Effective Inclusion of Electronic Polarization Improves the Description of Electrostatic Interactions: The prosECCo75 Biomolecular Force Field.


Journal

Journal of chemical theory and computation
ISSN: 1549-9626
Titre abrégé: J Chem Theory Comput
Pays: United States
ID NLM: 101232704

Informations de publication

Date de publication:
26 Aug 2024
Historique:
medline: 27 8 2024
pubmed: 27 8 2024
entrez: 26 8 2024
Statut: aheadofprint

Résumé

prosECCo75 is an optimized force field effectively incorporating electronic polarization via charge scaling. It aims to enhance the accuracy of nominally nonpolarizable molecular dynamics simulations for interactions in biologically relevant systems involving water, ions, proteins, lipids, and saccharides. Recognizing the inherent limitations of nonpolarizable force fields in precisely modeling electrostatic interactions essential for various biological processes, we mitigate these shortcomings by accounting for electronic polarizability in a physically rigorous mean-field way that does not add to computational costs. With this scaling of (both integer and partial) charges within the CHARMM36 framework, prosECCo75 addresses overbinding artifacts. This improves agreement with experimental ion binding data across a broad spectrum of systems─lipid membranes, proteins (including peptides and amino acids), and saccharides─without compromising their biomolecular structures. prosECCo75 thus emerges as a computationally efficient tool providing enhanced accuracy and broader applicability in simulating the complex interplay of interactions between ions and biomolecules, pivotal for improving our understanding of many biological processes.

Identifiants

pubmed: 39186899
doi: 10.1021/acs.jctc.4c00743
doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Auteurs

Ricky Nencini (R)

Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, CZ-160 00 Prague 6, Czech Republic.
Institute of Biotechnology, University of Helsinki, Viikinkaari 5, FI-00790 Helsinki, Finland.
Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Viikinkaari 5, FI-00790 Helsinki, Finland.

Carmelo Tempra (C)

Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, CZ-160 00 Prague 6, Czech Republic.

Denys Biriukov (D)

Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, CZ-160 00 Prague 6, Czech Republic.
CEITEC─Central European Institute of Technology, Masaryk University, Kamenice 753/5, CZ-62500 Brno, Czech Republic.
National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, CZ-62500 Brno, Czech Republic.

Miguel Riopedre-Fernandez (M)

Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, CZ-160 00 Prague 6, Czech Republic.

Victor Cruces Chamorro (V)

Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, CZ-160 00 Prague 6, Czech Republic.

Jakub Polák (J)

Department of Physical Chemistry, University of Chemistry and Technology, Prague, Technická 5, CZ-166 28 Prague 6, Czech Republic.

Philip E Mason (PE)

Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, CZ-160 00 Prague 6, Czech Republic.

Daniel Ondo (D)

Department of Physical Chemistry, University of Chemistry and Technology, Prague, Technická 5, CZ-166 28 Prague 6, Czech Republic.

Jan Heyda (J)

Department of Physical Chemistry, University of Chemistry and Technology, Prague, Technická 5, CZ-166 28 Prague 6, Czech Republic.

O H Samuli Ollila (OHS)

Institute of Biotechnology, University of Helsinki, Viikinkaari 5, FI-00790 Helsinki, Finland.
VTT Technical Research Centre of Finland, Tietotie 2, FI-02150 Espoo, Finland.

Pavel Jungwirth (P)

Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, CZ-160 00 Prague 6, Czech Republic.

Matti Javanainen (M)

Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, CZ-160 00 Prague 6, Czech Republic.
Institute of Biotechnology, University of Helsinki, Viikinkaari 5, FI-00790 Helsinki, Finland.

Hector Martinez-Seara (H)

Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, CZ-160 00 Prague 6, Czech Republic.

Classifications MeSH