The primary process of vision and the structure of bathorhodopsin: a mechanism for photoisomerization of polyenes.

Liu, Robert S. H.; Asato, Alfred E.

doi:10.1073/pnas.82.2.259

Cited by 232 publications

(173 citation statements)

References 36 publications

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“…This step initiates the isomerization and is characterized by a concerted double bicycle-pedal mechanism (40) (illustrated in Fig. 4B) with a minor contribution of hula twist (52) involving tiny pyramidalizations at C12 and C13 [this pyramidalization was also reported by Hayashi et al (31), but at a different location, C14, perhaps due to reduced QM moiety employed in the simulations]. As shown in Fig.…”

Section: Photoisomerization Photoproduct Formation and Retinal Dipolementioning

confidence: 84%

Aborted double bicycle-pedal isomerization with hydrogen bond breaking is the primary event of bacteriorhodopsin proton pumping

Altoè

Cembran

Olivucci

et al. 2010

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

111

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Quantum mechanics/molecular mechanics calculations based on ab initio multiconfigurational second order perturbation theory are employed to construct a computer model of Bacteriorhodopsin that reproduces the observed static and transient electronic spectra, the dipole moment changes, and the energy stored in the photocycle intermediate K. The computed reaction coordinate indicates that the isomerization of the retinal chromophore occurs via a complex motion accounting for three distinct regimes: (i) production of the excited state intermediate I, (ii) evolution of I toward a conical intersection between the excited state and the ground state, and (iii) formation of K. We show that, during stage ii, a space-saving mechanism dominated by an asynchronous double bicycle-pedal deformation of the C10 ═ C11 ─ C12 ═ C13 ─ C14 ═ N moiety of the chromophore dominates the isomerization. On this same stage a N ─ H∕water hydrogen bond is weakened and initiates a breaking process that is completed during stage iii.photoisomerization | quantum mechanics/molecular mechanics (QM/MM) | retinal proteins T he light-activated proton pump bacteriorhodopsin (bR) is an Archaea receptor contained in the purple membrane of Halobacterium salinarium. As shown in Scheme 1, upon photoexcitation, the all-trans retinal chromophore (PSBT) bounded to Lys216 via a protonated Schiff base linkage is converted to the 13-cis isomer (PSB13). This event triggers a series of conformational changes that ultimately result in a proton translocation from the cytoplasmic to the extracellular domain (1).The bR protein environment affects both the spectroscopic and photochemical properties of PSBT (2-4). First, the absorption maximum (568 nm) is red-shifted with respect to the one observed in solution (440 nm in methanol). Second, timeresolved spectroscopy reveals a dominant excited state lifetime component of 450 fs (5, 6) almost matching the 500-fs time scale for formation of the vibrationally hot primary photoproduct J (7,8). In contrast, PSBT in solution features a biexponential decay dynamics with a dominant (ca. 10-fold longer) 2-ps component (9-11). Finally, although bR photoisomerizes stereoselectively (leading exclusively to PSB13) with high (ca. 67%) quantum yield (9, 12), irradiation of PSBT in solution leads to a mixture of different stereoisomers with a smaller (ca. 25%) total quantum yield (9, 13).Low-temperature spectroscopic studies provided evidence for the existence of a tiny (≤1 kcal mol −1 ) energy barrier on the excited state (S 1 ) potential energy surface of bR (14,15). Such a barrier would explain the 450-fs short-lived quasistationary state observed by Ruhman et al. (5) that is assigned to the fluorescent state I (16-18) and precedes decay to the ground state (S 0 ). Recent experiments by Léonard et al. (19) have also revealed that the photoinduced changes in the permanent dipole moment of PSBT are mirrored by the absorption of Trp86 up to the first stable (i.e., cryogenically trapped) photoproduct K (7). Relative to bR, K bears 11.7-...

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Section: Photoisomerization Photoproduct Formation and Retinal Dipolementioning

confidence: 84%

Aborted double bicycle-pedal isomerization with hydrogen bond breaking is the primary event of bacteriorhodopsin proton pumping

Altoè

Cembran

Olivucci

et al. 2010

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

111

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“…Previous models, such as the bicycle-pedal model 36 and the hula-twist model, 37 suggested that, upon photoisomerization, rotation around the C11 = C12 bond propagated to neighboring double and/or single bonds. Our model for Batho shows that, besides the C11 = C12 bond, the C7 = C8 double bond undergoes a large rotation in a bicycle-pedal fashion; in addition, every bond between these double bonds also twists to form a curved structure.…”

Section: Discussionmentioning

confidence: 99%

Crystallographic Analysis of the Primary Photochemical Reaction of Squid Rhodopsin

Murakami

Kouyama

2011

Journal of Molecular Biology

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“…Liu et al [194] proposed a model for the primary process of vision involving a concertedtwist motion. Hayward et al [195] suggested that the isomerisation is complete within picoseconds after the absorption of a photon.…”

Section: Retinamentioning

confidence: 99%

Raman Spectroscopy in Ophthalmology: From Experimental Tool to Applications In Vivo

et al. 2001

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Raman spectroscopy is a qualitative and quantitative optical technique for determining the molecular composition of matter. Improvements in spectroscopic instruments, especially the modality to detect low light level signals extended the Raman technique to biomedical applications, even in delicate structures like the eye. The purpose of this paper was to make an inventory of performed applications of Raman spectroscopy in biomedical science and especially in ophthalmology. A literature search was done using Medline, Current Contents, a patent server on the Internet, and references found in articles and patents. This search revealed a variety of Raman techniques and applications in biomedical research, and an increasing flow of articles starting in the late 1970s on Raman spectroscopy in ophthalmology. This increase in literature about Raman spectroscopy in ophthalmology feeds the expectation that this valuable technique will be introduced in the future into clinical practice.

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The primary process of vision and the structure of bathorhodopsin: a mechanism for photoisomerization of polyenes.

Cited by 232 publications

References 36 publications

Aborted double bicycle-pedal isomerization with hydrogen bond breaking is the primary event of bacteriorhodopsin proton pumping

Aborted double bicycle-pedal isomerization with hydrogen bond breaking is the primary event of bacteriorhodopsin proton pumping

Crystallographic Analysis of the Primary Photochemical Reaction of Squid Rhodopsin

Raman Spectroscopy in Ophthalmology: From Experimental Tool to Applications In Vivo

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