title: Structure of the biliverdin cofactor in the Pfr state of bathy and prototypical phytochromes.
abstract: Phytochromes act as photoswitches between the red- and far-red absorbing parent states of phytochromes (Pr and Pfr). Plant phytochromes display an additional thermal conversion route from the physiologically active Pfr to Pr. The same reaction pattern is found in prototypical biliverdin-binding bacteriophytochromes in contrast to the reverse thermal transformation in bathy bacteriophytochromes. However, the molecular origin of the different thermal stabilities of the Pfr states in prototypical and bathy bacteriophytochromes is not known. We analyzed the structures of the chromophore binding pockets in the Pfr states of various bathy and prototypical biliverdin-binding phytochromes using a combined spectroscopic-theoretical approach. For the Pfr state of the bathy phytochrome from Pseudomonas aeruginosa, the very good agreement between calculated and experimental Raman spectra of the biliverdin cofactor is in line with important conclusions of previous crystallographic analyses, particularly the ZZEssa configuration of the chromophore and its mode of covalent attachment to the protein. The highly homogeneous chromophore conformation seems to be a unique property of the Pfr states of bathy phytochromes. This is in sharp contrast to the Pfr states of prototypical phytochromes that display conformational equilibria between two sub-states exhibiting small structural differences at the terminal methine bridges A-B and C-D. These differences may mainly root in the interactions of the cofactor with the highly conserved Asp-194 that occur via its carboxylate function in bathy phytochromes. The weaker interactions via the carbonyl function in prototypical phytochromes may lead to a higher structural flexibility of the chromophore pocket opening a reaction channel for the thermal (ZZE → ZZZ) Pfr to Pr back-conversion.
authors.affiliation: Institut für Chemie, Technische Universität Berlin, Sekr. PC 14, Strasse des 17. Juni 135, D-10623 Berlin, Germany.
authors.forename: Johannes
authors.initials: J
authors.lastname: Salewski
authors.affiliation: Institut für Chemie, Technische Universität Berlin, Sekr. PC 14, Strasse des 17. Juni 135, D-10623 Berlin, Germany.
authors.forename: Francisco Velazquez
authors.initials: FV
authors.lastname: Escobar
authors.affiliation: Institut für Chemie, Technische Universität Berlin, Sekr. PC 14, Strasse des 17. Juni 135, D-10623 Berlin, Germany.
authors.forename: Steve
authors.initials: S
authors.lastname: Kaminski
authors.affiliation: Institut für Chemie, Technische Universität Berlin, Sekr. PC 14, Strasse des 17. Juni 135, D-10623 Berlin, Germany; Structural Biology Group, European Synchrotron Radiation Facility, 38043 Grenoble, France.
authors.forename: David
authors.initials: D
authors.lastname: von Stetten
authors.affiliation: Institut für Chemie, Technische Universität Berlin, Sekr. PC 14, Strasse des 17. Juni 135, D-10623 Berlin, Germany.
authors.forename: Anke
authors.initials: A
authors.lastname: Keidel
authors.affiliation: Institut für Chemie, Technische Universität Berlin, Sekr. PC 14, Strasse des 17. Juni 135, D-10623 Berlin, Germany.
authors.forename: Yvonne
authors.initials: Y
authors.lastname: Rippers
authors.affiliation: Institut für Chemie, Technische Universität Berlin, Sekr. PC 14, Strasse des 17. Juni 135, D-10623 Berlin, Germany.
authors.forename: Norbert
authors.initials: N
authors.lastname: Michael
authors.affiliation: Institute of Medical Physics and Biophysics (CCO), D-10117 Berlin, Germany; AG Protein X-ray Crystallography, D-10117 Berlin, Germany.
authors.forename: Patrick
authors.initials: P
authors.lastname: Scheerer
authors.affiliation: Institute of Medical Physics and Biophysics (CCO), D-10117 Berlin, Germany; AG Spectroscopy, Charité-University Medicine Berlin, Charitéplatz 1, D-10117 Berlin, Germany.
authors.forename: Patrick
authors.initials: P
authors.lastname: Piwowarski
authors.affiliation: Institute of Medical Physics and Biophysics (CCO), D-10117 Berlin, Germany; AG Spectroscopy, Charité-University Medicine Berlin, Charitéplatz 1, D-10117 Berlin, Germany.
authors.forename: Franz
authors.initials: F
authors.lastname: Bartl
authors.affiliation: AG Physiologie der Mikroorganismen, Ruhr-Universität Bochum, Universitätsstrasse 150, D-44780 Bochum, Germany.
authors.forename: Nicole
authors.initials: N
authors.lastname: Frankenberg-Dinkel
authors.affiliation: Max-Planck-Institut für Chemische Energiekonversion, Stiftstrasse 34-36, D-45470 Mülheim, Germany.
authors.forename: Simone
authors.initials: S
authors.lastname: Ringsdorf
authors.affiliation: Max-Planck-Institut für Chemische Energiekonversion, Stiftstrasse 34-36, D-45470 Mülheim, Germany.
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Gärtner
authors.affiliation: Institut für Allgemeine Botanik, Karlsruher Institut für Technologie, Kaiserstrasse 2, D-76131 Karlsruhe, Germany.
authors.forename: Tilman
authors.initials: T
authors.lastname: Lamparter
authors.affiliation: Institut für Chemie, Technische Universität Berlin, Sekr. PC 14, Strasse des 17. Juni 135, D-10623 Berlin, Germany. Electronic address: andrea.mroginski@tu-berlin.de.
authors.forename: Maria Andrea
authors.initials: MA
authors.lastname: Mroginski
authors.affiliation: Institut für Chemie, Technische Universität Berlin, Sekr. PC 14, Strasse des 17. Juni 135, D-10623 Berlin, Germany. Electronic address: Hildebrandt@tu-berlin.de.
authors.forename: Peter
authors.initials: P
authors.lastname: Hildebrandt
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry*; D001665:Binding Sites; D010834:Phytochrome / Q000737:chemistry*; D011550:Pseudomonas aeruginosa / Q000737:chemistry*
chemical_list: D001426:Bacterial Proteins; D010834:Phytochrome
keywords: Computer Modeling; Infrared Spectroscopy; Photoreceptors; Phytochrome; QM/MM Calculations; Raman Spectroscopy; Resonance Raman; Spectroscopy