Molecular motions and conformational changes of HPPK. Proteins

ABSTRACT 6-Hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) belongs to a class of catalytic enzymes involved in phosphoryl transfer and is a new target for the development of novel antimicrobial agents. In the present study, the fun-damental consideration is to view the overall struc-ture of HPPK as a network of interacting residues and to extract the most cooperative collective mo-tions that define its global dynamics. A coarse-grainedmodel, harmonically constrained according to HPPK’s crystal structure is used. Four crystal structures of HPPK (one apo and three holo forms with different nucleotide and pterin analogs) are studiedwith the goal of providing insights about the function-dynamic correlation and ligand induced conformational changes. The dynamic differences are examined between HPPK’s apo- and holo-forms, because they are involved in the catalytic reaction steps. Our results indicate that the palm-like struc-ture of HPPK is nearly rigid, whereas the two flexible loops: L2 (residues 43–53) and L3 (residues 82–92) exhibit themost concertedmotions for ligand recognition and presumably, catalysis. These two flexible loops are involved in the recognition of HPPKs nucleotide and pterin ligands, whereas the rigid palm region is associatedwith binding of these cognate ligands. Six domains of collective motions are identified, comprised of structurally close but not necessarily sequential residues. Two of these domains correspond to the flexible loops (L2 and L3), whereas the remaining domains correspond to the rigid part of themolecule. Proteins 2002;49:191–205