Coupling between energy and residue position fluctuations in native proteins

Abstract

The coupling between energy fluctuations and positional fluctuations in molecular dynamics trajectories of Crambin at 310 K is studied. Coupling with energy fluctuation is evaluated for both atomic positions and residue positions. Couplings show values which fluctuate around the previously proposed theoretical value under harmonic approximation. The magnitude of these correlations is in agreement, on the average, with the harmonic approximation. Additionally coupling between energy fluctuations and atom-atom distance fluctuations are evaluated. This coupling indicates how much each interaction among different atoms/residues is correlated with the protein's total energy fluctuations. Some atom's/residue's interactions have shown outstanding correlation. Moreover coupling of residue fluctuations between different modes is studied. © 2009 IEEE.