Principal components analysis filters functionally significant peroxidase motions

Abstract

Molecular dynamics simulation of explicitly solvated horseradish peroxidase and of its Ca-depleted form have been carried out, and the trajectories have been analyzed by the essential dynamics method. The results indicate that the motion of the native species is defined by a few preferred directions identified by the first four eigenvectors. The eigenvectors are significantly sampled and reveal that collective motions are perturbed in the absence of calcium. The destabilization of HRP and the corresponding decrease in the catalytic activity of the enzyme is due to perturbed collective motions primarily in the region located around the proximal calcium site.