A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. III. Determination of scale-consistent backbone-local and correlation potentials in the UNRES force field and force-field calibration and validation

Józef Adam Liwo , Adam Sieradzan , Agnieszka Lipska , Cezary Czaplewski , InSuk Joung , Wioletta Żmudzińska , Anna Hałabis , Stanisław Ołdziej

Abstract

The general theory of the construction of scale-consistent energy terms in the coarse-grained force fields presented in Paper I of this series has been applied to the revision of the UNRES force field for physics-based simulations of proteins. The potentials of mean force corresponding to backbone-local and backbone-correlation energy terms were calculated from the ab initio energy surfaces of terminally blocked glycine, alanine, and proline, and the respective analytical expressions, derived by using the scale-consistent formalism, were fitted to them. The parameters of all these potentials depend on single-residue types, thus reducing their number and preventing over-fitting. The UNRES force field with the revised backbone-local and backbone-correlation terms was calibrated with a set of four small proteins with basic folds: tryptophan cage variant (TRP1; α), Full Sequence Design (FSD; α + β), villin headpiece (villin; α), and a truncated FBP-28 WW-domain variant (2MWD; β) (the NEWCT-4P force field) and, subsequently, with an enhanced set of 9 proteins composed of TRP1, FSD, villin, 1BDC (α), 2I18 (α), 1QHK (α + β), 2N9L (α + β), 1E0L (β), and 2LX7 (β) (the NEWCT-9P force field). The NEWCT-9P force field performed better than NEWCT-4P in a blind-prediction-like test with a set of 26 proteins not used in calibration and outperformed, in a test with 76 proteins, the most advanced OPT-WTFSA-2 version of UNRES with former backbone-local and backbone-correlation terms that contained more energy terms and more optimizable parameters. The NEWCT-9P force field reproduced the bimodal distribution of backbone-virtual-bond angles in the simulated structures, as observed in experimental protein structures.
Author Józef Adam Liwo (FCh / DTCh / LMM)
Józef Adam Liwo,,
- Laboratory of Molecular Modeling
, Adam Sieradzan (FCh / DTCh / LMM)
Adam Sieradzan,,
- Laboratory of Molecular Modeling
, Agnieszka Lipska (FCh / DTCh / LMM)
Agnieszka Lipska,,
- Laboratory of Molecular Modeling
, Cezary Czaplewski (FCh / DTCh / LSP)
Cezary Czaplewski,,
- Laboratory of Simulation of Polymers
, InSuk Joung - [Korea Institute for Advanced Study]
InSuk Joung,,
-
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, Wioletta Żmudzińska (IFB / IB / LBiopolS)
Wioletta Żmudzińska,,
- Laboratory of Biopolymers Structure
, Anna Hałabis (IFB)
Anna Hałabis,,
- Intercollegiate Faculty of Biotechnology UG
, Stanisław Ołdziej (IFB / IB / LBiopolS)
Stanisław Ołdziej,,
- Laboratory of Biopolymers Structure
Journal seriesJournal of Chemical Physics, ISSN 0021-9606, [1089-7690], (N/A 100 pkt)
Issue year2019
Vol150
No15
Pages1-25
Publication size in sheets1.2
Article number155104
ASJC Classification1606 Physical and Theoretical Chemistry; 3100 General Physics and Astronomy
DOIDOI:10.1063/1.5093015
URL https://doi.org/10.1063/1.5093015
Languageen angielski
Score (nominal)100
Score sourcejournalList
ScoreMinisterial score = 100.0, 06-12-2019, ArticleFromJournal
Publication indicators Scopus Citations = 3; Scopus SNIP (Source Normalised Impact per Paper): 2018 = 0.969; WoS Impact Factor: 2018 = 2.997 (2) - 2018=2.84 (5)
Citation count*3 (2019-12-09)
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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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