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

The result's identifiers

  • Result code in IS VaVaI

    <a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F62156489%3A43210%2F19%3A43915691" target="_blank" >RIV/62156489:43210/19:43915691 - isvavai.cz</a>

  • Alternative codes found

    RIV/00216305:26620/19:PU132593

  • Result on the web

    <a href="https://doi.org/10.1016/j.bpj.2019.04.017" target="_blank" >https://doi.org/10.1016/j.bpj.2019.04.017</a>

  • DOI - Digital Object Identifier

    <a href="http://dx.doi.org/10.1016/j.bpj.2019.04.017" target="_blank" >10.1016/j.bpj.2019.04.017</a>

Alternative languages

  • Result language

    angličtina

  • Original language name

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

  • Original language description

    Given 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.

  • Czech name

  • Czech description

Classification

  • Type

    J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database

  • CEP classification

  • OECD FORD branch

    10610 - Biophysics

Result continuities

  • Project

    <a href="/en/project/GA18-10251S" target="_blank" >GA18-10251S: Comprehensive insight into mechanisms of action and metabolism of tyrosine kinase inhibitors and a study of ways increasing their antitumor efficiency</a><br>

  • Continuities

    P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Others

  • Publication year

    2019

  • Confidentiality

    S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Data specific for result type

  • Name of the periodical

    Biophysical Journal

  • ISSN

    0006-3495

  • e-ISSN

  • Volume of the periodical

    116

  • Issue of the periodical within the volume

    11

  • Country of publishing house

    US - UNITED STATES

  • Number of pages

    11

  • Pages from-to

    2062-2072

  • UT code for WoS article

    000470092800003

  • EID of the result in the Scopus database

    2-s2.0-85065395420