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Mercator Fellow

Computational Photochemistry of Photoreceptor Proteins

Principal Investigators: Dr. Igor Schapiro (HUJI)

The Mercator project comprises accurate excited state calculations of chromophore-protein complexes and their dynamics. For this purpose a multiscale approach is used which is based on a combination of accurate ab initio calculation applied to the chromophore with a description of the surrounding protein using a lower level of theory, namely a classical force field. In order to study dynamics in the excited state non-adiabatic molecular dynamics simulations will be carried out. The aim is to simulate the ultrafast photo-induced processes and to obtain a detailed understanding of the molecular mechanism. Potential cooperation is conceivable with other SFB projects in the research area B “Chromophore-driven protonation dynamics – photoreceptors” and computational modelling in section C "The bridge toward fundamental processes - theory".

Publications

2017-2020

Battocchio G., González R., Rao A.G., Schapiro I., Mroginski M.A. (2020). Dynamic Properties of the Photosensory Domain of Deinococcus radiodurans Bacteriophytochrome. J. Phys. Chem. B 124, 1740–1750; doi: 10.1021/acs.jpcb.0c00612

Borin V., Wiebeler C., Schapiro I. (2018). A QM/MM study of the initial excited state dynamics of greenabsorbing proteorhodopsin. Faraday Discuss. 207, 137–152; doi: 10.1039/C7FD00198C

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.

Guo, Y., Wolff, F. E., Schapiro, I., Elstner, M., Marazzi, M. (2018). Different hydrogen bonding environments of the retinal protonated Schiff base control the photoisomerization in channelrhodopsin-2. Phys Chem Chem Phys 20, 27501-27509, doi: 10.1039/c8cp05210g.

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

Kraskov A., Nguyen A. D., Goerling J., Buhrke D., Velazquez F., Fernandez 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

Nogly, P., Weinert, T., James, D., Carbajo, S., Ozerov, D., Furrer, A., Gashi, D., Borin, V., Skopintsev, P., Jaeger, K., Nass, K., Bath, P., Bosman, R., Koglin, J., Seaberg, M., Lane, T., Kekilli, D., Brunle, S., Tanaka, T., Wu, W., Milne, C., White, T., Barty, A., Weierstall, U., Panneels, V., Nango, E., Iwata, S., Hunter, M., Schapiro, I., Schertler, G., Neutze, R., and Standfuss, J. (2018). Retinal isomerization in bacteriorhodopsin captured by a femtosecond x-ray laser. Science 361, 6398; doi: 10.1126/science.aat0094

Schnedermann, C., Yang, X., Liebel, M., Spillane, K. M., Lugtenburg, J., Fernandez, I., Valentini, A., Schapiro, I., Olivucci, M., Kukura, P., Mathies, R. A. (2018). Evidence for a vibrational phase isotope effect on the photochemistry of vision. Nature Chemistry, 2018, 10, 449-455, doi: 10.1038/s41557-018-0014-y.

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. doi: 10.1038/s41586-020-2307-8

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, 848; doi: 10.3390/molecules25040848

Wiebeler, Ch., Rao, A. G., Gärtner, W., and Schapiro, I. (2018). The Effective Conjugation Length is Responsible for the Red/Green Spectral Tuning in the Cyanobacteriochrome Slr1393g3. Angewandte Chemie 58(7), 1934-1938, doi: org/10.1002/anie.201810266.

Wiebeler C., Schapiro I. (2019). QM/MM Benchmarking of Cyanobacteriochrome Slr1393g3 Absorption Spectra. Molecules 24, 1720; doi: 10.3390/molecules24091720

Xu, X., Port, A., Wiebeler, Ch., Kai-Hong Zhao, K.-H., Schapiro, I., and Gärtner, W. (2020). Structural elements regulating the photochromicity in a cyanobacteriochrome. PNAS117 (5)2432-2440, doi: 10.1073/pnas.1910208117.