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Project B6

Award-Winning Poster by Dr. Bilal Qureshi (project B6 / AG Scheerer):  Towards crystal structures of bacterial phytochromes from Agrobacterium tumefaciens (Bad Schandau, 2014)

Award-Winning Poster by Dr. Bilal Qureshi (project B6 / AG Scheerer): Towards crystal structures of bacterial phytochromes from Agrobacterium tumefaciens (Bad Schandau, 2014)

Proton-coupled conformational changes in photoreceptors

Principal Investigators: Prof. Dr. Peter Hildebrandt (TU), Dr. Patrick Scheerer (Charité) 

The project aims at elucidating the role of protonation dynamics in the photoinduced processes of photoreceptors. Using resonance Raman spectroscopy, protein crystallography, free electron laser techniques (pump probe), electron microscopy and protein engineering, the project primarily focuses on bacterial and plant phytochromes to analyse the interplay of structural changes of the cofactor and the protein and transient proton translocations, which eventually lead to the activation or deactivation of the receptor protein. Resonance Raman spectroscopic and protein X-ray crystallography (LCP crystallisation) investigations are further extended to investigate the proton-coupled processes in channelrhodopsin and other microbial rhodopsins.

Publications

2017 - 2020

Buhrke. D., Battocchio, G., Wilkening, S., Blain-Hartung, M., Baumann, T., Schmitt, F. J., Friedrich, F., Mroginski, M. A., Hildebrandt, P. (2020) Red, orange, green: Light- and Temperature-dependent Color Tuning in a Cyanobacteriochrome. Biochemistry 59, 509-519, doi: 10.1021/acs.biochem.9b00931.

Buhrke, D., Gourinchas, G., Müller, M., Michael, N., Hildebrandt, P., Winkler, A. (2020). Distinct chromophore-protein environments enable asymmetric activation of a bacteriophytochrome activated diguanylate cyclase. Journal of Biological Chemistry 295, 539-551. doi: 10.1074/jbc.RA119.011915.

Buhrke, D., Hildebrandt, P. (2020). Probing Structure and Reaction Dynamics of Proteins Using Time-Resolved Resonance Raman Spectroscopy. Chemical Reviews 120, 3577-3630. doi: 10.1021/acs.chemrev.9b00429.

Buhrke, D., Tavraz, N. N., Shcherbakova, D. M., Sauthof, L., Moldenhauer, M., Vélazquez Escobar, F., Verkhusha, V. V., Hildebrandt, P., Friedrich, T. (2019). Chromophore binding to two cysteines increases quantum yield of near-infrared fluorescent proteins. Scientific Reports 9: 1866. doi: 10.1038/s41598-018-38433-2.

Buhrke, D., Kuhlmann, U., Michael, N., and Hildebrandt, P. (2018). The Photoconversion of Phytochrome Includes an Unproductive Shunt Reaction Pathway. ChemPhysChem 19, 566-570; doi: 10.1002/cphc.201701311

Fernandez Lopez, M., Nguyen A. D., Velazquez Escobar, F., González, R., Michael, N., Nogacz, Ż., Piwowarski, P., Bartl, F., Siebert, F., Heise, I., Scheerer, P., Gärtner, W., Mroginski, M. A., Hildebrandt, P. (2019). Role of the Propionic Side Chains for the Photoconversion of Bacterial Phytochromes. Biochemistry 58, 3504-3519. doi: 10.1021/acs.biochem.9b00526

Fudim, R., Szczepek, M., Vierock, J., Vogt, A., Schmidt, A., Kleinau, G., Fischer, P., Bartl, F., Scheerer, P., Hegemann, P. (2019). Design of a light-gated proton channel based on the crystal structure of Coccomyxa rhodopsin. Science Signaling 12, 573. doi: 10.1126/scisignal.aav4203

