Dr. Songhwan Hwang
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Email: songhwan.hwang@hu-berlin.de |
Molecular understanding of color vision in stomatopod crustaceans
Animal rhodopsins enable light perception and consist of a complex formed by opsin and 11-cis retinal as a chromophore via Schiff base with a lysine amino acid. The protonated form of retinal carries a positive charge that is stabilized by electrostatic interaction with a negatively charged amino acid, referred to as a counterion. Animal rhodopsins belong to the largest subfamily of G protein-coupled receptors (GPCRs).[1] Upon photon absorption, the isomerization of 11-cis retinal to all-trans retinal (Figure 1A) triggers structural changes in the protein, leading to the binding of G proteins on the intracellular side and subsequent downstream signaling. Stomatopod crustaceans (mantis shrimp) have gained a lot of attention because their visual systems span an extended wavelength range. [2] Recent studies utilized transcriptome and complementary DNA sequencing techniques and unveiled the existence of 33 distinct rhodopsins in the stomatopod’s eye.[3] The differences in light absorption can be attributed to evolutionary pressures, resulting in variations in amino acid compositions within the chromophore binding pocket. These differences contribute to the distinct
wavelengths observed in different rhodopsins. In my current project, I focus on studying the structural rearrangement of proteins influenced by retinal cis-trans isomerization in various rhodopsins of stomatopod, employing multiple microsecond molecular dynamics (MD) simulations (Figure 1B,C). By combining MD simulations with excitation energy calculations using quantum mechanics/molecular mechanics (QM/MM), I work on understanding color vision. By comparing the computational studies with experimental mutation and spectroscopic data with collaborators, the key determinants of specific wavelengths are unraveled.
My research interests include the following, based on theoretical approaches such as molecular modeling, all-atom molecular dynamics (MD) simulations, and hybrid quantum mechanics/molecular mechanics (QM/MM):
- Investigating the ion permeability and ion conduction mechanisms of the photointermediates of microbial rhodopsins, such as light-gated channelrhodopsins.
- Understanding the molecular basis for bistability and spectral shifts in invertebrate animal rhodopsins.
- Exploring properties such as pH sensitivity and thermostability of rhodopsins.
- Developing voltage-imaging sensors for optogenetic applications.
[1] K. L. Pierce, R. T. Premont, R. J. Lefkowitz, Nat. Rev. Mol. Cell Biol. 3, 639-650 (2002). https://doi.org/10.1038/nrm908
[2] J. Marshall, T. W. Cronin, S. Kleinlogel, Arthropod. Struct. Dev. 36, 420-448 (2007). https://doi.org/10.1016/j.asd.2007.01.006
[3] M. L. Porter, H. Awata, M. J. Bok, T. W. Cronin, Proc. Natl. Acad. Sci. U.S.A 117, 8948-8957 (2020). https://doi.org/10.1073/pnas.1917303117
[4] J. Jumper, R. Evans, A. Pritzel, T. Green, M. Figurnov, O. Ronneberger, K. Tunyasuvunakool, R. Bates, A. Zidek, A. Potapenko, A. Bridgland, C. Meyer, S. A. A. Kohl, A. J. Ballard, A. Cowie, B. Romera-Paredes, S. Nikolov, R. Jain, J. Adler, T. Back, S. Petersen, D. Reiman, E. Clancy, M. Zielinski, M. Steinegger, M. Pacholska, T. Berghammer, S. Bodenstein, D. Silver, O. Vinyals, A. W. Senior, K. Kavukcuoglu, P. Kohli, D. Hassabis, Nature 596, 583-589 (2021). https://doi.org/10.1038/s41586-021-03819-2