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

J 2024

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

NENCINI, Ricky; Carmelo TEMPRA; Denys BIRIUKOV; Miguel RIOPEDRE-FERNANDEZ; Victor Cruces CHAMORRO et. al.

Základní údaje

Originální název

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

Autoři

Vydání

Journal of Chemical Theory and Computation, American Chemical Society, 2024, 1549-9618

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

30404 Biomaterials

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 5.500

Kód RIV

RIV/00216224:14740/24:00139674

Organizační jednotka

Středoevropský technologický institut

DOI

https://doi.org/10.1021/acs.jctc.4c00743

UT WoS

001300137900001

EID Scopus

2-s2.0-85202480303

Klíčová slova anglicky

molecular dynamics; force field; electrostatic interactions; scaled charges; biomolecules

Štítky

rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 4. 3. 2025 10:10, Mgr. Eva Dubská

Anotace

V originále

prosECCo75 is an optimized force field effectively incorporating electronic polarization via charge scaling. It aims to enhance the accuracy of nominally nonpolarizable molecular dynamics (MD) 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 physical 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.

Návaznosti

GA24-11274S, projekt VaV

Název: Přizpůsobení povlaků polymerních implantátů proti uchycení bakterií: přístup založený na znalostech

Investor: Grantová agentura ČR, Přizpůsobení povlaků polymerních implantátů proti uchycení bakterií: přístup založený na znalostech

Citovat

NENCINI, Ricky; Carmelo TEMPRA; Denys BIRIUKOV; Miguel RIOPEDRE-FERNANDEZ; Victor Cruces CHAMORRO; Jakub POLÁK; Philip E. MASON; Daniel ONDO; Jan HEYDA; O. H. Samuli OLLILA; Pavel JUNGWIRTH; Matti JAVANAINEN a Hector MARTINEZ-SEARA. Effective Inclusion of Electronic Polarization Improves the Description of Electrostatic Interactions: The prosECCo75 Biomolecular Force Field. Journal of Chemical Theory and Computation. American Chemical Society, 2024, roč. 20, č. 17, s. 7546-7559. ISSN 1549-9618. Dostupné z: https://doi.org/10.1021/acs.jctc.4c00743.

@article{2465572,
   author = {Nencini, Ricky and Tempra, Carmelo and Biriukov, Denys and RiopedreandFernandez, Miguel and Chamorro, Victor Cruces and Polák, Jakub and Mason, Philip E. and Ondo, Daniel and Heyda, Jan and Ollila, O. H. Samuli and Jungwirth, Pavel and Javanainen, Matti and MartinezandSeara, Hector},
   article_number = {17},
   doi = {https://doi.org/10.1021/acs.jctc.4c00743},
   keywords = {molecular dynamics; force field; electrostatic interactions; scaled charges; biomolecules},
   language = {eng},
   issn = {1549-9618},
   journal = {Journal of Chemical Theory and Computation},
   title = {Effective Inclusion of Electronic Polarization Improves the Description of Electrostatic Interactions: The prosECCo75 Biomolecular Force Field},
   url = {https://pubs.acs.org/doi/10.1021/acs.jctc.4c00743},
   volume = {20},
   year = {2024}
}

TY  - JOUR
ID  - 2465572
AU  - Nencini, Ricky - Tempra, Carmelo - Biriukov, Denys - Riopedre-Fernandez, Miguel - Chamorro, Victor Cruces - Polák, Jakub - Mason, Philip E. - Ondo, Daniel - Heyda, Jan - Ollila, O. H. Samuli - Jungwirth, Pavel - Javanainen, Matti - Martinez-Seara, Hector
PY  - 2024
TI  - Effective Inclusion of Electronic Polarization Improves the Description of Electrostatic Interactions: The prosECCo75 Biomolecular Force Field
JF  - Journal of Chemical Theory and Computation
VL  - 20
IS  - 17
SP  - 7546-7559
EP  - 7546-7559
PB  - American Chemical Society
SN  - 15499618
KW  - molecular dynamics
KW  - force field
KW  - electrostatic interactions
KW  - scaled charges
KW  - biomolecules
UR  - https://pubs.acs.org/doi/10.1021/acs.jctc.4c00743
N2  - prosECCo75 is an optimized force field effectively incorporating electronic polarization via charge scaling. It aims to enhance the accuracy of nominally nonpolarizable molecular dynamics (MD) 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 physical 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.
ER  -

NENCINI, Ricky; Carmelo TEMPRA; Denys BIRIUKOV; Miguel RIOPEDRE-FERNANDEZ; Victor Cruces CHAMORRO; Jakub POLÁK; Philip E. MASON; Daniel ONDO; Jan HEYDA; O. H. Samuli OLLILA; Pavel JUNGWIRTH; Matti JAVANAINEN a Hector MARTINEZ-SEARA. Effective Inclusion of Electronic Polarization Improves the Description of Electrostatic Interactions: The prosECCo75 Biomolecular Force Field. \textit{Journal of Chemical Theory and Computation}. American Chemical Society, 2024, roč.~20, č.~17, s.~7546-7559. ISSN~1549-9618. Dostupné z: https://doi.org/10.1021/acs.jctc.4c00743.

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