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dc.contributor.authorJalalypour, Farzaneh
dc.contributor.authorŞensoy, Özge
dc.contributor.authorAtılgan, Canan
dc.date.accessioned2020-07-27T09:51:56Z
dc.date.available2020-07-27T09:51:56Z
dc.date.issued2020en_US
dc.identifier.citationJalalypour, F., Şensoy, Ö. ve Atılgan, C. (2020). Perturb-Scan-Pull: A novel method facilitating conformational transitions in proteins. Journal of Chemical Theory and Computation, 16(6), 3825-3841. https://dx.doi.org/10.1021/acs.jctc.9b01222en_US
dc.identifier.issn1549-9618
dc.identifier.issn1549-9626
dc.identifier.urihttps://dx.doi.org/10.1021/acs.jctc.9b01222
dc.identifier.urihttps://hdl.handle.net/20.500.12511/5611
dc.description.abstractConformational transitions in proteins facilitate precise physiological functions. Therefor; it is crucial to understand the mechanisms underlying these processes to modulate protein function. Yet, studying structural and dynamical properties of proteins is notoriously challenging due to the complexity of the underlying potential energy surfaces (PES). We have previously developed the perturbation-response scanning (PRS) method to identify key residues that participate in the communication network responsible for specific conformational transitions. PRS is based on a residue-by-residue scan of the protein to determine the subset of residues/forces which provide the closest conformational change leading to a target conformational state, inasmuch as linear response theory applies to these motions. Here, we develop a novel method to further evaluate if conformational transitions may be triggered on the PES. We aim to study functionally relevant conformational transitions in proteins by using results obtained from PRS and feeding them as inputs to steered molecular dynamics simulations. The success and the transferability of the method are evaluated on three protein systems having different complexities of motion on the PES: calmodulin, adenylate kinase, and bacterial ferric binding protein. We find that the method captures the target conformation, while providing key residues and the optimum paths with relatively low free energy profiles.en_US
dc.language.isoengen_US
dc.publisherAmerican Chemical Societyen_US
dc.rightsinfo:eu-repo/semantics/embargoedAccessen_US
dc.subjectPeptides and Proteinsen_US
dc.subjectCrystal Structureen_US
dc.subjectChemical Structureen_US
dc.subjectConformationen_US
dc.subjectConformational Transitionsen_US
dc.titlePerturb-Scan-Pull: A novel method facilitating conformational transitions in proteinsen_US
dc.typearticleen_US
dc.relation.journalJournal of Chemical Theory and Computationen_US
dc.departmentİstanbul Medipol Üniversitesi, Mühendislik ve Doğa Bilimleri Fakültesi, Bilgisayar Mühendisliği Bölümüen_US
dc.authorid0000-0001-5950-3436en_US
dc.identifier.volume16en_US
dc.identifier.issue6en_US
dc.identifier.startpage3825en_US
dc.identifier.endpage3841en_US
dc.relation.tubitakinfo:eu-repo/grantAgreement/TUBITAK/SOBAG/116F229
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanıen_US
dc.identifier.doi10.1021/acs.jctc.9b01222en_US


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