Research Projects

Microbial rhodopsins (MR) are membrane-bound proteins that convert light energy into ion transport across cell membranes. This process is mediated by an all-trans retinal chromophore embedded within the protein, which absorbs light and undergoes structural changes, triggering a cascade of conformational transitions that regulate ion pumping. However, the coupling between the chromophore and the protein scaffold remains poorly understood. Due to their ability to modulate membrane potential, MR play a crucial role in optogenetics and clinical research. This proposal seeks to elucidate the intricate relationship between the structure and function of MR and uncover the molecular mechanisms underlying light capture and energy conversion. We will adopt a bottom-up approach to investigate the photochemistry of retinal chromophores, focusing on the series of intermediate states that occur during the photocycle. It will further probe how the energy from retinal structural transitions drives functional protein dynamics and explore how this coupling enable ion uptake and release. The study also aims to reveal the chemical tuning of the retinal chromophore by its protein environment and the interdependence between photocycle and ion-uptake, with the ultimate goal of extending retinal absorbance to long-wavelength photons while retaining functional efficiency. Recent time-resolved X-ray crystallography has revealed an intricate hydrogen-bonding network near the retinal, characterized by ultrashort O–O distances (2.2–2.5 Å), suggestive of low-barrier hydrogen bonds (LBHB). This research will test the hypothesis that these LBHBs play a crucial role in excited-state tuning and long-range signaling, addressing a longstanding question in structural biology. To achieve these objectives, our research will integrate large-scale molecular dynamics simulations, advanced quantum chemistry methods, and spectroscopy. Specifically, hybrid quantum-classical (QM/MM) simulations with polarizable embedding, non-adiabatic QM/MM approaches, wavefunction-based excited-state quantum chemical methods, and free-energy calculations of proton transfer and ion transport using umbrella sampling within QM/MM and MM/MD frameworks will provide a comprehensive understanding. The outcomes of this research will significantly advance our fundamental understanding of the bioenergetics of light-driven proton transport and shed light on the evolutionary dynamics of the rhodopsin superfamily. By elucidating the role of ultrafast, light-induced structural changes in efficient long-range signaling, this work will enhance our understanding of spectral tuning mechanisms and provide insights applicable to other rhodopsins. These findings will further have direct applications in protein engineering and de novo protein design, and drive innovations in optogenetics and the development of artificial cells, paving the way for transformative advances in biotechnology and medicine.