A new protein nucleic-acid coarse-grained force field based on the UNRES and NARES-2P force fields

Adam Sieradzan , Artur Giełdoń , Yanping Yin , Yi He , Harold Scheraga , Józef Adam Liwo

Abstract

Based on the coarse-grained UNRES and NARES-2P models of proteins and nucleic acids, respectively, developed in our laboratory, in this work we have developed a coarse-grained model of systems containing proteins and nucleic acids. The UNRES and NARES-2P effective energy functions have been applied to the protein and nucleic-acid components of a system, respectively, while protein–nucleic-acid interactions have been described by the respective coarse-grained potentials developed in our recent work (Yin et al., J. Chem Theory Comput. 2015, 11, 1792). The Debye–Hückel screening has been applied to the electrostatic-interaction energy between the phosphate groups and charged amino-acid side chains. The model has been integrated into the UNRES package for coarse-grained molecular dynamics simulations of proteins and the implementation has been tested for energy conservation in microcanonical molecular dynamics runs and for temperature conservation in canonical molecular dynamics runs. Two case studies were performed: (i) the dynamics of the Ku protein heterodimer bound to DNA, for which it was found that the Ku70/Ku80 protein complex plays an active role in DNA repairing and (ii) conformational changes of the multiple antibiotic resistance (MarA) protein occurring during DNA binding, for which the functionally important motions occurring during this process were identified.
Author Adam Sieradzan (FCh / DTCh / LMM)
Adam Sieradzan,,
- Laboratory of Molecular Modeling
, Artur Giełdoń (FCh / DTCh / LSP)
Artur Giełdoń,,
- Laboratory of Simulation of Polymers
, Yanping Yin
Yanping Yin,,
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, Yi He
Yi He,,
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, Harold Scheraga
Harold Scheraga,,
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, Józef Adam Liwo (FCh / DTCh / LMM)
Józef Adam Liwo,,
- Laboratory of Molecular Modeling
Journal seriesJournal of Computational Chemistry, ISSN 0192-8651, [1096-987X], (A 35 pkt)
Issue year2018
Vol39
No28
Pages2360-2370
Publication size in sheets0.5
Keywords in Englishlocal conformational states; physics-based potentials; initio energy surfaces; united-residue model; molecular-dynamics; polypeptide-chains; dna-replication; simulations; backbone; systems
ASJC Classification2605 Computational Mathematics; 1600 General Chemistry
DOIDOI:10.1002/jcc.25571
URL https://doi.org/10.1002/jcc.25571
Languageen angielski
Score (nominal)35
ScoreMinisterial score = 35.0, 30-09-2019, ArticleFromJournal
Publication indicators WoS Citations = 0; Scopus SNIP (Source Normalised Impact per Paper): 2016 = 1.297; WoS Impact Factor: 2017 = 3.221 (2) - 2017=4.161 (5)
Citation count*2 (2019-10-09)
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* presented citation count is obtained through Internet information analysis and it is close to the number calculated by the Publish or Perish system.
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