Polarizable AMOEBA Model for Simulating Mg²⁺·Protein·Nucleotide Complexes.

ABSTRACT: Molecular mechanics (MM) simulations have the potential to provide detailed insights into the mechanisms of enzymes that utilize nucleotides as cofactors. In most cases, the activities of these enzymes also require the binding of divalent cations to catalytic sites. However, modeling divalent cations in MM simulations has been challenging. The inclusion of explicit polarization was considered promising, but despite improvements over nonpolarizable force fields and despite the inclusion of "Nonbonded-fix (NB-fix)" corrections, errors in interaction energies of divalent cations with proteins remain large. Importantly, the application of these models fails to reproduce the experimental structural data on Mg²⁺·Protein·ATP complexes. Focusing on these complexes, here we provide a sys

SUBMITTER: Delgado JM 

PROVIDER: S-EPMC11345861 | biostudies-literature | 2024 Jan

REPOSITORIES: biostudies-literature