Collective motions in proteins: A covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations

TLDR

The study presents a method to identify collective motions in proteins using molecular dynamics trajectories or normal mode simulations. It employs covariance analysis of atomic positional fluctuations to detect these motions. Applied to bovine pancreatic trypsin inhibitor, the method revealed that secondary‑structure regions move coherently, that anharmonic effects influence large‑scale motions, and that solvent presence affects long‑range dynamics, with covariance and cross‑correlation matrices showing comparable features across simulations.

Abstract

Abstract A method is described for identifying collective motions in proteins from molecular dynamics trajectories or normal mode simulations. The method makes use of the covariances of atomic positional fluctuations. It is illustrated by an analysis of the bovine pancreatic trypsin inhibitor. Comparison of the covariance and cross‐correlation matrices shows that the relative motions have many similar features in the different simulations. Many regions of the protein, especially regions of secondary structure, move in a correlated manner. Anharmonic effects, which are included in the molecular dynamics simulations but not in the normal analysis, are of some importance in determining the larger scale collective motions, but not the more local fluctuations. Comparisons of molecular dynamics simulations in the present and absence of solvent indicate that the environment is of significance for the long‐range motions.