Molecular modeling of phytochrome using constitutive C-phycocyanin from Fremyella diplosiphon as a putative...

Phytochrome, the ubiquitous photosensor in green plants, is similar to C-phycocyanin in a number of ways. We have produced a model of the phytochrome chromophore binding pocket based on the X-ray crystal structure of C-phycocyanin from Fremyella diplosiphon [Duerring et al. (1991) J. Mol. Biol. 217, 577-592]. Twenty residues around the chromophore binding site of C-phycocyanin were changed to the corresponding residues of Avena phytochrome A for the modeling. In the minimized model, Arg-318, Ala-319, the methylene of Ser-322, Leu-325, Gln-326, and Tyr-327 (using the numbering of the Avena sequence; Cys-323 is chromophore bound) form a pocket on one side of the chromophore. The other side of the chromophore lacks hydrogen-bond donors and is involved only in van der Waals contact with the chromophore. The overall structure of the model may be described as one peptide segment "anchoring" the chromophore hydrophobically, covalently, and electrostatically from several directions, while the other key peptide segment simply provides a hydrophobic surface for the chromophore to rest against. The red light absorbing (Pr) chromophore of the model is buried more deeply in the binding pocket than the far red light absorbing (Pfr) chromophore. This apparently reflects reduced compatibility of the chromophore with the pocket upon photoisomerization, which requires the insertion of hydrophilic parts of ring D into the hydrophobic core of the protein. This concept is consistent with the experimental evidence that photoisomerization of the Pr chromophore is followed by movement of the chromophore from its binding pocket. In the proposed model, increased exposure of hydrophobic portions of the Pfr chromophore compared to the Pr chromophore is consistent with the red shift observed in the first intermediate of the Pr to Pfr photoconversion. The proposed model may be tested by mutation experiments, thus providing a viable model to foster the current rapid progress of molecular biology in this field.