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Optimized Magnesium Force Field Parameters for Biomolecular Simulations with Accurate Solvation, Ion-Binding, and Water-Exchange Properties in SPC/E, TIP3P-fb, TIP4P/2005, TIP4P-Ew, and TIP4P-D
[Image: see text] Magnesium is essential in many vital processes. To correctly describe Mg(2+) in physiological processes by molecular dynamics simulations, accurate force fields are fundamental. Despite the importance, force fields based on the commonly used 12-6 Lennard-Jones potential showed sign...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Chemical Society
2021
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8757469/ https://www.ncbi.nlm.nih.gov/pubmed/34881568 http://dx.doi.org/10.1021/acs.jctc.1c00791 |
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author | Grotz, Kara K. Schwierz, Nadine |
author_facet | Grotz, Kara K. Schwierz, Nadine |
author_sort | Grotz, Kara K. |
collection | PubMed |
description | [Image: see text] Magnesium is essential in many vital processes. To correctly describe Mg(2+) in physiological processes by molecular dynamics simulations, accurate force fields are fundamental. Despite the importance, force fields based on the commonly used 12-6 Lennard-Jones potential showed significant shortcomings. Recently progress was made by an optimization procedure that implicitly accounts for polarizability. The resulting microMg and nanoMg force fields (J. Chem. Theory Comput.2021, 17, 2530–2540) accurately reproduce a broad range of experimental solution properties and the binding affinity to nucleic acids in TIP3P water. Since countless simulation studies rely on available water models and ion force fields, we here extend the optimization and provide Mg(2+) parameters in combination with the SPC/E, TIP3P-fb, TIP4P/2005, TIP4P-Ew, and TIP4P-D water models. For each water model, the Mg(2+) force fields reproduce the solvation free energy, the distance to oxygens in the first hydration shell, the hydration number, the activity coefficient derivative in MgCl(2) solutions, and the binding affinity and distance to the phosphate oxygens on nucleic acids. We present two parameter sets: MicroMg yields water exchange on the microsecond time scale and matches the experimental exchange rate. Depending on the water model, nanoMg yields accelerated water exchange in the range of 10(6) to 10(8) exchanges per second. The nanoMg parameters can be used to enhance the sampling of binding events, to obtain converged distributions of Mg(2+), or to predict ion binding sites in biomolecular simulations. The parameter files are freely available at https://github.com/bio-phys/optimizedMgFFs. |
format | Online Article Text |
id | pubmed-8757469 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | American Chemical Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-87574692022-01-14 Optimized Magnesium Force Field Parameters for Biomolecular Simulations with Accurate Solvation, Ion-Binding, and Water-Exchange Properties in SPC/E, TIP3P-fb, TIP4P/2005, TIP4P-Ew, and TIP4P-D Grotz, Kara K. Schwierz, Nadine J Chem Theory Comput [Image: see text] Magnesium is essential in many vital processes. To correctly describe Mg(2+) in physiological processes by molecular dynamics simulations, accurate force fields are fundamental. Despite the importance, force fields based on the commonly used 12-6 Lennard-Jones potential showed significant shortcomings. Recently progress was made by an optimization procedure that implicitly accounts for polarizability. The resulting microMg and nanoMg force fields (J. Chem. Theory Comput.2021, 17, 2530–2540) accurately reproduce a broad range of experimental solution properties and the binding affinity to nucleic acids in TIP3P water. Since countless simulation studies rely on available water models and ion force fields, we here extend the optimization and provide Mg(2+) parameters in combination with the SPC/E, TIP3P-fb, TIP4P/2005, TIP4P-Ew, and TIP4P-D water models. For each water model, the Mg(2+) force fields reproduce the solvation free energy, the distance to oxygens in the first hydration shell, the hydration number, the activity coefficient derivative in MgCl(2) solutions, and the binding affinity and distance to the phosphate oxygens on nucleic acids. We present two parameter sets: MicroMg yields water exchange on the microsecond time scale and matches the experimental exchange rate. Depending on the water model, nanoMg yields accelerated water exchange in the range of 10(6) to 10(8) exchanges per second. The nanoMg parameters can be used to enhance the sampling of binding events, to obtain converged distributions of Mg(2+), or to predict ion binding sites in biomolecular simulations. The parameter files are freely available at https://github.com/bio-phys/optimizedMgFFs. American Chemical Society 2021-12-09 2022-01-11 /pmc/articles/PMC8757469/ /pubmed/34881568 http://dx.doi.org/10.1021/acs.jctc.1c00791 Text en © 2021 The Authors. Published by American Chemical Society https://creativecommons.org/licenses/by/4.0/Permits the broadest form of re-use including for commercial purposes, provided that author attribution and integrity are maintained (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Grotz, Kara K. Schwierz, Nadine Optimized Magnesium Force Field Parameters for Biomolecular Simulations with Accurate Solvation, Ion-Binding, and Water-Exchange Properties in SPC/E, TIP3P-fb, TIP4P/2005, TIP4P-Ew, and TIP4P-D |
title | Optimized Magnesium Force Field Parameters for Biomolecular
Simulations with Accurate Solvation, Ion-Binding, and Water-Exchange
Properties in SPC/E, TIP3P-fb, TIP4P/2005, TIP4P-Ew, and TIP4P-D |
title_full | Optimized Magnesium Force Field Parameters for Biomolecular
Simulations with Accurate Solvation, Ion-Binding, and Water-Exchange
Properties in SPC/E, TIP3P-fb, TIP4P/2005, TIP4P-Ew, and TIP4P-D |
title_fullStr | Optimized Magnesium Force Field Parameters for Biomolecular
Simulations with Accurate Solvation, Ion-Binding, and Water-Exchange
Properties in SPC/E, TIP3P-fb, TIP4P/2005, TIP4P-Ew, and TIP4P-D |
title_full_unstemmed | Optimized Magnesium Force Field Parameters for Biomolecular
Simulations with Accurate Solvation, Ion-Binding, and Water-Exchange
Properties in SPC/E, TIP3P-fb, TIP4P/2005, TIP4P-Ew, and TIP4P-D |
title_short | Optimized Magnesium Force Field Parameters for Biomolecular
Simulations with Accurate Solvation, Ion-Binding, and Water-Exchange
Properties in SPC/E, TIP3P-fb, TIP4P/2005, TIP4P-Ew, and TIP4P-D |
title_sort | optimized magnesium force field parameters for biomolecular
simulations with accurate solvation, ion-binding, and water-exchange
properties in spc/e, tip3p-fb, tip4p/2005, tip4p-ew, and tip4p-d |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8757469/ https://www.ncbi.nlm.nih.gov/pubmed/34881568 http://dx.doi.org/10.1021/acs.jctc.1c00791 |
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