Chromophore In Bathorhodopsin Research Articles

Towards an interpretation of 13C chemical shifts in bathorhodopsin, a functional intermediate of a G-protein coupled receptor

Photoisomerization of the membrane-bound light receptor protein rhodopsin leads to an energy-rich photostate called bathorhodopsin, which may be trapped at temperatures of 120 K or lower. We recently studied bathorhodopsin by low-temperature solid-state NMR, using in situ illumination of the sample in a purpose-built NMR probe. In this way we acquired 13C chemical shifts along the retinylidene chain of the chromophore. Here we compare these results with the chemical shifts of the dark state chromophore in rhodopsin, as well as with the chemical shifts of retinylidene model compounds in solution. An earlier solid-state NMR study of bathorhodopsin found only small changes in the 13C chemical shifts upon isomerization, suggesting only minor perturbations of the electronic structure in the isomerized retinylidene chain. This is at variance with our recent measurements which show much larger perturbations of the 13C chemical shifts. Here we present a tentative interpretation of our NMR results involving an increased charge delocalization inside the polyene chain of the bathorhodopsin chromophore. Our results suggest that the bathochromic shift of bathorhodopsin is due to modified electrostatic interactions between the chromophore and the binding pocket, whereas both electrostatic interactions and torsional strain are involved in the energy storage mechanism of bathorhodopsin.

Water‐mediated Spectral Shifts in Rhodopsin and Bathorhodopsin†

The role of water molecules in spectral tuning of proteins has been left largely unexplored. This topic is important because changing hydrogen bond patterns during the activation process may lead to spectral shifts which can be of diagnostic value for the underlying structures. Arguments put forward in this article are based on spectral shift calculations of the rhodopsin and bathorhodopsin chromophore due to wat2a and 2b in the presence and absence of the counterion and of the amino acids lining the rhodopsin binding pocket. They show, among others, that a single water molecule can shift the absorbance by up to 0.1 eV or 34 nm depending on the environment of the chromophore.

Modelling of photointermediates suggests a mechanism of the flip of the beta-ionone moiety of the retinylidene chromophore in the rhodopsin photocascade.

Flip out! A model of the bathorhodopsin chromophore (see scheme) generated by molecular dynamics simulation suggests a twisted conformation of the C11C12 bond caused by steric interaction between the 13-methyl group and Cys183. The twisted double bond may be involved in the flip of the β-ionone moiety toward transmembrane segments 3 and 4 in the formation of lumirhodopsin.

A Mechanism of Primary Photoactivation Reactions of Rhodopsin: Modeling of the Intermediates in the Rhodopsin Photocycle

The photoisomerization of the retinylidene chromophore and the process of thermal relaxation of its strained conformation were examined by restrained molecular dynamic simulations in the transmembrane model of rhodopsin. This model was constructed based on the projection map obtained by electron cryomicroscopy. The photoconversion process from the 11-cis-retinylidene chromophore to the all-trans chromophore was traced by simultaneous rotation of the adjacent C12−C13 bond, leading to an all-trans chromophore having a C11−C12-twisted and C12−C13-s-cis conformation for the bathorhodopsin chromophore. In accord with the characteristic CD signals at 500 and 540 nm, the retinylidene chromophore of rhodopsin and bathorhodopsin showed characteristic right-handed and left-handed helical conformations, respectively. Subsequent rotation of the C12−C13 bond led to the lumirhodopsin chromophore with an all-trans C12−C13-s-trans conformation, affecting the backbone structure of transmembrane helix 3 by steric interaction between the 13-Me group of the chromophore and opsin. The conformational change of the chromophore from lumirhodopsin to metarhodopsin I placed the β-ionyl portion of the chromophore in an alternate binding site and the protonated Schiff base in a position appropriate for proton transfer to its counterion, Glu113. Estimation of UV absorption of the rhodopsin and photoactivated rhodopsin chromophores indicated the importance of the PSB−Glu113 carboxylate distance, the twist of the C11−C12 double bond, and the C12−C13 s-cis conformation of the 11,13-diene portion to the bathochromic shift of bathorhodopsin.

Structure around C6-C7 bond of the chromophore in bathorhodopsin: low-temperature spectroscopy of 6s-cis-locked bicyclic rhodopsin analogs.

