Large-scale molecular dynamics simulation: Effect of polarization on thrombin-ligand binding energy.

ABSTRACT: Molecular dynamics (MD) simulations lasting 500 ns were performed in explicit water to investigate the effect of polarization on the binding of ligands to human α-thrombin based on the standard nonpolarizable AMBER force field and the quantum-derived polarized protein-specific charge (PPC). The PPC includes the electronic polarization effect of the thrombin-ligand complex, which is absent in the standard force field. A detailed analysis and comparison of the results of the MD simulation with experimental data provided strong evidence that intra-protein, protein-ligand hydrogen bonds and the root-mean-square deviation of backbone atoms were significantly stabilized through electronic polarization. Specifically, two critical hydrogen bonds between thrombin and the ligand were broken at appro

SUBMITTER: Duan LL 

PROVIDER: S-EPMC4979035 | biostudies-literature | 2016 Aug

REPOSITORIES: biostudies-literature