Your browser doesn't support javascript.
loading
Effective Inclusion of Electronic Polarization Improves the Description of Electrostatic Interactions: The prosECCo75 Biomolecular Force Field.
Nencini, Ricky; Tempra, Carmelo; Biriukov, Denys; Riopedre-Fernandez, Miguel; Cruces Chamorro, Victor; Polák, Jakub; Mason, Philip E; Ondo, Daniel; Heyda, Jan; Ollila, O H Samuli; Jungwirth, Pavel; Javanainen, Matti; Martinez-Seara, Hector.
Afiliación
  • Nencini R; Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, CZ-160 00 Prague 6, Czech Republic.
  • Tempra C; Institute of Biotechnology, University of Helsinki, Viikinkaari 5, FI-00790 Helsinki, Finland.
  • Biriukov D; Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Viikinkaari 5, FI-00790 Helsinki, Finland.
  • Riopedre-Fernandez M; Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, CZ-160 00 Prague 6, Czech Republic.
  • Cruces Chamorro V; Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, CZ-160 00 Prague 6, Czech Republic.
  • Polák J; CEITEC─Central European Institute of Technology, Masaryk University, Kamenice 753/5, CZ-62500 Brno, Czech Republic.
  • Mason PE; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 753/5, CZ-62500 Brno, Czech Republic.
  • Ondo D; Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, CZ-160 00 Prague 6, Czech Republic.
  • Heyda J; Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, CZ-160 00 Prague 6, Czech Republic.
  • Ollila OHS; Department of Physical Chemistry, University of Chemistry and Technology, Prague, Technická 5, CZ-166 28 Prague 6, Czech Republic.
  • Jungwirth P; Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, CZ-160 00 Prague 6, Czech Republic.
  • Javanainen M; Department of Physical Chemistry, University of Chemistry and Technology, Prague, Technická 5, CZ-166 28 Prague 6, Czech Republic.
  • Martinez-Seara H; Department of Physical Chemistry, University of Chemistry and Technology, Prague, Technická 5, CZ-166 28 Prague 6, Czech Republic.
J Chem Theory Comput ; 20(17): 7546-7559, 2024 Sep 10.
Article en En | MEDLINE | ID: mdl-39186899
ABSTRACT
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.
Asunto(s)

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Electricidad Estática / Simulación de Dinámica Molecular Idioma: En Revista: J Chem Theory Comput Año: 2024 Tipo del documento: Article País de afiliación: República Checa Pais de publicación: Estados Unidos

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Electricidad Estática / Simulación de Dinámica Molecular Idioma: En Revista: J Chem Theory Comput Año: 2024 Tipo del documento: Article País de afiliación: República Checa Pais de publicación: Estados Unidos