To elucidate the structural changes near the beta-ionone ring region of the chromophore during the photobleaching process of rhodopsin, the photochemical and subsequent thermal reactions of rhodopsin analogs, whose retinylidene chromophores were fixed in a 6s-cis form with a five-membered ring (6,5-rhodopsin) and a seven-membered ring (6,7-rhodopsin), respectively, were investigated by low-temperature spectroscopy. Like rhodopsin, both the rhodopsin analogs convert to the respective batho-intermediates upon absorption of light at -190 degrees C. The extinction coefficient of batho-intermediate of 6,5-rhodopsin is similar to that of bathorhodopsin, while that of 6,7-rhodopsin is considerably smaller than that of bathorhodopsin. Like bathorhodopsin, the batho-intermediate of 6,5-rhodopsin directly converts to lumi-intermediate, while that of 6,7-rhodopsin first converts to a blue-shifted intermediate and then to lumi-intermediate. These results strongly suggest that the structure around the beta-ionone ring region of the bathorhodopsin chromophore resembles 6,5-retinal rather than 6,7-retinal. From the comparison of the structural features among retinal, 6,5-retinal, and 6,7-retinal, a possible conformation around C6-C7 bond of the bathorhodopsin chromophore is discussed.

A RESONANCE RAMAN STUDY OF OCTOPUS BATHORHODOPSIN WITH DEUTERIUM LABELED RETINAL CHROMOPHORES*

The resonance Raman spectrum of octopus bathorhodopsin in the fingerprint region and in the ethylenic-Schiff base region have been obtained at 80 K using the "pump-probe" technique as have its deuterated chromophore analogues at the C7D; C8D; C8,C7D2; C10D; C11D; C11, C12D2; C14D; C15D; C14, C15D2; and N16D positions. While these data are not sufficient to make definitive band assignments, many tentative assignments can be made. Because of the close spectral similarity between the octopus bathorhodopsin spectrum and that of bovine bathorhodopsin, we conclude that the essential configuration of octopus bathorhodopsin's chromophore is all-trans like. The data suggest that the Schiff base, C = N, configuration is trans (anti). The observed conformationally sensitive fingerprint bands show pronounced isotope shifts upon chromophore deuteration. The size of the shifts differ, in certain cases, from those found for bovine bathorhodopsin. Thus, the internal mode composition of the fingerprint bands differs somewhat from bovine bathorhodopsin, suggesting a somewhat different in situ chromophore conformation. An analysis of the NH bend frequency, the Schiff base C = N stretch frequency, and its shift upon Schiff base deuteration suggests that the hydrogen bonding between the protonated Schiff base with its protein binding pocket is weaker in octopus bathorhodopsin than in bovine bathorhodopsin but stronger than that found in bacteriorhodopsin's bR568 pigment.

13C magic-angle spinning NMR studies of bathorhodopsin, the primary photoproduct of rhodopsin.

Magic-angle spinning NMR spectra have been obtained of the bathorhodopsin photointermediate trapped at low temperature (less than 130 K) by using isorhodopsin samples regenerated with retinal specifically 13C-labeled at positions 8, 10, 11, 12, 13, 14, and 15. Comparison of the chemical shifts of the bathorhodopsin resonances with those of an all-trans-retinal protonated Schiff base (PSB) chloride salt show the largest difference (6.2 ppm) at position 13 of the protein-bound retinal. Small differences in chemical shift between bathorhodopsin and the all-trans PSB model compound are also observed at positions 10, 11, and 12. The effects are almost equal in magnitude to those previously observed in rhodopsin and isorhodopsin. Consequently, the energy stored in the primary photoproduct bathorhodopsin does not give rise to any substantial change in the average electron density at the labeled positions. The data indicate that the electronic and structural properties of the protein environment are similar to those in rhodopsin and isorhodopsin. In particular, a previously proposed perturbation near position 13 of the retinal appears not to change its position significantly with respect to the chromophore upon isomerization. The data effectively exclude charge separation between the chromophore and a protein residue as the main mechanism for energy storage in the primary photoproduct and argue that the light energy is stored in the form of distortions of the bathorhodopsin chromophore.

