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We have strong interest and expertise in computational modelling and the mechanistic understanding of rhodopsins. For a long time, rhodopsins were considered non-fluorescent until a peculiar voltage-sensitive fluorescence was reported for archaerhodopsin-3 (Arch3) derivatives. These proteins, known as QuasArs, have been used to image membrane voltage changes in cell cultures and small animals. However, due to their low fluorescence intensity, these constructs require significantly higher light intensities than other optogenetic tools. To develop the next generation of sensors, it is indispensable to understand the molecular basis of the fluorescence and its modulation by the membrane voltage. Based on an integrated study combining MD simulations, fluorescence imaging, and spectroscopy studies together with our collaborators, we obtained deeper insights into the effects of the transmembrane voltage on protein dynamics and fluorescence (Figure 2). Moreover, we identified the key residues responsible for enhancing the fluorescence quantum yield increase and voltage sensing [9].
Based on our computational expertise in ion channels, we recently combined time-resolved X-ray crystallography with atomistic MD and quantum-mechanics/molecular mechanics (QM/MM) simulations to investigate the opening mechanism of channelrhodopsins, which are light-gated ion channels and serve as essential tools in optogenetics. Our study provides critical insights into channel opening, ion conduction, and selectivity [10]. This method has also contributed to the structural and mechanistic investigation of a potassium-selective channelrhodopsin [11] and the biophysical investigation of optoenzymes, such as rhodopsin-guanylyl cyclases [12]. Our rhodopsin-related projects have previously been supported by a DFG funding within the SFB1078 and are currently continued through a project funded by the UniSysCat Excellence Cluster.
Figure 2. Schematic illustration of computational investigation of Archaerhodopsins [9].
[9] Silapetere, A.; Hwang, S.; Hontani, Fernandez Lahore, R. G.; Balke, J.; Escobar, F. V.; Tros, M.; Konold, P. E.; Matis, R.; Croce, R.; Walla, P. J.; Hildebrandt, P.; Alexiev, U.; Kennis, J. T. M.; Sun, H.; Utesch, T.; Hegemann, P. QuasAr odyssey: the origin of fluorescence and its voltage sensitivity in microbial rhodopsins, Nat. Commun., 2022, 13, 5501. doi: 10.1038/s41467-022-33084-4
[10] Mulder, M.; Hwang, S.; Broser, M.; Brünle, S.; Skopintsev, P.; Schattenberg, C.; Schnick, C.; Hartmann, S.; Church, J.; Schapiro, I.; Dworkowski, F.; Weinert, T.; Hegemann, P.; Sun, H.*; Standfuss, J.*, Structural Insights Into the Opening Mechanism of C1C2 Channelrhodopsin. J. Am. Chem. Soc., 2025, 147(1), 1282-1290. doi: 10.1021/jacs.4c15402
[11] Morizumi, T.; Kim, K.; Li, H.; Nag, P.; Dogon, T.; Sineshchekov, O. A.; Wang, Y.; Brown, L. S.; Hwang, S.; Sun, H.; Bondar, A.N.; Schapiro, I.; Govorunova, E. G.; Spudich, J. L.; Ernst, O. P., Structural insights into light-gating of potassium-selective channelrhodopsin, Nat. Commun., 2025, 16(1), 1283. doi: 10.1038/s41467-025-56491-9
[12] Broser, M.; Busse, W.; Spreen, A.; Reh, M.; Sierra, Y. A. B.; Hwang, S.; Utesch, T.; Sun, H.; Hegemann, P., Diversity of rhodopsin cyclases in zoospore-forming fungi, PNAS, 2023, 120. doi: 10.1073/pnas.2310600120
The Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) is part of the Forschungsverbund Berlin e.V. (FVB), which legally represents seven non-university research institutes - members of the Leibniz Association - in Berlin.
Leibniz-Forschungsinstitut für Molekulare Pharmakologie im Forschungsverbund Berlin e.V. (FMP)
Campus Berlin-Buch
Robert-Roessle-Str. 10,
13125 Berlin, Germany
