Dynamics of Ca2 -saturated calmodulin D129N mutant studied by multiple molecular dynamics simulations

Abstract

Fifteen independent 1-nsec MD simulations of fully solvated Ca 2+ saturated calmodulin (CaM) mutant D129N were performed from different initial conditions to provide a sufficient statistical basis to gauge the significance of observed dynamical properties. In all MD simulations the four Ca2+ ions remained in their binding sites, and retained a single water ligand as observed in the crystal structure. The coordination of Ca2+ ions in EF-hands I, II, and III was sevenfold. In EF-hand IV, which was perturbed by the mutation of a highly conserved Asp129, an anomalous eightfold Ca2+ coordination was observed. The Ca2+ binding loop in EF-hand II was observed to dynamically sample conformations rel..