Altered Dynamics of S. aureus Phosphofructokinase via Bond Restraints at Two Distinct Allosteric Binding Sites

dc.authoridCELEBI, METEHAN/0000-0002-2112-9124
dc.contributor.authorAkdoğan, Ebru Demet
dc.contributor.authorAkten, Ebru Demet
dc.date.accessioned2023-10-19T15:11:32Z
dc.date.available2023-10-19T15:11:32Z
dc.date.issued2022
dc.department-temp[Celebi, Metehan] Free Univ Berlin, Integrated Grad Sch, Dept Phys, AG Struct Dynam & Funct Biol Syst, Berlin, Germany; [Akten, Ebru Demet] Kadir Has Univ, Fac Engn & Nat Sci, Dept Mol Biol & Genet, Istanbul, Turkeyen_US
dc.description.abstractThe effect of perturbation at the allosteric site was investigated through several replicas of molecular dynamics (MD) simulations conducted on bacterial phosphofructokinase (SaPFK). In our previous work, an alternative binding site was estimated to be allosteric in addition to the experimentally reported one. To highlight the effect of both allosteric sites on receptor's dynamics, MD runs were carried out on apo forms with and without perturbation. Perturbation was achieved via incorporating multiple bond restraints for residue pairs located at the allosteric site. Restraints applied to the predicted site caused one dimer to stiffen, whereas an increase in mobility was detected in the same dimer when the experimentally resolved site was restrained. Fluctuations in C-alpha-C-alpha distances which is used to disclose residues with high potential of communication indicated a marked increase in signal transmission within each dimer as the receptor switched to a restrained state. Cross-correlation of positional fluctuations indicated an overall decrease in the magnitude of both positive and negative correlations when restraints were employed on the predicted allosteric site whereas an exact opposite effect was observed for the reported site. Finally, mutual correspondence between positional fluctuations noticeably increased with restraints on predicted allosteric site, whereas an opposite effect was observed for restraints applied on experimentally reported one. In view of these findings, it is clear that the perturbation of either one of two allosteric sites effected the dynamics of the receptor with a distinct and contrasting character. (c) 2022 Elsevier Ltd. All rights reserved.en_US
dc.description.sponsorshipScientific and Technological Research Council of Turkey (TUBI_TAK) [218M320]en_US
dc.description.sponsorshipThis work has been partially supported by The Scientific and Technological Research Council of Turkey (TUBI_TAK Project #218M320) .en_US
dc.identifier.citation2
dc.identifier.doi10.1016/j.jmb.2022.167646en_US
dc.identifier.issn0022-2836
dc.identifier.issn1089-8638
dc.identifier.issue17en_US
dc.identifier.pmid35623412en_US
dc.identifier.scopus2-s2.0-85131567323en_US
dc.identifier.scopusqualityQ1
dc.identifier.urihttps://doi.org/10.1016/j.jmb.2022.167646
dc.identifier.urihttps://hdl.handle.net/20.500.12469/5063
dc.identifier.volume434en_US
dc.identifier.wosWOS:000848635800011en_US
dc.identifier.wosqualityQ2
dc.khas20231019-WoSen_US
dc.language.isoenen_US
dc.publisherAcademic Press Ltd- Elsevier Science Ltden_US
dc.relation.ispartofJournal of Molecular Biologyen_US
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanıen_US
dc.rightsinfo:eu-repo/semantics/closedAccessen_US
dc.subjectMolecular-DynamicsEn_Us
dc.subjectProtein-StructureEn_Us
dc.subjectMotionsEn_Us
dc.subjectNetworksEn_Us
dc.subjectModeEn_Us
dc.subjectMolecular-Dynamics
dc.subjectallosteric siteen_US
dc.subjectProtein-Structure
dc.subjectmutual informationen_US
dc.subjectMotions
dc.subjectmean square fluctuationsen_US
dc.subjectNetworks
dc.subjectperturbationen_US
dc.subjectMode
dc.subjectsignal transmissionen_US
dc.titleAltered Dynamics of S. aureus Phosphofructokinase via Bond Restraints at Two Distinct Allosteric Binding Sitesen_US
dc.typeArticleen_US
dspace.entity.typePublication
relation.isAuthorOfPublication558d2b8e-c713-49e0-9350-d354abb5cd69
relation.isAuthorOfPublication.latestForDiscovery558d2b8e-c713-49e0-9350-d354abb5cd69

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