A Comparison of Bonded and Nonbonded Zinc(II) Force Fields with NMR Data.

ABSTRACT: Classical molecular dynamics (MD) simulations are widely used to inspect the behavior of zinc(II)-proteins at the atomic level, hence the need to properly model the zinc(II) ion and the interaction with its ligands. Different approaches have been developed to represent zinc(II) sites, with the bonded and nonbonded models being the most used. In the present work, we tested the well-known zinc AMBER force field (ZAFF) and a recently developed nonbonded force field (NBFF) to assess how accurately they reproduce the dynamic behavior of zinc(II)-proteins. For this, we selected as benchmark six zinc-fingers. This superfamily is extremely heterogenous in terms of architecture, binding mode, function, and reactivity. From repeated MD simulations, we computed the order parameter (S²) of

SUBMITTER: Bazayeva M 

PROVIDER: S-EPMC10055966 | biostudies-literature | 2023 Mar

REPOSITORIES: biostudies-literature