Hydroretinals and hydrorhodopsins

Arnaboldi, Maria; Motto, Michael G.; Tsujimoto, Kazuo; Balogh‐Nair, Valeria; Nakanishi, Koji

doi:10.1021/ja00517a059

Cited by 133 publications

(98 citation statements)

References 8 publications

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“…They concluded that B had a perturbed all-trans configuration and that it is protonated. (91), and Pardoen et al (92,93) there is a negative charge near the ionone ring in conformity with the proposal of Nakanishi et al (104). The third charge could be the counter-ion of the negative charge.…”

Section: Isomerizationsupporting

confidence: 75%

“…the difference being the opsin-shift. Methanol was chosen as a solvent (104,110), since A,,,, in this solvent is independent from the counter-ion ("levelling effect", Blatz and Mohler (126)). This is not an ideal choice, since methanol as a polar, hydrogen bonding solvent promotes protonation that is, helps to push the proton onto the nitrogen in a salt bridge.…”

Section: The Saga O F the Resonance Raman Assault On Rh And Br Startementioning

confidence: 99%

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The photochemical event in rhodopsins

Sándorfy¹,

Vocelle²

1986

Can. J. Chem.

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. 64, 225 1 (1986).The photochemical step in the functioning of visual and bacterial rhodopsins entails cis-trans or trans-cis isomerization and changes in the state of protonation of the retinylidene Schiff base chromophore. In this review our present knowledge on these two events is discussed as well as the role of interactions between the chromophore and the surrounding protein, opsin. The relation between protonation and hydrogen bonding at the Schiff base nitrogen, the problems of stabilization of the proton bridge and charge separation are also discussed. A new proposal is made which implies Schiff base to counter-ion proton translocation with concomitant isomerization and reprotonation of the chromophore.

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Section: Isomerizationsupporting

confidence: 75%

Section: The Saga O F the Resonance Raman Assault On Rh And Br Startementioning

confidence: 99%

The photochemical event in rhodopsins

Sándorfy¹,

Vocelle²

1986

Can. J. Chem.

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“…As previously reported (13), in Rh, the 34% of the chromophore charge, originally located on the -NHACH-moiety, is shifted toward the ␤-ionone upon S 0 3 S 1 vertical excitation. An electrostatic potential stabilizing, in the excited state, the positive charge near the ␤-ionone region or destabilizing it in the Schiff base region, for the ground state, will result in a decreased S 0 3 S 1 excitation energy (34).…”

Section: Resultsmentioning

confidence: 99%

The color of rhodopsins at theab initiomulticonfigurational perturbation theory resolution

Coto

Strambi

Ferré

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

131

204

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We demonstrate that ''brute force'' quantum-mechanics͞molecu-lar-mechanics computations based on ab initio (i.e., first principles) multiconfigurational perturbation theory can reproduce the absorption maxima of a set of modified bovine rhodopsins with an accuracy allowing for the analysis of the factors determining their colors. In particular, we show that the theory accounts for the changes in excitation energy even when the proteins display the same charge distribution. Three color-tuning mechanisms, leading to changes of close magnitude, are demonstrated to operate in these conditions. The first is based on the change of the conformation of the conjugated backbone of the retinal chromophore. The second operates through the control of the distance between the positive charge residing on the chromophore and the carboxylate counterion. Finally, the third mechanism operates through the changes in orientation of the chromophore relative to the protein. These results offer perspectives for the unbiased computational design of mutants or chemically modified proteins with wanted optical properties.excited states ͉ quantum mechanics͞molecular mechanics R ecently, protein mutants displaying properties such as high binding affinities and novel catalytic activities (1, 2) have been designed by using computational methods based on molecular mechanics. In a close context, substrate selectivity has been simulated by using more advanced tools based on density functional theory and molecular mechanics paving the way to the design of mutations that convert receptors into enzymes (3). However, the design of mutants with specific spectral properties, such as color and luminescence, represents a more complex problem. In these cases, the quantum chemical method used must be capable to describe both ground and electronically excited states of the protein chromophore. The ab initio (i.e., first-principles) complete-active-space self-consistent-field (CASSCF) method (4) is a multiconfigurational method offering maximum flexibility for an unbiased description of the electronic and equilibrium structure of a molecule (i.e., with no empirically derived parameters and avoiding single-reference wavefunctions). Furthermore, the CASSCF wave function can be used for subsequent multiconfigurational second-order perturbation theory (5) computations (CASPT2) of the dynamic correlation energy of each state ultimately leading to a nearly quantitative evaluation of the excitation energies of organic compounds (6, 7). The CASPT2 ability to describe exotic bonding has been recently assessed (8).In a previous study (9), we implemented the ab initio CASPT2͞͞CASSCF protocol (where equilibrium geometries and electronic energies are determined at the CASSCF and CASPT2 levels, respectively) in a quantum mechanics͞ molecular mechanics (QM͞MM) scheme (10-12) allowing for the evaluation of the excitation energy of chromophores (treated quantum mechanically) embedded in a protein environment (described by a MM force field).The absorption and fluorescence max...

