Molecular dynamics simulation of bovine pancreatic ribonuclease A-CpA and transition state-like complexes.

ABSTRACT: The mechanisms of enzymes are intimately connected with their overall structure and dynamics in solution. Experimentally, it is considerably challenging to provide detailed atomic level information about the conformational events that occur at different stages along the chemical reaction path. Here, theoretical tools may offer new potential insights that complement those obtained from experiments that may not yield an unambiguous mechanistic interpretation. In this study, we apply molecular dynamics simulations of bovine pancreatic ribonuclease A, an archetype ribonuclease, to study the conformational dynamics, structural relaxation, and differential solvation that occur at discrete stages of the transesterification and cleavage reaction. Simulations were performed with explicit solvation

SUBMITTER: Formoso E 

PROVIDER: S-EPMC2892782 | biostudies-literature | 2010 Jun

REPOSITORIES: biostudies-literature