Raman Optical Activity of Retinal Chromophore in Sensory Rhodopsin II

Abstract

Raman optical activity (ROA) spectroscopy was used to study the conformation of the retinal chromophore in sensory rhodopsin II (SRII), which is a blue−green light sensor of microbes. The ROA spectrum consisted of the negative vibrational bands of the chromophore, whose relative intensities are similar to those of the parent Raman spectrum. This spectral feature was explained by the left-handed helical twist of the retinal chromophore on the basis of quantum chemical calculations. On the other hand, we found that the chromophore conformation based on the crystal structures of SRII has a right-handed helical twist, which does not agree with the observation. This specific result suggests that the consistency with chirooptical properties can be a key criterion for the accurate prediction and/or evaluation of chromophore conformation in retinal-binding proteins.

Near-Infrared Excited Raman Optical Activity as a Tool to Uncover Active Sites of Photoreceptor Proteins

“…Figure ), we recently used the ROA spectrum to show that some crystal structures of PYP did not accurately represent the correct conformation of the p CA chromophore in solution . The crystal structures of sensory rhodopsin II were likewise found to exhibit a twist in the chromophore that contradicted with the ROA spectra in solution . Thus, ROA spectroscopy can be a unique tool to give the precise three-dimensional structures of protein active sites under physiological conditions.…”

“…From this perspective, we present general principles for ROA and briefly describe ROA instruments. We will then discuss several research topics where ROA spectroscopy has been instrumental in uncovering the active site structures of photoreceptor proteins. ,− …”

Configurational Changes of Retinal Schiff Base during Membrane Na+ Transport by a Sodium Pumping Rhodopsin

“…To confirm this idea, we performed density functional theory (DFT) calculations at the B3LYP/6-31+G** level. We used a model chromophore, , N ,3,7,10,11-pentamethyl­dodeca-2,4,6,8,10-pentaen-1-iminum, which represents the polyene moiety of the all-trans retinal Schiff base. This simplification of the chromophore is useful to obtain the primary features of its vibrational modes.…”

Spectroscopic Validation of Crystallographic Structures of a Protein Active Site by Chiroptical Spectroscopy

“…The sum of the two components ( I R + I L ) is the parent Raman spectrum. The method has been applied to photoreceptor proteins, and the ROA spectra provide an extraordinary sensitivity to a chromophore structure, including out-of-plane distortions within its protein environment. − ECD spectroscopy is widely used to study biological systems including photoreceptor proteins. However, detailed structural interpretations of these spectra have been limited so far.…”