FTIR study of the photoinduced processes of plant phytochrome phyA using isotope-labeled bilins and density functional theory calculations

Abstract

Fourier transform infrared spectroscopy was used to analyze the chromophore structure in the parent states Pr and Pfr of plant phytochrome phyA and the respective photoproducts lumi-R and lumi-F. The spectra were obtained from phyA adducts assembled with either uniformly or selectively isotope-labeled phytochromobilin and phycocyanobilin. The interpretation of the experimental spectra is based on the spectra of chromophore models calculated by density functional theory. Global (13)C-labeling of the tetrapyrrole allows for the discrimination between chromophore and protein bands in the Fourier transform infrared difference spectra. All infrared difference spectra display a prominent difference band attributable to a stretching mode with large contributions from the methine bridge between the inner pyrrole rings (B-C stretching). Due to mode coupling, frequencies and isotopic shifts of this mode suggest that the Pr chromophore may adopt a distorted ZZZssa or ZZZasa geometry with a twisted A-B methine bridge. The transition to lumi-R is associated with only minor changes of the amide I bands indicating limited protein structural changes during the isomerization site of the C-D methine bridge. Major protein structural changes occur upon the transition to Pfr in which the chromophore adopts a ZZEssa or ZZEasa-like state. In addition, specific interactions with the protein alter the structure of the B-C methine bridge as concluded from the substantial downshift of the respective stretching mode. These interactions are removed during the photoreaction to lumi-F (ZZE-->ZZZ), which involves only small protein structural changes.

FIGURE 1

Structure of phytochromobilin (PΦB; R = vinyl) and phycocyanobilin (PCB; R = ethyl). Positions for ¹³C labeling are at C(5) and C(10). ¹⁵N labeling has been uniformly carried out at all nitrogens. In the text the individual methine bridges are denoted by A-B, B-C, and C-D.

FIGURE 2

Comparison of FTIR difference spectra of phyA reconstituted with nonlabeled PΦB and phyA reconstituted with uniformly ¹³C-labeled PΦB. The spectra of the adducts with nonlabeled and labeled PΦB are given by the gray and black lines, respectively. The spectra (from top to bottom) refer to the “Pfr” minus “Pr” (A), “lumi-R” minus “Pr” (B), and “lumi-F” minus “Pfr” (C) differences. Protein changes are denoted by an asterisk. Further details are given in the text (Materials and Methods).

FIGURE 3

Comparison of FTIR difference spectra of phyA reconstituted with nonlabeled PΦB and phyA reconstituted with ¹³C(10)-labeled PΦB. The spectra of the adducts with nonlabeled and labeled PΦB are given by the gray and black lines, respectively. The spectra (from top to bottom) refer to the “Pfr” minus “Pr” (A), “lumi-R” minus “Pr” (B), and “lumi-F” minus “Pfr” (C) differences. Protein changes are denoted by an asterisk. Further details are given in the text (Materials and Methods).

FIGURE 4

Comparison of FTIR difference spectra of phyA reconstituted with nonlabeled PΦB and phyA reconstituted with uniformly ¹³C(5)-labeled PCB. The spectra of the adducts with nonlabeled and labeled PΦB are given by the gray and black lines, respectively. The spectra (from top to bottom) refer to the “Pfr” minus “Pr” (A), “lumi-R” minus “Pr” (B), and “lumi-F” minus “Pfr” (C) differences. Protein changes are denoted by an asterisk. Further details are given in the text (Materials and Methods).

FIGURE 5

Comparison of FTIR difference spectra of phyA reconstituted with nonlabeled PΦB and phyA reconstituted with uniformly ¹⁵N-labeled PCB. The spectra of the adducts with nonlabeled and labeled PΦB are given by the gray and black lines, respectively. The spectra (from top to bottom) refer to the “Pfr” minus “Pr” (A), “lumi-R” minus “Pr” (B), and “lumi-F” minus “Pfr” (C) differences. Protein changes are denoted by an asterisk. Further details are given in the text (Materials and Methods).

FIGURE 6

Comparison of FTIR difference spectra of phyA reconstituted with nonlabeled PΦB and phyA reconstituted with PΦB in H₂O (gray) and D₂O (black). The spectra (from top to bottom) refer to the “Pfr” minus “Pr” (A), “lumi-R” minus “Pr” (B), and “lumi-F” minus “Pfr” (C) differences. Protein changes are denoted by an asterisk. Further details are given in the text (Materials and Methods).