Chelator-Based Parameterization of the 12-6-4 Lennard-Jones Molecular Mechanics Potential for More Realistic Metal Ion-Protein Interactions.

ABSTRACT: Metal ions are associated with a variety of proteins and play critical roles in a wide range of biochemical processes. There are multiple ways to study and quantify protein-metal ion interactions, including molecular dynamics simulations. Recently, the AMBER molecular mechanics forcefield was modified to include a 12-6-4 Lennard-Jones potential, which allows for a better description of nonbonded terms through the additional pairwise C_ij coefficients. Here, we demonstrate a method of generating C_ij parameters that allows parametrization of specific metal ion-ligating groups in order to tune binding energies computed by thermodynamic integration. The new C_ij coefficients were tested on a series of chelators: ethylenediaminetetraacetic aci

SUBMITTER: Kantakevicius P 

PROVIDER: S-EPMC9171819 | biostudies-literature | 2022 Apr

REPOSITORIES: biostudies-literature