PHYTOCHROME STRUCTURE - A NEW METHODOLOGICAL APPROACH

Higher plants use the protein phytochrome as a photosensor. In physiol ogical temperatures phytochrome exists in two forms: Pr and Pfr. The c hromophore of phytochrome is an open-chain tetrapyrrole. On the pathwa y from Pr to Pfr four intermediates (Lumi-R, Meta-Ra, Meta-Rb, and Met a-Rc) can be distinguished, while only two (Lumi-F and Meta-F) can be seen on the way back from Pfr to Pr. We have used the x-ray structure of the C-Phycocyanin protein Fremyella diplosiphon bacteria as a templ ate to build a model (similar to 200 atoms) that includes only the chr omophore and five amino acids of the phytochrome (Arg316-Cys321-His322 -Leu323-Gln324) around it. Using the existing experimental evidences, we have proposed a three-dimensional (3D) structure for Pr, Pfr, and i ntermediates and a mechanism for the photoisomerization as well. Struc tures were fully optimized using AM1 (Unichem package on a Gray J90-NA CAD). Using the INDO/S method of Zerner and co-workers, we calculated the absorption spectra of the model compounds and compared them with t he experimental data. The oscillator strength ratio is an indicator of the chomophore conformation in biliproteins. The calculated spectra r eproduces well the spectra of the phytochrome (Pr, Pfr, and intermedia tes) except for the lower energy band. This result is attributed to th e small number of amino acids in the models. The calculated ratios (f( VIS)/f(UV) - f(osc) of visible band over f(osc) of UV band and f(2)/f( 1) - f(osc) of second absorption band over f(osc) of first absorption band) for the models match very well the experimental ratios obtained for the phytochrome (Pr, Pfr, and intermediates). This supports the pr oposed mechanism for the photoisomerization process. (C) 1998 John Wil ey & Sons, Inc.