Treatment of flexibility of protein backbone in simulations of protein-ligand interactions using steered molecular dynamics.

ABSTRACT: To ensure that an external force can break the interaction between a protein and a ligand, the steered molecular dynamics simulation requires a harmonic restrained potential applied to the protein backbone. A usual practice is that all or a certain number of protein's heavy atoms or Cα atoms are fixed, being restrained by a small force. This present study reveals that while fixing both either all heavy atoms and or all Cα atoms is not a good approach, while fixing a too small number of few atoms sometimes cannot prevent the protein from rotating under the influence of the bulk water layer, and the pulled molecule may smack into the wall of the active site. We found that restraining the Cα atoms under certain conditions is more relevant. Thus, we would propose an alternative solution in whi

SUBMITTER: Truong DT 

PROVIDER: S-EPMC11076533 | biostudies-literature | 2024 May

REPOSITORIES: biostudies-literature