Vibrational Spectroscopy of Optogenetic Rhodopsins: A Biophysical Study of Molecular Mechanisms

In this dissertation,the membrane protein channelrhodopsin-1 from the green flagellate algae Chlamydomonas agustae (Ca ChR1) is studied using a variety of spectroscopic techniques developed in the Rothschild Molecular Biophysics Laboratory at Boston University. Over the last decade, channelrhodopsins have proven to be effective optogenetic tools due to their ability to function as light-gated ion channels when expressed in neurons. This ability allows neuroscientists to optically activate an inward directed photocurrent which depolarizes the neuronal membranes and triggers an action potential. Although a variety of channelrhodopsins with different properties have been used, the underlying mechanisms of channelrhodopsin functionality is not yet fully understood.;The protein studied here has several advantageous properties compared to the more extensively studied channelrhodopsin-2 from Chlamydomonas reinhardtii including a red shifted visible absorption and slower light inactivation despite having a lower channel current. Elucidating the internal molecular mechanisms underlying the function of CaChR1 provides critical insight into the large class of channelrhodopsin proteins leading toward improved bioengineering for specific optogenetic applications. Here near-IR pre-resonance Raman spectroscopy of CaChR1 provides information on the structure of the unphotolyzed (P0) retinal chromophore, the Schiff base protonation state, and presence of carboxylic acid residues interacting with the Schiff base. Low-temperature FTIR difference spectroscopy combined with site-directed mutagenesis and isotope labeling provide information on changes occurring in the retinal chromophore and protein during the primary phototransition (P0 → P1).;This includes information about changes involving protonation state of binding-pocket residues, protein backbone structure, and internal water molecules. Further experiments combining low-temperature and time-resolved FTIR-difference spectroscopy reveal additional information about structural changes during the transition from the unphotolyzed state to the active (open channel) state of the protein (P0 → P2). This work has resulted in an initial model that describes key proton transfer events which occur between the Schiff base and carboxylic acid residues inside the active site of CaChR1. The model raises the possibility that ion channel gating and ion specificity is regulated by the protonation changes of two key residues (Glu 169 and Asp299) located near the Schiff base.