Molecular Mechanisms for Ion Transportation of Microbial Rhodopsins Studied by Light-Induced Difference FTIR Spectroscopy

Abstract

Microbial rhodopsins, many variants of which were developed via genetic engineering, have been widely utilized as optogenetic tools. Understanding the molecular mechanisms is important for designing such tools more efficiently. The dynamics of these proteins upon photoactivation can be studied by light-induced difference Fourier transform infrared (FTIR) spectroscopy. As the structural information involves hydrogen, which is not readily accessible via X-ray crystallography, light-induced difference FTIR spectroscopy is a powerful tool to study the molecular mechanisms of these light-receptive proteins. Low-temperature and time-resolved FTIR spectroscopy on two major microbial rhodopsins—bacteriorhodopsin (BR) and halorhodopsin (HR)—are summarized in this review. The low-temperature method stabilizes the intermediate states by decreasing temperature, whereas the time-resolved method allows direct observation at physiological temperature by using a measurement time short enough for their detection. By measuring the difference spectra in X–H and X–D stretching regions, changes in the hydrogen-bonding networks, including water molecules, were elucidated. It was demonstrated that water molecules played an important role in proton and ion translocation in BR and HR. Therefore, for develop optogenetic tools with favorable molecular properties, it may be important to design protein structures in the presence of internal water molecules.