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Project B7

Real-time tracking of hydrogen bond dynamics in phytochrome

Principal Investigators: Prof. Dr. Karsten Heyne (FU)

Project B7 aims to elucidate cause-effect relations in the coupling of proton dynamics to conformational changes in phytochromes, light-gated channels and light driven pumps. Femtosecond (fs) polarization resolved Vis-pump IR-probe spectroscopy (upvi) represents an excellent tool to investigate local structural changes of the chromophore, the protein backbone, amino acid side chains, and water clusters. Hydrogen bonds can be monitored by spectral changes of specific vibrational bands and their orientations. Ground state heterogeneity can be resolved into species with distinct quantum yields. Rate-determining proton-transfer steps will be identified by measurements at different pH and temperature. A new ns pump – upvi setup is going to be developed to investigate selected intermediate states of the photoreaction and determine structural changes during keto-enol transition involved in the phytochrome photocycle. Comparison of structural dynamics of various ground state conformations between different phytochromes (Cph1, Agp1, Agp2, plant phytochromes) will reveal general principles of the cause-effect relation.

Publications

2017 - 2020

Kraskov, A., Nguyen, A.D., Goerling, J., Buhrke, D., Velazquez 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., and Hildebrandt, P. (2020). Intramolecular proton transfer controls protein structural changes in phytochrome. Biochemistry 59, 1023-1037; doi: 10.1021/acs.biochem.0c00053

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

Sadeghi, M., Balke, J., Schneider, C., Nagano, S., Stellmacher, J., Lochnit, G.L., Lang, C., Weise, C., Hughes, J., and Alexiev, U. (2020). Transient deprotonation of the chromophore affects protein dynamics proximal and distal to the linear tetrapyrrole chromophore in phytochrome Cph1. Biochemistry 59, 1051-1062; doi: 10.1021/acs.biochem.9b00967

Song, C., Mroginski, M.A., Lang, C., Kopycki, J., Gärtner, W., Matysik, J., and Hughes, J. (2018). 3D structures of plant phytochrome A as Pr and Pfr from solid-state NMR: Implications for molecular function. Front. Plant Sci. 9: 498; doi: 10.3389/fpls.2018.00498

Stensitzki, T., Adam, S., Schlesinger, R., Schapiro, I., and Heyne, K. (2020). Ultrafast backbone protonation in Channelrhodopsin-1 captured by polarization resolved fs vis-pump-IR-probe spectroscopy and computational methods. Molecules 25, pii: E848; doi: 10.3390/molecules25040848

Stensitzki, T., Yang, Y., Wölke, A.L., Knapp, E.-W., Hughes, J., Mroginski, M. A., and Heyne, K. (2017). Influence of Heterogeneity on the Ultrafast Photoisomerization Dynamics of Pfr in Cph1 Phytochrome. Photochemistry and Photobiology 93, 703-712; doi: 10.1111/php.12743

Velázquez 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. J. Phys. Chem. B 121, 47-57; doi: 10.1021/acs.jpcb.6b09600

Velázquez Escobar, F., Buhrke, D., Fernandez Lopez, M., Shenkutie, S., 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

2013 - 2016

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.

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.