Rotamer Dynamics: Analysis of Rotamers in Molecular Dynamics Simulations of Proteins

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dc.contributor"European Union (EU)" & "Horizon 2020"en
dc.contributor.authorHaddad, Yazan Abdulmajeed Eyadhcs
dc.contributor.authorAdam, Vojtěchcs
dc.contributor.authorHeger, Zbyněkcs
dc.coverage.issue11cs
dc.coverage.volume116cs
dc.date.accessioned2020-11-05T15:55:34Z
dc.date.available2020-11-05T15:55:34Z
dc.date.issued2019-06-04cs
dc.description.abstractGiven by chi torsional angles, rotamers describe the side-chain conformations of amino acid residues in a protein based on the rotational isomers (hence the word rotamer). Constructed rotamer libraries, based on either protein crystal structures or dynamics studies, are the tools for classifying rotamers (torsional angles) in a way that reflect their frequency in nature. Rotamer libraries are routinely used in structure modeling and evaluation. In this perspective article, we would like to encourage researchers to apply rotamer analyses beyond their traditional use. Molecular dynamics (MD) of proteins highlight the in silico behavior of molecules in solution and thus can identify favorable side-chain conformations. In this article, we used simple computational tools to study rotamer dynamics (RD) in MD simulations. First, we isolated each frame in the MD trajectories in separate Protein Data Bank files via the cpptraj module in AMBER. Then, we extracted torsional angles via the Bio3D module in R language. The classification of torsional angles was also done in R according to the penultimate rotamer library. RD analysis is useful for various applications such as protein folding, study of rotamer-rotamer relationship in protein-protein interaction, real-time correlation between secondary structures and rotamers, study of flexibility of side chains in binding site for molecular docking preparations, use of RD as guide in functional analysis and study of structural changes caused by mutations, providing parameters for improving coarse-grained MD accuracy and speed, and many others. Major challenges facing RD to emerge as a new scientific field involve the validation of results via easy, inexpensive wet-lab methods. This realm is yet to be explored.en
dc.formattextcs
dc.format.extent2062-2072cs
dc.format.mimetypeapplication/pdfcs
dc.identifier.citationBIOPHYSICAL JOURNAL. 2019, vol. 116, issue 11, p. 2062-2072.en
dc.identifier.doi10.1016/j.bpj.2019.04.017cs
dc.identifier.issn0006-3495cs
dc.identifier.other157616cs
dc.identifier.urihttp://hdl.handle.net/11012/195616
dc.language.isoencs
dc.publisherElseviercs
dc.relation.ispartofBIOPHYSICAL JOURNALcs
dc.relation.projectIdinfo:eu-repo/grantAgreement/EC/H2020/759585/EU//ToMeTuMen
dc.relation.urihttps://www.sciencedirect.com/science/article/abs/pii/S0006349519303352cs
dc.rightsCreative Commons Attribution-NonCommercial-NoDerivatives 4.0 Internationalcs
dc.rights.accessopenAccesscs
dc.rights.sherpahttp://www.sherpa.ac.uk/romeo/issn/0006-3495/cs
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/4.0/cs
dc.subjectrotameren
dc.subjectmolecular dynamicsen
dc.subjectproteinsen
dc.titleRotamer Dynamics: Analysis of Rotamers in Molecular Dynamics Simulations of Proteinsen
dc.type.driverarticleen
dc.type.statusPeer-revieweden
dc.type.versionacceptedVersionen
sync.item.dbidVAV-157616en
sync.item.dbtypeVAVen
sync.item.insts2020.11.05 16:55:34en
sync.item.modts2020.11.05 16:14:28en
thesis.grantorVysoké učení technické v Brně. Středoevropský technologický institut VUT. Chytré nanonástrojecs
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