Kacprzak, S., Njimona, I., Renz, A., Feng, J., Reijerse, E., Lubitz, W., Krauss, N., Scheerer, P., Nagano, S., Lamparter, T., and Weber, S. (2017). Inter-subunit distances in full-length, dimeric, bacterial phytochrome Agp1, as measured by PELDOR between different spin label positions, remain unchanged upon photoconversion. Journal  of Biological Chemistry 292, 7598-7606; doi: 10.1074/jbc.m116.761882

Kielb, P., Utesch, T., Kozuch, J., Jeoung, J.-H., Dobbek, H., Mroginski, M.A., Hildebrandt, P., and Weidinger, I. (2017). Switchable Redox Chemistry of the Hexameric Tyrosine-Coordinated Heme Protein. Journal of Physical Chemistry B 121, 3955-3964; doi: 10.1021/acs.jpcb.7b01286

Kraskow, A., Nguyen, D. A., Buhrke, D., Velasquez Escobar, F., Fernandez Lopez, M., Michael, N., Sauthof, L., Schmidt, A., Piwowarski, P., Yang, Y., Stensitzki, T., Adam, S., Bartl, F., Schapiro, I., Heyne, K., Siebert, F., Scheerer, P., Mroginski, M. A., Hildebrandt, P. (2020) Intramolecular Proton Transfer Controls Protein Structural Changes in Phytochrome. Biochemistry 59, 1023-1037; doi: 10.1021/acs.biochem.0c00053.

Lamparter, T., Krauß, N., and Scheerer, P. (2017). Phytochromes from Agrobacterium fabrum. Photochemistry and Photobiology 93, 642-655; doi: 10.1111/php.12761

Luck, M., Velázquez Escobar, F., Glass, K., Sabotke, M. I., Hagedorn, R., Corellou, F., Siebert, F., Hildebrandt, P.Hegemann, P. (2019). Photoreactions of the histidine kinase rhodopsin Ot-HKR from the marine picoalga Ostreococcus tauri. Biochemistry 58, 1878-1891. doi: 10.1021/acs.biochem.8b01200.

Nagano, S., Guan, K., Shenkutie, S., Feiler, C., Weiss, M. S., Kraskov, A., Buhrke, D., Hildebrandt, P., Hughes, J. (2020). Structural insights into photoactivation and signalling in plant phytochromes. Nature Plants 6, 581-588; doi: 10.1038/s41477-020-0638-y

Oberthuer, D., Knoška, J., Wiedorn, M.O., Beyerlein, K.R., Bushnell, D.A-, Kovaleva, E.G., Heymann, M., Gumprecht, L., Kirian, R.A., Barty, A., Mariani, V., Tolstikova, A., Adriano, L., Awel, S., Barthelmess, M., Dörner, K., Xavier, P.L., Yefanov, O., James, D.R., Nelson, G., Wang, D., Calvey, G., Chen, Y., Schmidt, A., Szczepek, M., Frielingsdorf, S., Lenz, O., Snell, E., Robinson, P.J., Šarler, B., Belšak, G., Maček, M., Wilde, F., Aquila, A., Boutet, S., Liang, M., Hunter, M.S., Scheerer, P., Lipscomb, J.D., Weierstall, U., Kornberg, R.D., Spence, J.C., Pollack, L., Chapman, H.N., and Bajt, S. (2017). Double-flow focused liquid injector for efficient serial femtosecond crystallography. Scientific Reports 7, 44628; doi: 10.1038/srep44628

Oppermann, J., Fischer, P., Silapetere, A., Liepe, B., Rodriguez-Rozada, S., Flores-Uribe, J., Peter, E., Keidel, A., Vierock, J., Kaufmann, J., Broser, M., Luck, M., Bartl, F., Hildebrandt, P., Wiegert, J. S., Béjà, O., Hegemann, P., Wietek, J. (2019). MerMAIDs: a family of metagenomically discovered marine anion-conducting and intensely desensitizing channelrhodopsins. Nature Communications 10: 3315; doi: 10.1038/s41467-019-11322-6

