A molecular dynamics study of glutathione reductase

Abstract

A 200 ps molecular dynamics trajectory for the 8634 atoms corresponding to the enzyme glutathione reductase were calculated with the GROMOS program. This enzyme is formed by two identical subunits, with 478 residues and a flavinadenine dinucleotide (FAD) molecule each. Four regions are well distinguished in its crystallographic structure, the dimer interface, the FAD binding site, the active site and the crystal contact region. The analysis shows an equilibrated trajectory after 40 ps. The r.m.s. difference between the X-ray structure and the conformation along the simulation is 2.4 Å when considering the r.m.s. of the whole molecule. The structure is locally well conserved. Values of r.m.s. lower than 2.0 Å are found for all regions, with the exception of the crystal contact region. The results give evidence of a fairly stable fold, especially for the catalytically active regions even in the absence of explicit solvent collisions.