MODELING OF THE D1 D2 PROTEINS AND COFACTORS OF THE PHOTOSYSTEM-II REACTION-CENTER - IMPLICATIONS FOR HERBICIDE AND BICARBONATE BINDING/

A three-dimensional model of the photosystem IT (PSII) reaction center from the cyanobacterium Synechocystis sp. PCC 6803 was generated base d on homology with the anoxygenic purple bacterial photosynthetic reac tion centers of Rhodobacter sphaeroides and Rhodopseudomonas viridis, for which the X-ray crystallographic structures are available. The mod el was constructed with an alignment of D1 and D2 sequences with the L and M subunits of the bacterial reaction center, respectively, and by using as a scaffold the structurally conserved regions (SCRs) from ba cterial templates. The structurally variant regions were built using a novel sequence-specific approach of searching for the best-matched pr otein segments in the Protein Data Bank with the ''basic local alignme nt starch tool'' (Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ, 1990, J Mol Biol 215:403-410), and imposing the matching conformationa l preference on the corresponding D1 and D2 regions. The structure thu s obtained was refined by energy minimization. The modeled D1 and D2 p roteins contain five transmembrane alpha-helices each, with cofactors (4 chlorophylls, 2 pheophytins, 2 plastoquinones, and a non-heme iron) essential for PSII primary photochemistry embedded in them. A beta-ca rotene, considered important for PSII photoprotection, was also includ ed in the model. Four different possible conformations of the primary electron donor P680 chlorophylls were proposed, one based on the homol ogy with the bacterial template and the other three on existing experi mental suggestions in literature. The P680 conformation based on homol ogy was preferred because it has the lowest energy. Redox active tyros ine residues important for P680(+) reduction as well as residues impor tant for PSII cofactor binding were analyzed. Residues involved in int erprotein interactions in the model were also identified. Herbicide 3- (3,4-dichlorophenyl)1,1-dimethylurea (DCMU) was also modeled in the pl astoquinone Q(B) binding niche using the structural information availa ble from a DCMU-binding bacterial reaction center. A bicarbonate anion , known to play a role in PSII, but not in anoxygenic photosynthetic b acteria, was modeled in the non-heme iron site, providing a bidentate ligand to the iron. By modifying the previous hypothesis of Blubaugh a nd Govindjee (1988, Photosyn Res 19:85-128), we modeled a second bicar bonate and a water molecule in the Q(B) Site and we proposed a hypothe sis to explain the mechanism of Q(B) protonation mediated by bicarbona te and water. The bicarbonate, stabilized by D1-R257, donates a proton to Q(B)(2-) through the intermediate of D1-H252; and a water molecule donates another proton to Q(B)(2-). Based on the discovery of a ''wat er transport channel'' in the bacterial reaction center, an analogous channel for transporting water and bicarbonate is proposed in our PSII model. The putative channel appears to be primarily positively charge d near Q(B) and the non-heme iron, in contrast to the polarity distrib ution in the bacterial water transport channel. The constructed model has been found to be consistent with most existing data.