Identification of proton and hydrogen bond dynamics in channelrhodopsin and related systems

Principal Investigators: Prof. Dr. Joachim Heberle (FU)

We aim at revealing the gating mechanism of channelrhodopsins, such as the cation channelrhodopsin CaChR1 and the anion channelrhodopsin GtACR1, by applying time-resolved IR spectroscopic techniques developed in this CRC. Our expertise in time-resolved IR spectroscopy on protein crystals will be employed in collaborations with XFEL groups. Here, we will study the mechanism of sodium pumping in the microbial rhodopsin KR2 and of chloride pumping in NmHR by contributing changes in protonation states and hydrogen bonds to finally achieve a 4D understanding of protein function at the atomic level.

Publications

2021 - 2024

Baserga, F., Vorkas, A., Crea, F., Schubert, L., Chen, J.L., Redlich, A., La Greca, M., Storm, J., Oldemeyer, S., Hoffmann, K., Schlesinger, R. and Heberle, J. (2022). Membrane Protein Activity Induces Specific Molecular Changes in Nanodiscs Monitored by FTIR Difference Spectroscopy. Front Mol Biosci, 9, 915328. doi: 10.3389/fmolb.2022.915328.

Bühl, E., Resler, T., Lam, R., Asido, M., Bamberg, E., Schlesinger, R., Bamann, C., Heberle, J. and Wachtveitl, J. (2023). Assessing the Role of R120 in the Gating of CrChR2 by Time-Resolved Spectroscopy from Femtoseconds to Seconds. J Am Chem Soc 145, 40: 21832-21840. doi: 10.1021/jacs.3c05399.

Crea, F., Vorkas, A., Redlich, A., Cruz, R., Shi, C., Trauner, D., Lange, A., Schlesinger, R. and Heberle, J. (2022). Photoactivation of a Mechanosensitive Channel. Front Mol Biosci. doi: 10.3389/fmolb.2022.905306. 

La Greca, M., Chen, J.-L., Schubert, L., Kozuch, J., Berneiser, T., Terpitz, U., Heberle, J., and Schlesinger, R. (2022). The Photoreaction of the Proton-Pumping Rhodopsin 1 From the Maize Pathogenic Basidiomycete Ustilago maydis. Front Mol Biosci. doi: 10.3389/fmolb.2022.826990.

Maia, R.N., Ehrenberg, D., Oldemeyer, S., Knieps-Grünhagen, E., Krauss, U., and Heberle, J. (2021). Real-Time Tracking of Proton Transfer from the Reactive Cysteine to the Flavin Chromophore of a Photosensing Light Oxygen Voltage Protein. J Am Chem Soc, 143, 32, 12535–12542. doi: 10.1021/jacs.1c03409.

Mous, S., Gotthard, G., Ehrenberg, D., Sen, S., Weinert, T., Johnson, P.J.M., James, D., Nass, K., Furrer, A., Kekilli, D., Ma, P., Brünle, S., Casadei, C.M., Martiel, I., Dworkowski, F., Gashi, D., Skopintsev, P., Wranik, M., Knopp, G., Panepucci, E., Panneels, V., Cirelli, C., Ozerov, D., Schertler, G., Wang, M., Milne, C., Standfuss, J., Schapiro, I., Heberle, J., and Nogly, P. (2022). Dynamics and mechanism of a light-driven chloride pump. Science. doi: 10.1126/science.abj6663.

Oldemeyer, S., La Greca, M., Langner, P., Lê Công, K.L., Schlesinger, R. and Heberle, J. (2024). Nanosecond Transient IR Spectroscopy of Halorhodopsin in Living Cells. J Am Chem Soc, 146, 28: 19118-19127. doi: 10.1021/jacs.4c03891.

Saliminasab, M., Yamazaki, Y., Palmateer, A., Harris, A., Schubert, L., Langner, P., Heberle, J., Bondar, A.-N. and Brown, L.S. (2023). A Proteorhodopsin-Related Photosensor Expands the Repertoire of Structural Motifs Employed by Sensory Rhodopsins. J Phys Chem B, 127, 37: 7872-7886. doi: 10.1021/acs.jpcb.3c04032.

