MODELING THE QUINONE-B BINDING-SITE OF THE PHOTOSYSTEM-II REACTION-CENTER USING NOTIONS OF COMPLEMENTARITY AND CONTACT-SURFACE BETWEEN ATOMS

Functional identity and significant similarities in cofactors and sequence exist between the L and M reaction center proteins of the photosynthetic bacteria and the D1 and D2 photosystem-II reaction center proteins of cyanobacteria, algae, and plants. A model of the quinone (Q(B)) binding site of the D1 protein is presented based upon the resolved structure of the Q(B) binding pocket of the L subunit, and introducing novel quantitative notions of complementarity and contact surface between atoms. This model, built without using traditional methods of molecular mechanics and restricted to residues in direct contact with Q(B), accounts for the experimentally derived functional state of mutants of the D1 protein in the region of Q(B). It predicts the binding of both the classical and phenol-type PSII herbicides and rationalizes the relative levels of tolerance of mutant phenotypes. (C) 1995 Wiley-Liss, Inc.