A KNOWLEDGE-BASED 3-DIMENSIONAL MODEL OF THE PHOTOSYSTEM-II REACTION-CENTER OF CHLAMYDOMONAS-REINHARDTII

In this Minireview, a comparison of the binding niches of the PS II co factors from several existing models of the PS II reaction center is p rovided. In particular, it discusses a three dimensional model of the Photosystem II (PS II) reaction center including D1, D2 and cytochrome b559 proteins from the green alga Chlamydomonas reinhardtii that was specifically generated for this Minireview. This model is the most com plete to date and includes accessory chlorophyll(z)s, a manganese clus ter, two molecules of beta-carotene and cytochrome b559, all of which are essential components of the PS II reaction center. The modeling of the D1 and D2 proteins was primarily based on homology with the L and M subunits of the anoxygenic purple bacterial photosynthetic reaction centers. The non-homologous loop regions were built using a sequence specific approach by searching for the best-matched protein segments i n the Protein Data Bank, and by imposing the matching conformations on the corresponding D1 and D2 regions. Cytochrome b559 which is in clos e proximity to D1 and D2 was tentatively modeled in alpha/beta conform ation and docked on the Q(B) side of the PS II reaction center accordi ng to experimental suggestions. An alternate docking on the Q(A) side is also shown for comparison. The cofactors in the PS II reaction cent er were modeled either by adopting the structures from the bacterial c ounterparts, when available, with modifications based on existing expe rimental data or by de novo modeling and docking in the most probable positions in the reaction center complex. The specific features of thi s model are the inclusion of the tetramanganese cluster (with calcium and chloride ions) in a open, C-shaped structure modeled within the D1 /D2/cytochrome b559 complex with D1-D170, D1-E189, D1-D342 and D1-A344 as putative ligands; and the modeling of two cis beta-carotenes and t wo accessory chlorophyll(z)s liganded by D1-H118 and D2-H117. We also analyzed residues in the model which may be involved in the D1 and D2 inter-protein interactions, as well as residues which may be involved in putative bicarbonate and water binding and transport.