Schubert, L., Chen, J.-L., Fritz, T., Marxer, F., Langner, P., Hoffmann, K., Gamiz-Hernandez, A.P., Kaila, V.R.I., Schlesinger, R. and Heberle, J. (2023). Proton Release Reactions in the Inward H+ Pump NsXeR. J Phys Chem B. doi: 10.1021/acs.jpcb.3c04100.

Schubert, L., Langner, P., Ehrenberg, D., Lorenz-Fonfria, V.A. and Heberle, J. (2022). Protein conformational changes and protonation dynamics probed by a single shot using quantum-cascade-laser-based IR spectroscopy. J Chem Phys, 156, 20: 204201. doi: 10.1063/5.0088526

Walter, M., Schubert, L., Heberle, J., Schlesinger, R. and Losi, A. (2023). Time-resolved photoacoustics of channelrhodopsins: early energetics and light-driven volume changes. Photochem Photobiol Sci. doi: 10.1007/s43630-022-00327-8

Yaguchi, M., Jia, X., Schlesinger, R., Jiang, X., Ataka, K., and Heberle, J. (2023). Near-Infrared Activation of Sensory Rhodopsin II Mediated by NIR-to-Blue Upconversion Nanoparticles. Front Mol Biosci. doi: 10.3389/fmolb.2021.782688.

2017 - 2020

Daldrop, J.O., Saita, M., Heyden, M., Lorenz-Fonfria, V. A., Heberle. J., and Netz, R.R. (2018). Orientation of non-spherical protonated water clusters revealed by infrared absorption dichroism. Nature Communications 9, 311 doi: 10.1038/s41467-017-02669-9

Ehrenberg, D., Krause, N., Saita, M., Bamann, C., Kar, R.K., Hoffmann, K., Heinrich, D., Schapiro, I., Heberle, J., and Schlesinger, R. (2019) Atomistic insight into the role of threonine 127 in the functional mechanism of channelrhodopsin-2. Appl. Sci., 9 (22), 4905; https://doi.org/10.3390/app9224905.

Ehrenberg, D., Varma, N., Deupi, X., Koyanagi, M., Terakita, A., Schertler, GFX., Heberle, J., and Lesca, E. (2019).The two-photon reversible reaction of the bistable jumping spider rhodopsin-1. Biophysical Journal 116, 1248-1258, doi: https://doi.org/10.1016/j.bpj.2019.02.025.

Harris, A., Lazaratos, M., Siemers, M., Watt, E., Hoang, A., Tomida, S., Schubert, L., Saita, M., Heberle, J., Furutani, Y., Kandori, H., Bondar, A. N., and Brown, L. S. (2020). Mechanism of Inward Proton Transport in an Antarctic Microbial Rhodopsin. Journal of Physical Chemistry B 124, 4851-4872. doi: 10.1021/acs.jpcb.0c02767

Harris N.J., Reading E., Ataka K., Grzegorzewski L., Charalambous K., Liu X., Schlesinger R., Heberle J., and Booth P.J. (2017). Structure formation during translocon-unassisted co-translational membrane protein folding. Scientific Reports 7: 8021; doi: 10.1038/s41598-017-08522-9

Harris, A., Saita, M., Resler, T., Hughes-Visentin, A., Maia, R., Pranga-Sellnau, F., Bondar, A.-N., Heberle, J., and Brown, L. S. (2018). Molecular details of the unique mechanism of chloride transport by a cyanobacterial rhodopsin. Physical Chemistry Chemical Physics 20, 3184-3199; doi: 10.1039/C7CP06068H

Hu, H.^., Ataka, K., Menny, A., Fourati, Z., Sauguet, L., Corringer, P. J., Koehl, P., Heberle, J., Delarue, M. (2018). Electrostatics, proton sensor, and networks governing the gating transition in GLIC, a proton-gated pentameric ion channel. Proc Natl Acad Sci USA 115 (52), doi: 10.1073/pnas.1813378116.

Kottke, T., Lórenz-Fonfría V.A., and Heberle J. (2017). The Grateful Infrared – Sequential Protein Structural Changes Resolved by IR Difference Spectroscopy. Journal of Physical Chemistry B 121, 335-350. [Link to news section.]

