SEARCH

SEARCH BY CITATION

Keywords:

  • molecular dynamics;
  • isotropic reorientational eigenmode dynamics;
  • iRED;
  • villin headpiece subdomain;
  • NMR relaxation;
  • Lipari-Szabo model-free

Abstract

The separability between overall and internal motions is evaluated over multiple folding trajectories of the villin headpiece subdomain. The analysis, which relies on the Prompers-Brüschweiler separability index, offers a potentially useful perspective on protein folding. The protein is considered folded in this study, not when it reaches some static target, but rather when it tumbles as a dynamically constrained object. The analysis also demonstrates how the separability index, when applied to protein folding simulations, can facilitate the analysis of NMR relaxation data. Proteins 2012;. © 2012 Wiley Periodicals, Inc.