Spectroscopic investigations of proton transfer processes and hydrogen bonded networks in channelrhodopsins and phytochromes

Principal Investigator: Prof. Dr. Franz Bartl (Charité)

In this project the focus is laid on the spectroscopic investigation of different representatives of channelrhodopsins and phytochromes. The aim is to explore the photochemistry and the protonation dynamics that direct the photocycles and consequently the function of these photoreceptors on a molecular level. The mechanisms of the different representatives of channelrhodopsins and phytochromes investigated in B5 and in other projects of the CRC will be compared in order to reveal differences and similarities and thus generic principles of the reaction pathways within the two classes of photoreceptors.

Publications

2021 - 2024

Fischer, P., Mukherjee, S., Peter, E., Broser, M., Bartl, F.J., and Hegemann, P. (2021). The inner mechanics of rhodopsin guanylyl cyclase during cGMP-formation revealed by real-time FTIR spectroscopy. Elife, 10, e71384. doi: 10.7554/eLife.71384.

Fischer, P., Schiewer, E., Broser, M., Busse, W., Spreen, A., Grosse, M., Hegemann, P., and Bartl, F. (2024). The functionality of the DC pair in a Rhodopsin Guanylyl Cyclase from Catenaria anguillulae. Journal Mol Biol, 168375. Advance online publication. doi: 10.1016/j.jmb.2023.168375.

Merga, G., Lopez, M.F., Fischer, P., Piwowarski, P., Nogacz, Ż., Kraskov, A., Buhrke, D., Escobar, F.V., Michael, N., Siebert, F., Scheerer, P., Bartl, F.J., and Hildebrandt, P. (2021). Light- and temperature-dependent dynamics of chromophore and protein structural changes in bathy phytochrome Agp2. Phys Chem Chem Phys, 23, 33, 18197-18205. doi: 10.1039/d1cp02494a.

Yang, Y., Stensitzki, T., Sauthof, L., Schmidt, A., Piwowarski, P., Velazquez Escobar, F., Michael, N., Nguyen, A.D., Szczepek, M., Brünig, F. N., Netz, R.R., Mroginski, M.A., Adam, S., Bartl, F.J., Schapiro, I., Hildebrandt, P., Scheerer, P., and Heyne, K. (2022). Ultrafast proton-coupled isomerization in the phototransformation of phytochrome. Nat Chem. doi: 10.1038/s41557-022-00944-x.

2017 - 2020

Fudim, R., Szczepek, M., Vierock, J., Vogt, A., Schmidt, A., Kleinau, G., Fischer, P., Bartl, F.J., Scheerer, P., Hegemann, P. (2019). Design of a light-gated proton channel based on the crystal structure of Coccomyxa rhodopsin. Sci Signal. 2019 Mar 19;12(573). pii: eaav4203. doi: 10.1126/scisignal.aav4203

Kaufmann, J.C.D., Krause, B.S., Grimm, C., Ritter, E., Hegemann, P., Bartl, F.J. (2017). Proton transfer reactions in the red light-activatable channelrhodopsin variant ReaChR and their relevance for its function. J Biol Chem. 2017 Aug 25;292(34):14205-14216. doi: 10.1074/jbc.M117.779629.

Kaufmann, J.C.D., Krause B.S., Adam S., Ritter E., Schapiro I., Hegemann P., and Bartl, F.J. (2020). Modulation of Light Energy Transfer from Chromophore to Protein in the Channelrhodopsin ReaChR. Biophysical Journal; doi: 10.1016/j.bpj.2020.06.031

Krause, B.S., Grimm, C., Kaufmann, J.C.D., Schneider, F., Sakmar, T.P., Bartl, F.J., and Hegemann, P. (2017). Complex Photochemistry within the Green-Absorbing Channelrhodopsin ReaChR. Biophysical Journal 112, 1166-1175; doi. 10.1016/j.bpj.2017.02.001

Krause, B. S., Kaufmann, J. C. D., Kuhne,^, J., Vierock, J. T. T., Huber, T., Sakmar, T. P., Gerwert, K., Bartl, F.J., and Hegemann, P. (2019). Tracking pore hydration in channelrhodopsin by site-directed infrared-active azido probes. Biochemistry. Feb 19. doi: 10.1021/acs.biochem.8b01211

Kraskov, A., Nguyen, A.D., Goerling, J., Buhrke, D., Velazquez-Escobar, F., Lopez, M. F., Michael, N. Sauthof, L., Schmidt, A., Piwowarski, P., Yang, Y., Stensitzki, T., Adam, S., Bartl, F.J., Schapiro, I., Heyne, K., Siebert, F., Scheerer, P., Mroginski, M.A., and Hildebrandt, P. (2020). Intramolecular proton transfer controls protein structural changes in phytochrome. Biochemistry 59, 1023-1037; doi: 10.1021/acs.biochem.0c00053

Lopez, M.F., Nguyen, A.D., Velazquez-Escobar, F., González, R., Michael, N., Nogacz, Z., Piwowarski, P., Bartl, F.J., Siebert, F., Heise, I., Scheerer, P., Gärtner, W., Mroginski, M.A, Hildebrandt, P. (2019). Role of the propionic side chain for the photoconversion of bacterial phytochromes. Biochemistry 58, 3504-3519; doi: 10.1021/acs.biochem.9b00526

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

Ritter, E., Puskar, L., Kim, S.Y., Park, J.H., Hofmann, K.P., Bartl, F.J., Hegemann, P., Schade, U. (2019). Féry infrared spectrometer for single shot analysis of protein dynamics. J. Phys. Chem. 10, 7672-7677; doi: 10.1021/acs.jpclett.9b03099

Takiden, A., Velazquez-Escobar, F., Dragelj, J., Woelke, A.L., Knapp E.-W., Piwowarski, P., Bartl, F.J., 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

2013 - 2016

Escobar, F.V., Piwowarski, P., Salewski, J., Michael, N., Fernandez Lopez, M., Rupp, A., Muhammad Qureshi, B., Scheerer, P., Bartl, F.J., 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.]

Kuhne, J., Eisenhauer, K., Ritter, E., Hegemann, P., Gerwert, K., and Bartl, F.J. (2015). Early Formation of the Ion-Conducting Pore in Channelrhodopsin-2. Angewandte Chemie International Edition 54, 4953-4957.

Pyta, K., Przybylski, P., and Bartl, F.J. (2015). Regioselective Long-Range Proton Transfer in New Rifamycin Antibiotics: A Process in which Crown Ethers Act as Stronger Br circle divide nsted Bases than Amines. ChemPhysChem 16, 938-942.

Ritter, E., Piwowarski, P., Hegemann, P., and Bartl, F.J. (2013). Light-dark Adaptation of Channelrhodopsin C128T Mutant. Journal of Biological Chemistry 288, 10451-10458.

Salewski, J., Escobar, F.V., Kaminski, S., von Stetten, D., Keidel, A., Rippers, Y., Michael, N., Scheerer, P., Piwowarski, P., Bartl, F.J., 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.