Altered Dynamics of S. aureus Phosphofructokinase via Bond Restraints at Two Distinct Allosteric Binding Sites
dc.authorid | CELEBI, METEHAN/0000-0002-2112-9124 | |
dc.contributor.author | Akdoğan, Ebru Demet | |
dc.contributor.author | Akten, Ebru Demet | |
dc.date.accessioned | 2023-10-19T15:11:32Z | |
dc.date.available | 2023-10-19T15:11:32Z | |
dc.date.issued | 2022 | |
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, Turkey | en_US |
dc.description.abstract | The 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.sponsorship | Scientific and Technological Research Council of Turkey (TUBI_TAK) [218M320] | en_US |
dc.description.sponsorship | This work has been partially supported by The Scientific and Technological Research Council of Turkey (TUBI_TAK Project #218M320) . | en_US |
dc.identifier.citation | 2 | |
dc.identifier.doi | 10.1016/j.jmb.2022.167646 | en_US |
dc.identifier.issn | 0022-2836 | |
dc.identifier.issn | 1089-8638 | |
dc.identifier.issue | 17 | en_US |
dc.identifier.pmid | 35623412 | en_US |
dc.identifier.scopus | 2-s2.0-85131567323 | en_US |
dc.identifier.scopusquality | Q1 | |
dc.identifier.uri | https://doi.org/10.1016/j.jmb.2022.167646 | |
dc.identifier.uri | https://hdl.handle.net/20.500.12469/5063 | |
dc.identifier.volume | 434 | en_US |
dc.identifier.wos | WOS:000848635800011 | en_US |
dc.identifier.wosquality | Q2 | |
dc.khas | 20231019-WoS | en_US |
dc.language.iso | en | en_US |
dc.publisher | Academic Press Ltd- Elsevier Science Ltd | en_US |
dc.relation.ispartof | Journal of Molecular Biology | en_US |
dc.relation.publicationcategory | Makale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanı | en_US |
dc.rights | info:eu-repo/semantics/closedAccess | en_US |
dc.subject | Molecular-Dynamics | En_Us |
dc.subject | Protein-Structure | En_Us |
dc.subject | Motions | En_Us |
dc.subject | Networks | En_Us |
dc.subject | Mode | En_Us |
dc.subject | Molecular-Dynamics | |
dc.subject | allosteric site | en_US |
dc.subject | Protein-Structure | |
dc.subject | mutual information | en_US |
dc.subject | Motions | |
dc.subject | mean square fluctuations | en_US |
dc.subject | Networks | |
dc.subject | perturbation | en_US |
dc.subject | Mode | |
dc.subject | signal transmission | en_US |
dc.title | Altered Dynamics of S. aureus Phosphofructokinase via Bond Restraints at Two Distinct Allosteric Binding Sites | en_US |
dc.type | Article | en_US |
dspace.entity.type | Publication | |
relation.isAuthorOfPublication | 558d2b8e-c713-49e0-9350-d354abb5cd69 | |
relation.isAuthorOfPublication.latestForDiscovery | 558d2b8e-c713-49e0-9350-d354abb5cd69 |