ChemRxiv
These are preliminary reports that have not been peer-reviewed. They should not be regarded as conclusive, guide clinical practice/health-related behavior, or be reported in news media as established information. For more information, please see our FAQs.
1/1
0/0

Parameterization of Divalent Cations for Coarse-Grained Simulations

preprint
submitted on 21.02.2020 and posted on 24.02.2020 by Florencia Klein, Daniela Cáceres-Rojas, Monica Carrasco, Juan Carlos Tapia, Julio Caballero, Jans Alzate-Morales, Sergio Pantano

Although molecular dynamics simulations allow for the study of interactions among virtually all biomolecular entities, metal ions still pose significant challenges to achieve an accurate structural and dynamical description of many biological assemblies. This is particularly the case for coarse-grained (CG) models. Although the reduced computational cost of CG methods often makes them the technique of choice for the study of large biomolecular systems, the parameterization of metal ions is still very crude or simply not available for the vast majority of CG- force fields. Here, we show that incorporating statistical data retrieved from the Protein Data Bank (PDB) to set specific Lennard-Jones interactions can produce structurally accurate CG molecular dynamics simulations. Using this simple approach, we provide a set of interaction parameters for Calcium, Magnesium, and Zinc ions, which cover more than 80% of the metal-bound structures reported on the PDB. Simulations performed using the SIRAH force field on several proteins and DNA systems show that using the present approach it is possible to obtain non-bonded interaction parameters that obviate the use of topological constraints.

History

Email Address of Submitting Author

fklein@pasteur.edu.uy

Institution

Institut Pasteur de Montevideo

Country

Uruguay

ORCID For Submitting Author

0000-0003-4099-9907

Declaration of Conflict of Interest

No conflict of interest

Exports

Logo branding

Exports