Transmembrane helix 6 observed at the interface of beta(2)AR homodimers in blind docking studies

dc.contributor.authorKoroğlu, Ayça
dc.contributor.authorAkten, Ebru Demet
dc.date.accessioned2019-06-27T08:02:16Z
dc.date.available2019-06-27T08:02:16Z
dc.date.issued2015
dc.departmentFakülteler, Mühendislik ve Doğa Bilimleri Fakültesi, Biyoinformatik ve Genetik Bölümüen_US
dc.description.abstractPeptide- and protein-protein dockings were carried out on beta(2)-adrenergic receptor (beta(2)AR) to confirm the presence of transmembrane helix 6 (TM6) at the interface region between two beta(2)AR monomers thereby its possible role in dimerization as suggested in numerous experimental and computational studies. Initially a portion of TM6 was modeled as a peptide consisting of 23 residues and blindly docked to beta(2)AR monomer using a rigid body approach. Interestingly all highest score conformations preferred to be near TM5 and TM6 regions of the receptor. Furthermore longer peptides generated from a whole TM region were blindly docked to beta(2)AR using the same rigid body approach. This yielded a total of seven docked peptides each derived from one TM helix. Most interestingly for each peptide TM6 was among the most preferred binding site region in the receptor. Besides the peptide dockings two beta(2)AR monomers were blindly docked to each other using a full rigid-body search of docking orientations which yielded a total of 16000 dimer conformations. Each dimer was then filtered according to a fitness value based on the membrane topology. Among 149 complexes that met the topology requirements 102 conformers were composed of two monomers oriented in opposite directions whereas in the remaining 47 the monomers were arranged in parallel. Lastly all 149 conformers were clustered based on a root mean-squared distance value of 6 angstrom. In agreement with the peptide results the clustering yielded the largest population of conformers with the highest Z-score value having TM6 at the interface region.en_US]
dc.identifier.citation3
dc.identifier.doi10.1080/07391102.2014.962094en_US
dc.identifier.endpage1515
dc.identifier.issn0739-1102en_US
dc.identifier.issn1538-0254en_US
dc.identifier.issn0739-1102
dc.identifier.issn1538-0254
dc.identifier.issue7
dc.identifier.pmid25262920en_US
dc.identifier.scopus2-s2.0-84939946049en_US
dc.identifier.scopusqualityQ2
dc.identifier.startpage1503en_US
dc.identifier.urihttps://hdl.handle.net/20.500.12469/584
dc.identifier.urihttps://doi.org/10.1080/07391102.2014.962094
dc.identifier.volume33en_US
dc.identifier.wosWOS:000353720700009en_US
dc.identifier.wosqualityN/A
dc.institutionauthorAkten, Ebru Demeten_US
dc.language.isoenen_US
dc.publisherTaylor & Francis Incen_US
dc.relation.journalJournal Of Biomolecular Structure & Dynamicsen_US
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanıen_US
dc.rightsinfo:eu-repo/semantics/openAccessen_US
dc.subjectProtein-protein dockingen_US
dc.subjectInterfaceen_US
dc.subjectBeta(2)AR dimeren_US
dc.subjectHomodimeren_US
dc.subjectPeptide-protein dockingen_US
dc.subjectBeta(2)-adrenergic receptoren_US
dc.subjectTransmembrane helix 6en_US
dc.titleTransmembrane helix 6 observed at the interface of beta(2)AR homodimers in blind docking studiesen_US
dc.typeArticleen_US
dspace.entity.typePublication

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