Collective motions in proteins: A covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations
Article first published online: 3 FEB 2004
Copyright © 1991 Wiley-Liss, Inc.
Proteins: Structure, Function, and Bioinformatics
Volume 11, Issue 3, pages 205–217, November 1991
How to Cite
Ichiye, T. and Karplus, M. (1991), Collective motions in proteins: A covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations. Proteins, 11: 205–217. doi: 10.1002/prot.340110305
- Issue published online: 3 FEB 2004
- Article first published online: 3 FEB 2004
- Manuscript Received: 14 MAR 1991
- Manuscript Accepted: 14 MAR 1991
- molecular dynamics;
- normal modes;
- collective motions
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.