Molecular Dynamics Simulations on the Coenzyme Thiamin Diphosphate in Apoenzyme Environment

Thiamin diphosphate (ThDP) is an essential cofactor for a number of enzymes, and especially involved in the nonoxidative decarboxylation of α-keto acids by pyruvate decarboxylase (PDC). Recently the crystal structure of PDC bound ThDP has been determined. Based on these X-ray data MD simulations of the isolated coenzyme as well as of ThDP in its enzymatic environment were performed, using the GROMOS87 software package. For the ThDP-apoenzyme modelling all significant amino acid residues with a cut-off radius less than 8.5 A from the cofactor were taken into account. Because the activity of the coenzyme mainly depends on the formation of a specific structure, the conformational behavior of ThDP and enzyme bound ThDP were investigated within the MD simulations in more detail. Therefore, trajectories of significant structural parameters such as the ring torsion angles ΦT and ΦP as well as essential hydrogen bonds were analyzed by our graphics tool. Moreover, Ramachandran-like plots with respect to the torsion angles ΦT and ΦP were used for the illustration of preferred orientations of the two aromatic rings in ThDP. Finally, MD simulations on ThDP analogs with less or none catalytic activity and apoenzyme mutants were included, in order to get hints of conformational effects and significant interactions in relation to cofactor-apoenzyme binding and the catalytic mechanism.