Molecular simulations of IDPs: From ensemble generation to IDP interactions leading to disorder-to-order transitions

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dc.authorid0000-0002-0772-9350
dc.contributor.authorFatafta, Hebah
dc.contributor.authorSamantray, Suman
dc.contributor.authorSayyed-Ahmad, Abdallah
dc.contributor.authorWeber, Orkide Coşkuner
dc.contributor.authorStrodel, Birgit
dc.contributor.editorN. Uversky, Vladimir
dc.date.accessioned2022-08-17T09:59:14Z
dc.date.available2022-08-17T09:59:14Z
dc.date.issued2021
dc.departmentTAÜ, Fen Fakültesi, Moleküler Biyoteknoloji Bölümüen_US
dc.description.abstractIntrinsically disordered proteins (IDPs) lack a well-defined three-dimensional structure but do exhibit some dynamical and structural ordering. The structural plasticity of IDPs indicates that entropy-driven motions are crucial for their function. Many IDPs undergo function-related disorder-to-order transitions upon by their interaction with specific binding partners. Approaches that are based on both experimental and theoretical tools enable the biophysical characterization of IDPs. Molecular simulations provide insights into IDP structural ensembles and disorder-to-order transition mechanisms. However, such studies depend strongly on the chosen force field parameters and simulation techniques. In this chapter, we provide an overview of IDP characteristics, review all-atom force fields recently developed for IDPs, and present molecular dynamics-based simulation methods that allow IDP ensemble generation as well as the characterization of disorder-to-order transitions. In particular, we introduce meta-dynamics, replica exchange molecular dynamics simulations, and also kinetic models resulting from Markov State modeling, and provide various examples for the successful application of these simulation methods to IDPs.
dc.identifier.citationFatafta, H., Samantray, S., Sayyed-Ahmad, A., Coskuner-Weber, O., & Strodel, B. (2021). Molecular simulations of IDPs: From ensemble generation to IDP interactions leading to disorder-to-order transitions. Progress in Molecular Biology and Translational Science, 183, 135-185.
dc.identifier.doi10.1016/bs.pmbts.2021.06.003
dc.identifier.endpage185en_US
dc.identifier.issn1877-1173
dc.identifier.scopus2-s2.0-85111490745
dc.identifier.startpage135en_US
dc.identifier.urihttps://hdl.handle.net/20.500.12846/651
dc.identifier.volume183en_US
dc.identifier.wosWOS:000748722300006
dc.identifier.wosqualityN/A
dc.indekslendigikaynakWeb of Science
dc.institutionauthorWeber, Orkide Coşkuner
dc.language.isoen
dc.publisherAcademic Press Inc Elsevier Science
dc.relation.ispartofDancing Protein Clouds: Intrinsically Disordered Proteins In The Norm And Pathology, Pt C
dc.relation.publicationcategoryDiğer
dc.rightsinfo:eu-repo/semantics/closedAccess
dc.subjectHamiltonian Replica Exchangeen_US
dc.subjectCreb-Binding Proteinen_US
dc.subjectPolarizable Force-Fielden_US
dc.subjectPolarize Edilebilir Kuvvet Alanıen_US
dc.subjectHamiltonian Kopya Değişimien_US
dc.subjectHamiltonscher Replika-Austauschen_US
dc.subjectCreb-Bindendes Proteinen_US
dc.subjectPolarisierbares Kraftfelden_US
dc.titleMolecular simulations of IDPs: From ensemble generation to IDP interactions leading to disorder-to-order transitions
dc.typeReview Article

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