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“…It is, therefore, a process which is typical for the transition from the stable species rhodopsin or isorhodopsin to their first photoproduct, bathorhodopsin. The modification of carboxylic groups may play a role in point-charge models of the chromophore in rhodopsin [6,32].…”

Section: Discussionmentioning

confidence: 99%

Fourier‐transform infrared spectroscopy applied to rhodopsin

Siebert

Mäntele

Gerwert

1983

European Journal of Biochemistry

110

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By measuring the rhodopsin -bathorhodopsin, isorhodopsin -bathorhodopsin, rhodopsin -isorhodopsin and rhodopsin --eta-I1 difference spectra with the method of Fourier-transform infrared spectroscopy we have identified the C=N stretching vibration of the protonated retinylidene Schiff base of rhodopsin, isorhodopsin and bathorhodopsin. In contrast to resonance Raman spectroscopy additional strong bands were observed between 1700cm-'and 1620cni-'. Most ofthemdependon theisomericstateofthechromophore. Theoriginofthese bands will be discussed. In the fingerprint region isorhodopsin and bathorhodopsin are quite similar but no similarities with infrared spectra of model compounds of any isomeric composition are observed. Therefore, no conclusions on the isomeric state of the retinal in bathorhodopsin can be drawn. We provide evidence for the modification of one or two carboxylic group(s) during the rhodopsin -bathorhodopsin and isorhodopsin -bathorhodopsin transition.During the last years evidence has accumulated to show that the main role of rhodopsin in the visual transduction process consists in its function as an activator of enzymatic reactions, switched on by the action of light (e.g. [I]). The molecular events leading to the activation of rhodopsin are still not well enough understood. A prerequisite for the understanding of this mechanism is the knowledge of the molecular events in the chromophore 1 I-cis retinal and in the protein, as well as the knowledge of the chromophore-protein interaction, especially of the nature of the chromophore-protein bond. Resonance Raman spectroscopy has provided evidence that the retinal-protein link constitutes a protonated Schiff base [2-51. This finding has been questioned on the basis of theoretical and experimental arguments [6 -121. To explain the discrepancy processes in the electronic excited state involved in resonance Raman spectroscopy have been proposed. With the method of time-resolved infrared spectroscopy we have previously measured the rhodopsin -meta-I and rhodopsin --eta-11 difference spectra [12]. In these measurements it was not possible to identify clearly the Cz=N stretching vibration of the protonated retinylidene Schiff base in rhodopsin, and a protonation via a hydrogen bond has, therefore, been suggested. These investigations were hampered by low spectral resolution (5 cm-' -8 cm-'). In addition, protein changes, which cause spectral changes, have been invoked to explain these observations. Nevertheless, since infrared difference spectroscopy does not involve the electronic excited state, it still would be desirable to apply this method at a higher spectral resolution to solve the problem of the nature of the retinal-protein link in rhodopsin. Recently, Fourier-transform infrared (FTIR) difference spectroscopy has been successfully employed to measure the static difference spectra in the systems of CO-myoglobin and bacteriorhoAhhrez;iutions. FTTR spectroscopy, Fourier-transform infrared spectroscopy; BR568r light-adapted form of bacteriorhodopsin; Kslo...

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Hydroretinals and hydrorhodopsins

Cited by 133 publications

References 8 publications

The photochemical event in rhodopsins

The photochemical event in rhodopsins

The color of rhodopsins at theab initiomulticonfigurational perturbation theory resolution

Fourier‐transform infrared spectroscopy applied to rhodopsin

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