Molecular Dynamics Investigation of Phenolic Oxidative Coupling Protein Hyp-1 Derived from Hypericum perforatum

Molecular dynamics (MD) simulations provide a physics-based approach to understanding protein structure and dynamics. Here, we used this intriguing tool validate the experimental structural model of Hyp-1, pathogenesis-related class 10 (PR-10) from medicinal herb Hypericum perforatum, with potential application in various pharmaceutical therapies. A nanosecond MD simulation using all-atom optimized potentials for liquid (OPLS–AA) force field was performed reveal that atomic displacement parameters (ADPs) underestimate their values calculated simulation. The average factors obtained confirmed some extent relatively high compliance simulated Hyp-1 models. We found, however, many outliers between side-chain conformations within model, which prompted us propose more reasonable energetically preferred rotameric forms. Therefore, may be applicable verification refined, models explanation intricacies.