Comparative Assessment of Water Models in Protein-Glycan Interaction: Insights from Alchemical Free Energy Calculations and Molecular Dynamics Simulations.

ABSTRACT: Accurate computational simulations of protein-glycan dynamics are crucial for a comprehensive understanding of critical biological mechanisms, including host-pathogen interactions, immune system defenses, and intercellular communication. The accuracy of these simulations, including molecular dynamics (MD) simulation and alchemical free energy calculations, critically relies on the appropriate parameters, including the water model, because of the extensive hydrogen bonding with glycan hydroxyl groups. However, a systematic evaluation of water models' accuracy in simulating protein-glycan interaction at the molecular level is still lacking. In this study, we used full atomistic MD simulations and alchemical absolute binding free energy (ABFE) calculations to investigate the performance of fi

SUBMITTER: Li D 

PROVIDER: S-EPMC11684738 | biostudies-literature | 2024 Dec

REPOSITORIES: biostudies-literature