A model for the organization of chlorophyll-protein complex of photosystem II and analysis of its photochemical efficiency and excitation migration.

A model is proposed for the organization of chlorophyll-protein complex in photosystem II (PS II) of higher plants. The rates of exciton migration and exciton trapping have been computed using stochastic method to find out the photochemical efficiency of the dimeric PS II. Three dimeric PS II units are assumed to form a group, as transfer of the exciton to the light harvesting bed of the nearest neighbour on either side may only be effective. A relationship has been deduced between the fractions of the reaction centre traps closed and the number of jumps (J) required by the exciton for trapping. The photochemical efficiency and fluorescence quantum yield are computed using J as the parameter in an empirical equation.

Modelling a binuclear metal binding site in the photosynthetic reaction centre II.

Based on the experimental data and homologous sites in Protein Data Bank (PDB) a model for metal binding sites in D1/D2 heterodimer has been proposed. On searching for tetranuclear and binuclear Mn binding sites in the PDB, a suitable sequence homology in thermolysin and D1 could be observed. From the homology and site-directed mutagenesis data, a model for binuclear Mn-Ca or Mn-Mn has been built and it is extended to a tetranuclear Mn centre.

Prediction of structure of antenna proteins of photosystem II.

Membrane spanning regions of 43 kDa and 47 kDa antenna proteins of photosystem II of thylakoid membranes are theoretically predicted. Prediction of topology of chlorophyll-a and beta-carotene molecules in the proteins and interaction of the proteins with 33 kDa extrinsic protein on the lumenal side of thylakoid membrane is based on the findings reported earlier. Each antenna protein is predicted to have six transmembrane alpha-helices with twelve chlorophyll-a and five beta-carotene molecules binding to it. Both N- and C- terminal ends are proposed to be on the stromal side of thylakoid membrane. The proposed structural model conforms to the reported experimental results from the literature.

Prediction of structure and organisation of chlorophyll a/b binding polypeptides in PS I and II.

Secondary structures, functionally important residues, antigenic sites, membrane spanning segments and hydropathicity of light harvesting chlorophyll a/b binding polypeptides (LHC) are predicted by theoretical methods from the amino acid sequence of the polypeptides. The reported structural features of the Pea LHC (Lhcb 1 gene product) from electron crystallographic studies have been compared by alignment with other types of chlorophyll a/b binding polypeptides for structural prediction. Fifteen conserved residues D85, D89, E113, H116, E/Q133, E/Q181, E189, D/N233, E252, N/H255, Q/E269, E/D/Q280, N281, H285, D288 (number indicates position in the aligned sequence), are identified which are potential ligands to Mg2+ of chlorophylls. Three amino acid residues D89, E/Q131 and D/N 233 are proposed as ligands to chlorophylls b2, a7 and b2 respectively, for which ligands are not identified in electron crystallographic study.