Kovacsova, G., Grünbein, M.L., Kloos, M., Barends, T.R.M., Schlesinger, R., Heberle, J., Kabsch, W., Shoeman, R.L., Doak, R.B., Schlichting, I. (2017). Viscous hydrophilic injection matrices for serial crystallography. IUCrJ 4, 400-410; doi: 10.1107/S2052252517005140

Lorenz-Fonfria V.A., Saita M., Lazarova T., Schlesinger R., and Heberle J. (2017). pH-sensitive vibrational probe reveals a cytoplasmic protonated cluster in bacteriorhodopsin. Proceedings of the National Academy of Sciences of the United States of America 114, E10909-E10918; doi: 10.1073/pnas.1707993114

Nass Kovacs, G., Colletier, J.-P., Grünbein, M. L., Yang, Y., Stensitzki, T., Batyuk, A., Carbajo, S., Doak, R. B., Ehrenberg, D., Foucar, L., Gasper, R., Gorel, A., Hilpert, M., Kloos, M., Koglin, J. E., Reinstein, J., Roome, C. M., Schlesinger, R., Seaberg, M., Shoeman, R. L., Stricker, M., Boutet, S., Haacke, S., Heberle, J., Heyne, K., Domratcheva, T., Barends, T. R. M., and Schlichting, I.(2019). Three-dimensional view of ultrafast dynamics in photoexcited bacteriorhodopsin. Nature Communications 10, Article Number 3177. doi: 10.1038/s41467-019-10758-0

Saita, M., Pranga-Sellnau, F., Resler, T., Schlesinger, R., Heberle, J., and Lorenz-Fonfria, V. A. (2018). Photoexcitation of the P4(480) state induces a secondary photocycle that potentially desensitizes channelrhodopsin-2. J Am Chem Soc 140, 9899-9903; doi: 10.1021/jacs.8b03931

Schultz, B.-J., Mohrmann, H., Lórenz-Fonfría, V.A., and Heberle J. (2018). Protein dynamics observed by tunable mid-IR quantum cascade lasers across the time range from 10 ns to 1 s. Spectrochimica Acta A 188, 666-674; doi: 10.1016/j.saa.2017.01.010

Skopintsev, P., Ehrenberg, D., Weinert, T., James, D., Kar, R. K., Johnson, P. J. M., Ozerov, D., Furrer, A., Martiel, I., Dworkowski, F., Nass, K., Knopp, G., Cirelli, C., Arrell, C., Gashi, D., Mous, S., Wranik, M., Gruhl, T., Kekilli, D., Brünle, S., Deupi, X., Schertler, G. F. X., Benoit, R. M., Panneels, V., Nogly, P., Schapiro, I., Milne, C., Heberle, J., and Standfuss, J. (2020). Femtosecond-to-millisecond structural changes in a light-driven sodium pump. Nature 583, 314-318. doi: 10.1038/s41586-020-2307-8

2013 - 2016

Heberle, J., Deupi, X., and Schertler, G. (2014). Retinal proteins — You can teach an old dog new tricks. Biochimica et Biophysica Acta (BBA) - Bioenergetics 1837, 531-532.

Krause, N., Engelhard, C., Heberle, J., Schlesinger, R., and Bittl, R. (2013). Structural differences between the closed and open states of channelrhodopsin-2 as observed by EPR spectroscopy. FEBS Letters 587, 3309-3313.

Linke, M., Yang, Y., Zienicke, B., Hammam, M.A.S., von Haimberger, T., Zacarias, A., Inomata, K., Lamparter, T., and Heyne, K. (2013). Electronic transitions and heterogeneity of the bacteriophytochrome Pr absorption band: An angle balanced polarization resolved femtosecond VIS pump-IR probe study. Biophysical Journal 105, 1756-1766.

Lórenz-Fonfría, V.A., Bamann, C., Resler, T., Schlesinger, R., Bamberg, E., and Heberle, J. (2015). Temporal evolution of helix hydration in a light-gated ion channel correlates with ion conductance. Proceedings of the National Academy of Sciences of the United States of America 112, E5796-E5804.

Lórenz-Fonfría, V.A., and Heberle, J. (2014). Channelrhodopsin unchained: Structure and mechanism of a light-gated cation channel. Biochimica et Biophysica Acta (BBA) - Bioenergetics 1837, 626-642.