Scheerer, P., Unger, E., and Tian, L. (2018). Protein structures guide the design of a much-needed tool for neuroscience. Nature 561, 312-313; doi: 10.1038/d41586-018-06670-0

Schmidt, A., Sauthof, L., Szczepek, M., Lopez, M., Velázquez, F., Qureshi, B. M., Michael, N., Buhrke, D., Stevens, T., Kwiatkowski, D., von Stetten, D., Mroginski, M. A., Krauß, N., Lamparter, T. , Hildebrandt, P., and Scheerer, P. (2018). Structural snapshot of a bacterial phytochrome in its functional intermediate state. Nature Communications 9, 4912; doi: 10.1038/s41467-018-07392-7

Takiden, A., Velazquez-Escobar, F., Dragelj, J., Woelke, A.L., Knapp E.-W., Piwowarski, P., Bartl, F., Hildebrandt, P., and Mroginski, M.A. (2017). Structural and Vibrational Characterization of the Chromophore Binding Site of Bacterial Phytochrome Agp1. Photochemistry and Photobiology 93, 713-723; doi: 10.1111/php.12737

Velázquez Escobar, F., Buhrke, D., Fernandez Lopez, M., Shenkutie, S.M., von Horsten., S, Essen, L.O., Hughes, J., and Hildebrandt, P. (2017). Structural communication between the chromophore-binding pocket and the N-terminal extension in plant phytochrome phyB. FEBS Letters 591, 1258-1265; doi: 10.1002/1873-3468.12642

Velázquez Escobar, F., Buhrke, D., Michael, N., Sauthof, L., Wilkening, S., Tavraz, N.N., Salewski, J., Frankenberg-Dinkel, N., Mroginski, M.A., Scheerer, P., Friedrich, T., Siebert, F., and Hildebrandt, P. (2017). Common Structural Elements in the Chromophore Binding Pocket of the Pfr State of Bathy Phytochromes. Photochemistry and Photobiology 93, 724-732; doi: 10.1111/php.12742

Velazquez Escobar, F., Kneip, C., Michael, N., Hildebrandt, T., Tavraz, N., Gärtner, W., Hughes, J., Friedrich, T., Scheerer, P., Mroginski, M.A., and Hildebrandt, P. (2020). The Lumi-R Intermediates of Prototypical Phytochromes. Journal of Physical Chemistry B 124, 4044-4055. doi: 10.1021/acs.jpcb.0c01059.

Velazquez Escobar, F., Lang, C., Takiden, A., Schneider, C., Balke, J., Hughes, J., Alexiev, U., Hildebrandt, P., and Mroginski, M.A. (2017). Protonation-Dependent Structural Heterogeneity in the Chromophore Binding Site of Cyanobacterial Phytochrome Cph1. Journal of Physical Chemistry B 121, 47-57; doi: 10.1021/acs.jpcb.6b09600

2013 - 2016

Bruun, S., Stoeppler, D., Keidel, A., Kuhlmann, U., Luck, M., Diehl, A., Geiger, M.-A., Woodmansee, D., Trauner, D., Hegemann, P., Oschkinat, H., Hildebrandt, P., and Stehfest, K. (2015). Light–Dark Adaptation of Channelrhodopsin Involves Photoconversion between the all-trans and 13-cis Retinal Isomers. Biochemistry 54, 5389-5400.

Buhrke, D., Velazquez Escobar, F., Sauthof, L., Wilkening, S., Herder, N., Tavraz, N.N., Willoweit, M., Keidel, A., Utesch, T., Mroginski, M.A., Schmitt, F.J., Hildebrandt, P., and Friedrich, T. (2016). The role of local and remote amino acid substitutions for optimizing fluorescence in bacteriophytochromes: A case study on iRFP. Scientific Reports 6, 28444.

