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dc.contributor.authorÇalışkan, Murat
dc.contributor.authorMandacı, Sunay Y.
dc.contributor.authorUversky, Vladimir N.
dc.contributor.authorWeber, Orkide Coşkuner
dc.date.accessioned2021-03-08T10:22:22Z
dc.date.available2021-03-08T10:22:22Z
dc.date.issued2021en_US
dc.identifier.citationÇalışkan, M., Mandacı, S. Y., Uversky, V. N., & Coskuner‐Weber, O. (2021). Secondary Structure Dependence of Amyloid‐ß (1‐40) on Simulation Techniques and Force Field Parameters. Chemical Biology & Drug Design.en_US
dc.identifier.issn1747-0285
dc.identifier.urihttps://hdl.handle.net/20.500.12846/529
dc.description.abstractOur recent studies revealed that none of the selected widely used force field parameters and molecular dynamics simulation techniques yield structural properties for the intrinsically disordered alpha-synuclein that are in agreement with various experiments via testing different force field parameters. Here, we extend our studies on the secondary structure properties of the disordered amyloid-beta(1-40) peptide in aqueous solution. For these purposes, we conducted extensive replica exchange molecular dynamics simulations and obtained extensive molecular dynamics simulation trajectories from David E. Shaw group. Specifically, these molecular dynamics simulations were conducted using various force field parameters and obtained results are compared to our replica exchange molecular dynamics simulations and experiments. In this study, we calculated the secondary structure abundances and radius of gyration values for amyloid-beta(1-40) that were simulated using varying force field parameter sets and different simulation techniques. In addition, the intrinsic disorder propensity, as well as sequence-based secondary structure predisposition of amyloid-beta(1-40) and compared the findings with the results obtained from molecular simulations using various force field parameters and different simulation techniques. Our studies clearly show that the epitope region identification of amyloid-beta(1-40) depends on the chosen simulation technique and chosen force field parameters. Based on comparison with experiments, we find that best computational results in agreement with experiments are obtained using the a99sb*-ildn, charmm36m, and a99sb-disp parameters for the amyloid-beta(1-40) peptide in molecular dynamics simulations without parallel tempering or via replica exchange molecular dynamics simulations.en_US
dc.language.isoengen_US
dc.publisherWileyen_US
dc.relation.isversionofdoi.org/10.1111/cbdd.13830en_US
dc.rightsinfo:eu-repo/semantics/closedAccessen_US
dc.subjectEpitope Regionen_US
dc.subjectIntrinsic Disorder Propensityen_US
dc.subjectAmyloiden_US
dc.subjectAmiloiden_US
dc.subjectEpitop Bölgesien_US
dc.subjectİçsel Bozukluk Eğilimien_US
dc.titleSecondary structure dependence of amyloid-beta(1-40) on simulation techniques and force field parametersen_US
dc.typearticleen_US
dc.relation.journalChemical Biology & Drug Designen_US
dc.contributor.authorID0000-0002-0772-9350en_US
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanıen_US
dc.contributor.departmentTAÜ, Fen Fakültesi, Moleküler Biyoteknoloji Bölümüen_US
dc.contributor.institutionauthorWeber, Orkide Coşkuner
dc.identifier.wosqualityQ3en_US
dc.identifier.scopusqualityN/Aen_US
dc.identifier.wosWOS:000620334700001en_US


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