Lórenz-Fonfría, V.A., and Heberle, J. (2014). Proton Transfer and Protein Conformation Dynamics in Photosensitive Proteins by Time-resolved Step-scan Fourier-transform Infrared Spectroscopy. Journal of Visualized Experiments 88, e51622. [Link to news section.]

Lórenz-Fonfría, V.A., Muders, V., Schlesinger, R., and Heberle, J. (2014). Changes in the hydrogen-bonding strength of internal water molecules and cysteine residues in the conductive state of channelrhodopsin-1. Journal of Chemical Physics 141, 22D507.

Lorenz-Fonfria, V.A., Resler, T., Krause, N., Nack, M., Gossing, M., von Mollard, G.F., Bamann, C., Bamberg, E., Schlesinger, R., and Heberle, J. (2013). Transient protonation changes in channelrhodopsin-2 and their relevance to channel gating. Proceedings of the National Academy of Sciences of the United States of America 110, E1273-E1281.

Lórenz-Fonfría, V.A., Schultz, B.-J., Resler, T., Schlesinger, R., Bamann, C., Bamberg, E., and Heberle, J. (2015). Pre-Gating Conformational Changes in the ChETA Variant of Channelrhodopsin-2 Monitored by Nanosecond IR Spectroscopy. Journal of the American Chemical Society 137, 1850-1861.

Mohrmann, H., Kube, I., Lórenz-Fonfría, V.A., Engelhard, M., and Heberle, J. (2016). Transient Conformational Changes of Sensory Rhodopsin II Investigated by Vibrational Stark Effect Probes. Journal of Physical Chemistry B 120, 4383-4387.

Muders, V., Kerruth, S., Lorenz-Fonfria, V.A., Bamann, C., Heberle, J., and Schlesinger, R. (2014). Resonance Raman and FTIR spectroscopic characterization of the closed and open states of channelrhodopsin-1. FEBS Letters 588, 2301-2306.

Neumann-Verhoefen, M.-K., Neumann, K., Bamann, C., Radu, I., Heberle, J., Bamberg, E., and Wachtveitl, J. (2013). Ultrafast Infrared Spectroscopy on Channelrhodopsin-2 Reveals Efficient Energy Transfer from the Retinal Chromophore to the Protein. Journal of the American Chemical Society 135, 6968-6976.

Resler, T., Schultz, B.-J., Lorenz-Fonfria, V.A., Schlesinger, R., and Heberle, J. (2015). Kinetic and Vibrational Isotope Effects of Proton Transfer Reactions in Channelrhodopsin-2. Biophysical Journal 109, 287-297.

Schnedermann, C., Muders, V., Ehrenberg, D., Schlesinger, R., Kukura, P., and Heberle, J. (2016). Vibronic Dynamics of the Ultrafast all-trans to 13-cis Photoisomerization of Retinal in Channelrhodopsin-1. Journal of the American Chemical Society 138, 4757-4762.

Stensitzki, T., Muders, V., Schlesinger, R., Heberle, J., and Heyne, K. (2015). The primary photoreaction of channelrhodopsin-1: Wavelength dependent photoreactions induced by ground-state heterogeneity. Frontiers in Molecular Biosciences 2, 41.

Stensitzki, T., Yang, Y., Berg, A., Mahammed, A., Gross, Z., and Heyne, K. (2016). Ultrafast electronic and vibrational dynamics in brominated aluminum corroles: Energy relaxation and triplet formation. Structural Dynamics 3, 043210.

Stensitzki, T., Yang, Y., Muders, V., Schlesinger, R., Heberle, J., and Heyne, K. (2016). Femtosecond infrared spectroscopy of channelrhodopsin-1 chromophore isomerization. Structural Dynamics 3, 043208.

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.

Yang, Y., Heyne, K., Mathies, R.A., and Dasgupta, J. (2016). Non-Bonded Interactions Drive the Sub-Picosecond Bilin Photoisomerization in the Pfr State of Phytochrome Cph1. ChemPhysChem 17, 369-374.

Yang, Y., Linke, M., von Haimberger, T., Matute, R., González, L., Schmieder, P., and Heyne, K. (2014). Active and silent chromophore isoforms for phytochrome Pr photoisomerization: An alternative evolutionary strategy to optimize photoreaction quantum yields. Structural Dynamics 1, 014701.