Molecular dynamics simulations of DNA-DNA and DNA-protein interactions.

DNA Entropy Molecular Dynamics Simulation Proteins

Journal

Current opinion in structural biology
ISSN: 1879-033X
Titre abrégé: Curr Opin Struct Biol
Pays: England
ID NLM: 9107784

Informations de publication

Date de publication:
10 2020
Historique:
received: 24 02 2020
revised: 03 06 2020
accepted: 08 06 2020
pubmed: 19 7 2020
medline: 16 10 2021
entrez: 19 7 2020
Statut: ppublish

Résumé

The all-atom molecular dynamics method can characterize the molecular-level interactions in DNA and DNA-protein systems with unprecedented resolution. Recent advances in computational technologies have allowed the method to reveal the unbiased behavior of such systems at the microseconds time scale, whereas enhanced sampling approaches have matured enough to characterize the interaction free energy with quantitative precision. Here, we describe recent progress toward increasing the realism of such simulations by refining the accuracy of the molecular dynamics force field, and we highlight recent application of the method to systems of outstanding biological interest.

Identifiants

DOI: 10.1016/j.sbi.2020.06.007 PMID: 32682257
pubmed: 32682257
pii: S0959-440X(20)30105-6
doi: 10.1016/j.sbi.2020.06.007
pii:
doi:

Substances chimiques

Proteins 0
DNA 9007-49-2

Types de publication

Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. Review

Langues

eng

Sous-ensembles de citation

IM

Pagination

88-96

Informations de copyright

Copyright © 2020 Elsevier Ltd. All rights reserved.

Auteurs

Jejoong Yoo (J)

Department of Physics, Sungkyunkwan University, Suwon 16419, Republic of Korea; Center for Self-assembly and Complexity, Institute for Basic Science, Pohang 37673, Republic of Korea. Electronic address: jejoong@skku.edu.

David Winogradoff (D)

Department of Physics and the Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.

Aleksei Aksimentiev (A)

Department of Physics and the Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. Electronic address: aksiment@illinois.edu.

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Classifications MeSH

questionsmedicales.fr › Acides nucléiques, nucléotides et nucléosides › Acides nucléiques › ADN › Molecular dynamics simulations of DNA-DNA and...
questionsmedicales.fr › Phénomènes physiques › Thermodynamique › Entropie › Molecular dynamics simulations of DNA-DNA and...
questionsmedicales.fr › Sciences de l'information › Méthodologies informatiques › Simulation numérique › Simulation de dynamique moléculaire › Molecular dynamics simulations of DNA-DNA and...
questionsmedicales.fr › Acides aminés, peptides et protéines › Protéines › Molecular dynamics simulations of DNA-DNA and...