Structures of MERS-CoV macro domain in aqueous solution with dynamics: Impacts of parallel tempering simulation techniques and\n CHARMM36m\n and\n AMBER99SB\n force field parameters

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dc.authorid0000-0002-0772-9350
dc.contributor.authorAkbayrak, İbrahim Yağız
dc.contributor.authorÇağlayan, Şule İrem
dc.contributor.authorDurdağı, Serdar
dc.contributor.authorKurgan, Lukasz
dc.contributor.authorUversky, Vladimir N.
dc.contributor.authorUlver, Burak
dc.contributor.authorDervişoğlu, Havvanur
dc.contributor.authorHaklıdır, Mehmet
dc.contributor.authorHasekioğlu, Orkun
dc.contributor.authorCoşkuner Weber, Orkid
dc.date.accessioned2024-05-07T06:26:43Z
dc.date.available2024-05-07T06:26:43Z
dc.date.issued2021
dc.departmentTAÜ, Fen Fakültesi, Moleküler Biyoteknoloji Bölümüen_US
dc.description.abstractA novel virus, severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2), causing coronavirus disease 2019 (COVID-19) worldwide appeared in 2019. Detailed scientific knowledge of the members of the Coronaviridae family, including the Middle East Respiratory Syndrome Coronavirus (MERS-CoV) is currently lacking. Structural studies of the MERS-CoV proteins in the current literature are extremely limited. We present here detailed characterization of the structural properties of MERS-CoV macro domain in aqueous solution. Additionally, we studied the impacts of chosen force field parameters and parallel tempering simulation techniques on the predicted structural properties of MERS-CoV macro domain in aqueous solution. For this purpose, we conducted extensive Hamiltonian-replica exchange molecular dynamics simulations and Temperature-replica exchange molecular dynamics simulations using the CHARMM36m and AMBER99SB parameters for the macro domain. This study shows that the predicted secondary structure properties including their propensities depend on the chosen simulation technique and force field parameter. We perform structural clustering based on the radius of gyration and end-to-end distance of MERS-CoV macro domain in aqueous solution. We also report and analyze the residue-level intrinsic disorder features, flexibility and secondary structure. Furthermore, we study the propensities of this macro domain for protein-protein interactions and for the RNA and DNA binding. Overall, results are in agreement with available nuclear magnetic resonance spectroscopy findings and present more detailed insights into the structural properties of MERS CoV macro domain in aqueous solution. All in all, we present the structural properties of the aqueous MERS-CoV macro domain using different parallel tempering simulation techniques, force field parameters and bioinformatics tools.
dc.identifier.citationAkbayrak İ. Y., Cağlayan Ş. İ., Durdağı, S., Coşkuner Weber, O., Hasekioğlu, O., Haklıdır, M., Dervişoğlu, H. (2021). Structures of MERS-CoV macro domain in aqueous solution with dynamics: Impacts of parallel tempering simulation techniques and\n CHARMM36m\n and\n AMBER99SB\n force field parameters. 89(10):1289–1299.
dc.identifier.doi10.1002/prot.26150
dc.identifier.endpage1299en_US
dc.identifier.issn0887-3585
dc.identifier.issue10en_US
dc.identifier.scopus2-s2.0-85106399387
dc.identifier.startpage1289en_US
dc.identifier.urihttps://hdl.handle.net/20.500.12846/1220
dc.identifier.volume89en_US
dc.identifier.wosWOS:000654202700001
dc.indekslendigikaynakWeb of Science
dc.language.isoen
dc.publisherWiley
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanı
dc.rightsinfo:eu-repo/semantics/openAccess
dc.subjectBioinformaticsen_US
dc.subjectForce field parametersen_US
dc.subjectH-REMD simulationsen_US
dc.subjectMERS-CoVen_US
dc.subjectSimulation protocolsen_US
dc.subjectT-REMD simulationsen_US
dc.titleStructures of MERS-CoV macro domain in aqueous solution with dynamics: Impacts of parallel tempering simulation techniques and\n CHARMM36m\n and\n AMBER99SB\n force field parameters
dc.typeArticle

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