Structure and fluctuations of bacteriophage T4 glutaredoxin modelled by molecular dynamics

A 120 ps molecular dynamics (MD) trajectory for bacteriophage T4 glutaredoxin was calculated including non-inertial solvent effects. The potential energy attains an equilibrated regime after the first 20 ps. The r.m.s. difference of all non-hydrogen atoms between X-ray and average MD structures for the regular secondary structure is 0.99A which shows that the MD simulation reproduces the essentials of the structure with high accuracy. Loop displacements are detected, shown by the larger full structure all non-hydrogen atom r.m.s. difference of 1.2A. The fluctuation pattern derived from MD agrees fairly well with that derived from X-ray isotropic temperature factors. The active site is a stable structural region in this MD modellization. Structural changes are put in context with the protein's function.