Retinal-binding proteins are found in all three domains of life: archaea, eubacteria and eukarya, and are classified into either type 1 or type 2 rhodopsins. These light-transducing proteins share a similar three-dimensional structure consisting of seven transmembrane α-helices. Visual pigments are type 2 rhodopsins and serve as G protein coupled receptors responsible for vision. Bacteriorhodopsin, a type 1 rhodopsin, functions as a light-driven ion pump and has various applications in memory devices. The photophysical properties of these retinal proteins are studied by spectroscopic and theoretical methods. Chapter 1 presents a detailed background on these two retinal-bound proteins. Chapter 2 presents a theoretical study of the spectral tuning mechanism of red cone pigments. This chapter suggests that the deep red cone pigments contain a different ring chromophore geometry compared to that of the other red cone pigments. Chapter 3 seeks to determine the protonation state of Glu 181 in the dark state of rhodopsin by examining the photobleaching sequence of a rhodopsin variant, E181Q. The photobleaching sequence is studied through cryogenic UV-Vis methods. This study shows that E181Q has a different photobleaching sequence compared to that of wild-type rhodopsin. We conclude in this study that E181 is a negatively charged residue in the dark state. Chapter 4 seeks to determine the source of the 70 nm blue-shift observed in a bacteriorhodopsin analog, 4-keto bacteriorhodopsin. In this study, the shift is assigned in part to the interactions of the side chain of Arg 82, with the two aspartic acid residues, Asp 85 and Asp 212, that are near the chromophore Schiff base.
