Paper Citing NAMD - Abstract
Likic, V.A.; Strehler, E.E.; Gooley, P.R.
Dynamics of Ca2+-saturated calmodulin D129N mutant studied by multiple molecular dynamics simulations
PROTEIN SCIENCE, 12:2215-2229, OCT 2003
Fifteen independent 1-nsec MD simulations of fully solvated Ca2+ 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 related to the Ca2+-free form. Repeated MD simulations implicate two well-defined conformations of Ca2+ binding loop II, whereas similar effect was not observed for loops I, III, and IV. In 8 out of 15 MD simulations Ca2+ binding loop II adopted an alternative conformation in which the Thr62 >C = 0 group was displaced from the Ca2+ coordination by a water molecule, resulting in the Ca2+ ion ligated by two water molecules. The alternative conformation of the Ca2+ binding loop II appears related to the "closed" state involved in conformational exchange previously detected by NMR in the N-terminal domain fragment of CaM and the C-terminal domain fragment of the mutant E140Q. MD simulations suggest that conformations involved in microsecond exchange exist partially preformed on the nanosecond time scale.
