaz, Selçuk/AAU-4677-2020
dc.authorwosidZARARSIZ, GOKMEN/ABH-7959-2020
dc.authorwosidDuarte, Jose M/I-6178-2018
dc.authorwosidGOKSULUK, DINCER/E-9175-2013
dc.authorwosidZararsız, Gökmen/E-8818-2013
dc.contributor.authorKorkmaz, Selcuk
dc.contributor.authorDuarte, Jose M.
dc.contributor.authorPrlic, Andreas
dc.contributor.authorGoksuluk, Dincer
dc.contributor.authorZararsiz, Gokmen
dc.contributor.authorSaracbasi, Osman
dc.contributor.authorBurley, Stephen K.
dc.date.accessioned2024-06-12T11:18:41Z
dc.date.available2024-06-12T11:18:41Z
dc.date.issued2018
dc.departmentTrakya Üniversitesien_US
dc.description.abstractThe Protein Data Bank (PDB) is the single worldwide archive of experimentally-determined three-dimensional (3D) structures of proteins and nucleic acids. As of January 2017, the PDB housed more than 125,000 structures and was growing by more than 11,000 structures annually. Since the 3D structure of a protein is vital to understand the mechanisms of biological processes, diseases, and drug design, correct oligomeric assembly information is of critical importance. Unfortunately, the biologically relevant oligomeric form of a 3D structure is not directly obtainable by X-ray crystallography, whilst in solution methods (NMR or single particle EM) it is known from the experiment. Instead, this information may be provided by the PDB Depositor as metadata coming from additional experiments, be inferred by sequence-sequence comparisons with similar proteins of known oligomeric state, or predicted using software, such as PISA (Proteins, Interfaces, Structures and Assemblies) or EPPIC (Evolutionary Protein Protein Interface Classifier). Despite significant efforts by professional PDB Biocurators during data deposition, there remain a number of structures in the archive with incorrect quaternary structure descriptions (or annotations). Further investigation is, therefore, needed to evaluate the correctness of quaternary structure annotations. In this study, we aim to identify the most probable oligomeric states for proteins represented in the PDB. Our approach evaluated the performance of four independent prediction methods, including text mining of primary publications, inference from homologous protein structures, and two computational methods (PISA and EPPIC). Aggregating predictions to give consensus results outperformed all four of the independent prediction methods, yielding 83% correct, 9% wrong, and 8% inconclusive predictions, when tested with a well-curated benchmark dataset. We have developed a freely-available web-based tool to make this approach accessible to researchers and PDB Biocurators (http://quatstruct.rcsb.org/).en_US
dc.description.sponsorshipScientific and Technological Research Council of Turkey (TUBITAK); International Research Fellowship Program (2214/A) [10596141401028]; National Science Foundation; National Institutes of Health; U.S. Department of Energy [NSF DBI1338415]en_US
dc.description.sponsorshipThis work was supported by Scientific and Technological Research Council of Turkey (TUBITAK), International Research Fellowship Program (2214/A) [10596141401028 to SK]; National Science Foundation, National Institutes of Health, and U.S. Department of Energy [NSF DBI1338415 to RCSB PDB (Protein Data Bank): to JMD, AP, SKB, PWR].en_US
dc.identifier.doi10.1371/journal.pone.0197176
dc.identifier.issn1932-6203
dc.identifier.issue6en_US
dc.identifier.pmid29864163en_US
dc.identifier.scopus2-s2.0-85048041585en_US
dc.identifier.scopusqualityQ1en_US
dc.identifier.urihttps://doi.org/10.1371/journal.pone.0197176
dc.identifier.urihttps://hdl.handle.net/20.500.14551/24917
dc.identifier.volume13en_US
dc.identifier.wosWOS:000434097100003en_US
dc.identifier.wosqualityQ2en_US
dc.indekslendigikaynakWeb of Scienceen_US
dc.indekslendigikaynakScopusen_US
dc.indekslendigikaynakPubMeden_US
dc.language.isoenen_US
dc.publisherPublic Library Scienceen_US
dc.relation.ispartofPlos Oneen_US
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanıen_US
dc.rightsinfo:eu-repo/semantics/openAccessen_US
dc.subjectData-Banken_US
dc.subjectInterfacesen_US
dc.subjectComplexesen_US
dc.subjectCrystalsen_US
dc.subjectEvolutionen_US
dc.subjectInferenceen_US
dc.titleInvestigation of protein quaternary structure via stoichiometry and symmetry informationen_US
dc.typeArticleen_US

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