Proton exchange processes in phytochromes and retinal proteins investigated by MAS NMR

Principal Investigators: Prof. Dr. Hartmut Oschkinat (FMP)

Protonation dynamics associated with structural changes in phytochromes are investigated by very fast magic-angle-spinning (MAS) NMR, detecting exchangeable protons directly. Proton exchange pattern within the chromophore and with residues towards the tongue region between the Pr, Meta-F, and Pfr states of the bacteriophytochromes Agp2 (batho), Agp1 (prototypic), and Cph1 will be analyzed. In this context, the proposal of a keto-enol tautomerism in the biliverdin of Agp2 will be scrutinized including a derivation of kinetic parameters. Furthermore, we will localize exchangeable protons in the channels of channelrhodopsins C1C2 and iC++slow and study their exchange pattern.

Publications

2021 - 2024 (PI Oschkinat)

Bell, D., Lindemann, F., Gerland, L., Aucharova, H., Klein, A., Friedrich, D., Hiller, M., Grohe, K., Meier, T., van Rossum, B., Diehl, A., Hughes, J., Mueller, L.J., Linser, R., Miller, A.F. and Oschkinat, H. (2024). Sedimentation of large, soluble proteins up to 140 kDa for ¹H-detected MAS NMR and ¹³C DNP NMR - practical aspects. J Biomol NMR, 78, 3: 179-192. doi: 10.1007/s10858-024-00444-9.

2017 - 2020 (PIs Hegemann & Oschkinat)

Friedrich, D., Brünig, F.N., Nieuwkoop, A.J., Netz, R., Hegemann, P. and Oschkinat, H. (2020). Collective exchange processes reveal an active site proton cage in bacteriorhodopsin. Commun. Biol. 3, doi: 10.1038/s42003-019-0733-7.

Friedrich, D., Perodeau, J., Nieuwkoop, A.J., and Oschkinat, H. (2020). MAS NMR detection of hydrogen bonds for protein secondary structure characterization. J. Biomol. NMR 74(4-5):247-256; doi: 10.1007/s10858-020-00307-z

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. Sci Signal. 2019 Mar 19;12(573). pii: eaav4203. doi: 10.1126/scisignal.aav4203.

Geiger, M.-A., Jagtap, A.P., Kaushik, M., Sun, H., Stöppler, D., Sigurdsson, S.T., Corzilius, B., and Oschkinat, H. (2018). Efficiency of Water‐Soluble Nitroxide Biradicals for Dynamic Nuclear Polarization in Rotating Solids at 9.4 T: bcTol‐M and cyolyl‐TOTAPOL as New Polarizing Agents. Chemistry 24(51), doi: 10.1002/chem.201801251.

Gerland, L.M., Friedrich, D., Hopf, L., Donovan, E., Wallmann, A., Erdmann, N., Diehl, A., Bommer, M., Buzar, K., Ibrahim, M., Schmieder, P., Dobbek, H., Zouni, A., Bondar, A.-N., Dau, H., and Oschkinat, H. (2020). pH‐Dependent Protonation of Surface Carboxylates in PsbO Enables Local Buffering and Triggers Structural Changes. ChemBioChem 21, 1597-1604. doi: 10.1002/cbic.201900739.

Grimm, C., Silapetere, A., Vogt, A., Bernal S., Yinth A., and Hegemann, P. (2018). Electrical properties, substrate specificity and optogenetic potential of the engineered light-driven sodium pump eKR2. Sci Rep 8, 9316; doi: 10.1038/s41598-018-27690-w

Krause, B.S., Grimm, C., Kaufmann, J.C.D., Schneider, F., Sakmar, T.P., and Hegemann, P. (2017). Complex photochemistry within the green-absorbing channelrhodopsin ReaChR. Biophys. J. 112, 1166-1175; doi: 10.1016/j.bpj.2017.02.001

Krause, B.S., Kaufmann, J.C.D., Kuhne, J., Vierock, V., Huber, T., Sakmar, T.P., Gerwert, K., Bartl, F.J., and Hegemann, P. (2019). Tracking pore hydration in channelrhodopsin by site-directed infraredactive azido probes. Biochemistry 58, 1275-1286; doi: 10.1021/acs.biochem.8b01211

Mukherjee, S., Hegemann, P., Broser, M. (2019). Enzymerhodopsins: novel photoregulated catalysts for optogenetics. Curr Opin Struct Biol. 57:118-126. doi: 10.1016/j.sbi.2019.02.003.

Oda, K., Vierock, J., Oishi, S., Rodriguez-Rozada, S., Taniguchi, R., Yamashita, K., Wiegert, J.S., Nishizawa, T., Hegemann, P., and Nureki, O. (2018). Crystal structure of the red light-activated channelrhodopsin Chrimson. Nat. Commun. 9:3949; doi: 10.1038/s41467-018-06421-9

Scheib, U., Broser, M., Constantin, O. M., Yang, S.,Gao, S., Mukherjee, S., Stehfest, K., Nagel, G., Gee, C. E., and Hegemann, P. (2018). Rhodopsin-cyclases for photocontrol of cGMP/cAMP and 2.3 Å structure of the adenylyl cyclase domain. Nature Commun 9, 2046.; doi: 10.1038/s41467-018-04428-w

Stöppler. D., Macpherson. A., Smith-Penzel, S., Basse, N., Lecomte, F., Deboves, H., Taylor, R.D., Norman, T., Porter, J., Waters, L.C., Westwood, M., Cossins, B., Cain, K., White, J., Griffin, R., Prosser, C., Kelm, S., Sullivan, A.H., Fox, D. 3rd, Carr, M.D., Henry, A., Taylor, R., Meier, B.H., Oschkinat, H., and Lawson, A.D. (2018). Insight into small molecule binding to the neonatal Fc receptor by X-ray crystallography and 100 kHz magic-angle-spinning NMR. PLoS Biol. 16(5), doi: 10.1371/journal.pbio.2006192

Vierock, J., Grimm, C., Nitzen, N., and Hegemann, P. (2017). Molecular determinants of proton selectivity and gating in the red-light activated channelrhodopsin Chrimson. Sci. Rep. 7, 9928; doi: 10.1038/s41598-017-09600-8

2013 - 2016 (PIs Hegemann & Oschkinat)

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.

Ernst, O.P., Lodowski, D.T., Elstner, M., Hegemann, P., Brown, L.S., and Kandori, H. (2014). Microbial and Animal Rhodopsins: Structures, Functions, and Molecular Mechanisms. Chemical Reviews 114, 126-163.

Jagtap, A.P., Geiger, M.-A., Stöppler, D., Orwick-Rydmark, M., Oschkinat, H., and Sigurdsson, S.T. (2016). bcTol: A highly water-soluble biradical for efficient dynamic nuclear polarization of biomolecules. Chemical Communications 52, 7020-7023.

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

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.

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.

Scheib, U., Stehfest, K., Gee, C.E., Korschen, H.G., Fudim, R., Oertner, T.G., and Hegemann, P. (2015). The rhodopsin-guanylyl cyclase of the aquatic fungus Blastocladiella emersonii enables fast optical control of cGMP signaling. Science Signaling 8, rs8.

Stöppler, D., Song, C., van Rossum, B.-J., Geiger, M.-A., Lang, C., Mroginski, M.-A., Jagtap, A.P., Sigurdsson, S.T., Matysik, J., Hughes, J., and Oschkinat, H. (2016). Dynamic nuclear polarization provides new insights into chromophore structure in phytochrome photoreceptors. Angew Chem Int Ed 55, 16017–16020, doi: doi: 10.1002/anie.201608119.