Luck, M., Bruun, S., Keidel, A., Hegemann, P., and Hildebrandt, P. (2015). Photochemical chromophore isomerization in histidine kinase rhodopsin HKR1. FEBS Letters 589, 1067-1071.

Nagano S., Scheerer P., Zubow K., Michael N., Inomata K., Lamparter T., Krauß N. (2016). The Crystal Structures of the N-terminal Photosensory Core Module of Agrobacterium Phytochrome Agp1 as Parallel and Anti-parallel Dimers. Journal of Biological Chemistry 291, 20674-20691.

Otero, L.O., Klinke, S., Rinaldi, J., Velazquez Escobar, F., Mroginski, M.A., Fernandez Lopez, M., Malamud, F., Vojnov, A., Hildebrandt, P., Goldbaum, F.A., and Bonomi, H.R. (2016). Structure of the full-length bacteriophytochrome from the plant pathogen Xanthomonas campestris provides clues to its long-range signaling mechanism. Journal of Molecular Biology 428, 3702-3720.

Salewski, J., Escobar, F.V., Kaminski, S., von Stetten, D., Keidel, A., Rippers, Y., Michael, N., Scheerer, P., Piwowarski, P., Bartl, F., Frankenberg-Dinkel, N., Ringsdorf, S., Gaertner, W., Lamparter, T., Mroginski, M.A., and Hildebrandt, P. (2013). Structure of the Biliverdin Cofactor in the Pfr State of Bathy and Prototypical Phytochromes. Journal of Biological Chemistry 288, 16800-16814.

Song, C., Velazquez Escobar, F., Xu, X.-L., Narikawa, R., Ikeuchi, M., Siebert, F., Gärtner, W., Matysik, J., and Hildebrandt, P. (2015). A Red/Green Cyanobacteriochrome Sustains Its Color Despite a Change in the Bilin Chromophore’s Protonation State. Biochemistry 54, 5839-5848.

Velazquez Escobar, F., Hildebrandt, T., Utesch, T., Schmitt, F.J., Seuffert, I., Michael, N., Schulz, C., Mroginski, M.A., Friedrich, T., and Hildebrandt, P. (2014). Structural Parameters Controlling the Fluorescence Properties of Phytochromes. Biochemistry 53, 20-29.

Velazquez Escobar, F., Piwowarski, P., Salewski, J., Michael, N., Fernandez Lopez, M., Rupp, A., Muhammad Qureshi, B., Scheerer, P., Bartl, F., Frankenberg-Dinkel, N., Siebert, F., Mroginski, M.A., and Hildebrandt, P. (2015). A protonation-coupled feedback mechanism controls the signalling process in bathy phytochromes. Nature Chemistry 7, 423-430. [Link to news section.]

Velazquez Escobar, F., Utesch, T., Narikawa, R., Ikeuchi, M., Mroginski, M.A., Gaertner, W., and Hildebrandt, P. (2013). Photoconversion Mechanism of the Second GAF Domain of Cyanobacteriochrome AnPixJ and the Cofactor Structure of Its Green-Absorbing State. Biochemistry 52, 4871-4880.

Velazquez Escobar, F., von Stetten, D., Günther-Lütkens, M., Keidel, A., Michael, N., Lamparter, T., Essen, L.-O., Hughes, J., Gärtner, W., Yang, Y., Heyne, K., Mroginski, M.A., and Hildebrandt, P. (2015). Conformational heterogeneity of the Pfr chromophore in plant and cyanobacterial phytochromes. Frontiers in Molecular Biosciences 2, 37.

Zienicke, B., Molina, I., Glenz, R., Singer, P., Ehmer, D., Escobar, F.V., Hildebrandt, P., Diller, R., and Lamparter, T. (2013). Unusual spectral properties of bacteriophytochrome Agp2 result from a deprotonation of the chromophore in the red-absorbing form Pr. Journal of Biological Chemistry 288, 31738-31751.