Higher plants use the protein phytochrome as a photosensor. In physiological temperatures phytochrome exists in two forms: Pr and Pfr. The chromophore of phytochrome is an open-chain tetrapyrrole. On the pathway from Pr to Pfr four Ž . intermediates Lumi-R, Meta-Ra, Meta-Rb, and Meta-Rc can be distinguished, while Ž . 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 Ž . template to build a model ; 200 atoms that includes only the chromophore and five Ž . amino acids of the phytochrome Arg316᎐Cys321᎐His322᎐Leu323᎐Gln324 around it.
Ž . Using the existing experimental evidences, we have proposed a three-dimensional 3D structure for Pr, Pfr, and intermediates and a mechanism for the photoisomerization as Ž well. Structures were fully optimized using AM1 Unichem package on a Cray J90-. NACAD . Using the INDOrS method of Zerner and co-workers, we calculated the absorption spectra of the model compounds and compared them with the experimental data. The oscillator strength ratio is an indicator of the chomophore conformation in Ž biliproteins. The calculated spectra reproduces well the spectra of the phytochrome Pr, . Pfr, and intermediates except for the lower energy band. This result is attributed to the Ž small number of amino acids in the models. The calculated ratios f rf y f of VIS UV osc visible band over f of UV band and f rf y f of second absorption band over f of osc 2 1 osc osc
. first absorption band for the models match very well the experimental ratios obtained Ž . for the phytochrome Pr, Pfr, and intermediates . This supports the proposed mechanism for the photoisomerization process.