Molecular Dynamic Simulation of Malate Dehydrogenase

The activity of cytoplasmic malate dehydrogenase (cMDH)is perturbed by solution crowding. Since specific movements of a surface loop in the region of the enzyme's active site have been implicated in the activity of this enzyme, it seems likely that flexibility of this and other portions of cMDH are important for kinetic activity. Solution crowding might limit that flexibility. We have examined the flexibility and conformational mobility of cMDH using molecular dynamic simulations. The enzyme, in the absence of cofactor and substrate, in the presence of cofactor only, and in the presence of cofactor and substrate, was examined in 100 ps simulations using the AMBER force field. In all simulations the protein was placed in a box of solvent water. The structure of cMDH, crystallized at high ammonium sulfate concentrations in the presence of NAD,was used as the starting structure. The cofactor was removed from the pdb file, the apo enzyme energy_minimized, and the dynamic simulation performed. Cofactor (NADH) was added to the structure that evolved during the molecular dynamics simulation of the apo enzyme. The complex was energy_minimized, and the simulation of the enzyme_cofactor complex performed. A similar process was followed for an enzyme_NADH_oxaloacetate complex. Results show the structure of cMDH changes relative to the crystalline enzyme during simulations. Active site ligand additions cause further perturbations. Flexible areas include the active site and the subunit interface. We gratefully acknowledge the support of the Ohio Supercomputer Center.