Zobrazit minimální záznam

dc.contributor.authorHaddad, Yazan Abdulmajeed Eyadh
dc.contributor.authorAdam, Vojtěch
dc.contributor.authorHeger, Zbyněk
dc.date.accessioned2021-06-19T00:02:19Z
dc.date.available2021-06-19T00:02:19Z
dc.date.issued2019
dc.identifier43917132
dc.identifier.issn0006-3495 Sherpa/RoMEO, JCR
dc.identifier.urihttps://repozitar.mendelu.cz/xmlui/handle/20.500.12698/1326
dc.description.abstractGiven by χ 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.format2062-2072
dc.publisherBiophysical Society
dc.relation.ispartofBiophysical Journal
dc.relation.urihttps://doi.org/10.1016/j.bpj.2019.04.017
dc.rightsCC BY-NC-ND 3.0
dc.rights.urihttps://creativecommons.org/licenses/by-nc-nd/3.0/
dc.subjectforce-field biasen
dc.subjecttryptophanen
dc.subjectneurotrophinen
dc.subjectfluorescenceen
dc.subjectdipeptideen
dc.subjectpeptidesen
dc.titleRotamer Dynamics: Analysis of Rotamers in Molecular Dynamics Simulations of Proteinsen
dc.typeJ_ČLÁNEK
dc.date.updated2021-06-19T00:02:19Z
dc.description.versionPreprint
local.identifier.doi10.1016/j.bpj.2019.04.017
local.identifier.scopus2-s2.0-85065395420
local.identifier.wos000470092800003
local.number11
local.volume116
local.identifier.obd43917132
local.identifier.e-issn1542-0086
dc.project.IDGA18-10251S
dc.project.IDKomplexní pohled na mechanismus působení a metabolismus inhibitorů tyrosinkinas a studium přístupů k potenciaci jejich protinádorové účinnosti
dc.identifier.orcidHaddad, Yazan Abdulmajeed Eyadh 0000-0002-7844-4336
dc.identifier.orcidAdam, Vojtěch 0000-0002-8527-286X
dc.identifier.orcidHeger, Zbyněk 0000-0002-3915-7270
local.contributor.affiliationAF
dc.embargo.lift04.07.2020


Soubory tohoto záznamu

Thumbnail

Tento záznam se objevuje v následujících kolekcích

Zobrazit minimální záznam

CC BY-NC-ND 3.0
Kromě případů, kde je uvedeno jinak, licence tohoto záznamu je CC BY-NC-ND 3.0