Complete assignment of the hydrogen out-of-plane wagging vibrations of bathorhodopsin: chromophore structure and energy storage in the primary photoproduct of vision

Resonance Raman vibrational spectra of the retinal chromophore in bathorhodopsin have been obtained after regenerating bovine visual pigments with an extensive series of 13C- and deuterium-labeled retinals. A low-temperature spinning cell technique was used to produce high-quality bathorhodopsin spectra exhibiting resolved hydrogen out-of-plane wagging vibrations at 838, 850, 858, 875, and 921 cm-1. The isotopic shifts and a normal coordinate analysis permit the assignment of these lines to the HC7 = C8H Bg, C14H, C12H, C10H, and C11H hydrogen out-of-plane wagging modes, respectively. The coupling constant between the C11H and C12H wags as well as the C12H wag force constant are unusually low compared to those of retinal model compounds. This quantitatively confirms the lack of coupling between the C11H and C12H wags and the low C12H wag vibrational frequency noted earlier by Eyring et al. [(1982) Biochemistry 21, 384]. The force constants for the C10H and C14H wags are also significantly below the values observed in model compounds. We suggest that the perturbed hydrogen out-of-plane wagging and C-C stretching force constants for the C10-C11 = C12-C13 region of the chromophore in bathorhodopsin result from electrostatic interactions with a charged protein residue. This interaction may also contribute to the 33 kcal/mol energy storage in bathorhodopsin.

Interpretation of the resonance Raman spectrum of bathorhodopsin based on visual pigment analogues.

Resonance Raman spectra of visual pigment analogues have been used to evaluate various models for the structure of the retinal chromophore in bathorhodopsin. Deuteration or removal of the 18-methyl on the beta-ionyl ring or of the 19-methyl on the polyene chain demonstrates that the three intense low wavenumber bands of bathorhodopsin at 853, 875, and 920 cm-1 are not due to exomethylene or ring modes. Rather, assignment of these lines to out-of-plane vinyl hydrogen motions on the chain best accounts for the experimental data. Our calculations show that the intensity of these vibrations can be explained by twists of 10-30 degrees about chain single bonds. The 1100-1400-cm-1 Raman fingerprint indicates that the configuration of the double bonds is trans. This suggests that the structure of the bathorhodopsin chromophore is twisted all-trans.

Resonance Raman studies of bathorhodopsin: Evidence for a protonated Schiff base linkage

A dual beam pump/probe technique has been used with a 585-nm probe wavelength to obtain maximal resonance enhancement of the Raman lines of bathorhodopsin in a photostationary steady-state mixture at -160 degrees C. These studies show that bathorhodopsin has a protonated Schiff base vibration at 1657 cm(-1) which shifts upon deuteration to 1625 cm(-1). Within our experimental error (+/-2 cm(-1)) these frequencies are identical to those observed in rhodopsin and isorhodopsin. These effects show that the strength of the C=N bond and the degree of protonation of the Schiff base nitrogen are the same in bathorhodopsin, rhodopsin, and isorhodopsin. The implication of these results for the structure of the retinal chromophore in bathorhodopsin are discussed. The resonance Raman spectrum of pure bathorhodopsin has been generated by accurately subtracting the residual contributions of rhodopsin and isorhodopsin from spectra of the low temperature photostationary mixture. Bathorhodopsin is found to have lines at 853, 875, 920, 1006, 1166, 1210, 1278, 1323, 1536, and 1657 cm(-1). Also, by using an intensified vidicon detector, we have observed Raman scattering from bathorhodopsin at room temperature by generating a photostationary steady state with pulsed laser excitation. At room temperature the three characteristic lines of bathorhodopsin are found at 858, 873, and 920 cm(-1). The fact that the frequencies of these bathorhodopsin lines are nearly identical at both temperatures implies that the retinal conformation in bathorhodopsin formed at -160 degrees C is the same as that formed at room temperature.

The structure of the retinylidene chromophore in bathorhodopsin

Resonance Raman data on bathorhodopsin (bovine and squid) at 95,77, and 4 degrees K support a mechanism of excitation proposed by Lewis in which both a protein conformational transition and chromophore structural alteration to a "dicisoid" configuration are required to generate the bathorhodopsin species observed in steady-state photostationary mixtures. However, these results also suggest that the molecular structure with a red-shifted chromophore absorption detected at room temperatures in 1 ps using picosecond absorption spectroscopy may not necessarily have the same chromophore conformation as the steady-state bathorhodopsin species.