Temperature Dependence of Femtosecond Excited State Dynamics of Bacteriorhodopsin Analyzed by the Fourier Transform of Optical Absorption Spectra

Akiyama, Ryo; Kakitani, Toshiaki; Imamoto, Yasushi; Shichida, Yoshinori; Hatano, Yasuyo

doi:10.1021/j100018a056

Cited by 14 publications

(43 citation statements)

References 12 publications

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“…Much detailed analysis of the temperature dependence of tcf was made for bacteriorhodopsin. 18 Theoretical analyses of these |C(t)| were made 16,18 by assuming harmonic approximation for the vibration and using the values of frequencies and displacements of normal coordinates of 25 and 29 vibrational modes, for rhodopsin and bacteriorhodopsin, respectively, which were determined by the resonance Raman scattering experiments. 21,22 The result was that the theoretically obtained |C(t)| of rhodopsin decreased by 1.5 orders of magnitude (the ordinate of the graphs of Figure 2 in ref 16 was erroneously written in log 10 unit instead of log e unit) in 20-50 fs and remained almost constant after it.…”

Section: Introductionmentioning

confidence: 99%

“…This aspect is consistent with the result of the temperature dependence of the tcf of bacteriorhodopsin, whose initial stage had a remarkable temperature dependence, but the tcf in the later stage was nearly temperature independent and had much vibrational structure. 18 On the basis of these considerations, we aim to extract the molecular picture of the cis-trans photoisomerization around C 11 dC 12 from the tcf of rhodopsin. For this objective, in this paper, we make the FTOA analysis for the modified rhodopsins where [11-D]retinal and [11,12-D 2 ]retinal in 11-cis form (see Figure 1) are incorporated into opsin and compare those results with the FTOA data of native rhodopsin.…”

Section: Introductionmentioning

confidence: 99%

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Deuterium Substitution Effect on the Excited-State Dynamics of Rhodopsin

Kakitani¹,

Akiyama²,

Hatano

et al. 1998

J. Phys. Chem. B

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We investigated the excited-state dynamics of the cis-trans photoisomerization of rhodopsin by analyzing deuterium substitution effects for hydrogen atoms bonded to C 11 and C 12 of the retinal chromophore by the method of Fourier transform of optical absorption spectra (FTOA). Plotting the absolute value of the time correlation function of modified vibrational wave packet, we found that the deuterium substitution effects do not appear in the excited-state dynamics until about 20 fs after photon absorption, weakly appear in the time range 20-60 fs, significantly appear in the time range 70-110 fs, and complicatedly appear in the time range 110-170 fs. By analyzing those deuterium substitution effects, we obtained a result that the concerted motions of hydrogen out-of-plane (HOOP) waggings at C 11 and C 12 , which are found to exist in native rhodopsin in the time range 20-60 fs, do not contribute to the excited-state dynamics in its time range appreciably and that the coupled motions of hydrogen atoms at C 11 and C 12 , which are significantly coupled with the skeletal twisting motion of the chromophore in the time range 70-110 fs, contribute to the excited dynamics in its time range substantially. The hydrogen motions after 110 fs contribute to the excited-state dynamics in a complicate way. This cis-trans photoisomerization process of rhodopsin is basically similar to that of bacteriorhodopsin, which was obtained by the comparative analysis of the FTOA of 13-trans-lockedbacteriorhodopsin with native bacteriorhodopsin. † Abbreviations: CHAPS, 3-[(3-cholamidopropyl)dimethylammonio]-1propanesulfonate; PC, L-R-phosphatidylcholine from fresh egg yolk; HEPES, N-(2-hydroxyethyl)piperazine-N′-2-ethanesulfonic acid.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Deuterium Substitution Effect on the Excited-State Dynamics of Rhodopsin

Kakitani¹,

Akiyama²,

Hatano

et al. 1998

J. Phys. Chem. B

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“…1) have been studied intensively (11, 13-33), but there are still unanswered questions regarding the electronic potential energy surfaces (PES) of retinal, the interaction with its surroundings in the protein, and related ultrafast vibrational coupling. A number of models have been proposed, each explaining parts of the large number of experiments (4,13,14,16,(34)(35)(36)(37)(38)(39)(40). Attempts have been made to reconcile the differences between these models (4).…”

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confidence: 99%

Control of retinal isomerization in bacteriorhodopsin in the high-intensity regime

Florean

Cardoza

White

et al. 2009

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

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A learning algorithm was used to manipulate optical pulse shapes and optimize retinal isomerization in bacteriorhodopsin, for excitation levels up to 1.8 ؋ 10 16 photons per square centimeter. Below 1/3 the maximum excitation level, the yield was not sensitive to pulse shape. Above this level the learning algorithm found that a Fourier-transform-limited (TL) pulse maximized the 13-cis population. For this optimal pulse the yield increases linearly with intensity well beyond the saturation of the first excited state. To understand these results we performed systematic searches varying the chirp and energy of the pump pulses while monitoring the isomerization yield. The results are interpreted including the influence of 1-photon and multiphoton transitions. The population dynamics in each intermediate conformation and the final branching ratio between the all-trans and 13-cis isomers are modified by changes in the pulse energy and duration.coherent control ͉ photoisomerization ͉ ultrafast science B acteriorhodopsin (bR) is a photosynthetic protein found in the purple membrane of Halobacterium salinarum and capable of conversion of solar energy into chemical energy. This energy conversion is efficient (1-3) and has several possible applications (4-12). A retinal chromophore is responsible for photon absorption. After photoexcitation retinal undergoes ultrafast isomerization from the all-trans to a 13-cis configuration, accompanied by additional changes in the conformation of bR (3,8). The initial steps of the bR photocycle (see Fig. 1) have been studied intensively (11, 13-33), but there are still unanswered questions regarding the electronic potential energy surfaces (PES) of retinal, the interaction with its surroundings in the protein, and related ultrafast vibrational coupling. A number of models have been proposed, each explaining parts of the large number of experiments (4,13,14,16,(34)(35)(36)(37)(38)(39)(40). Attempts have been made to reconcile the differences between these models (4).We aim to understand how the optical pulse shape and intensity affect the all-trans 3 13-cis yield and to explore potential pathways for producing high photoproduct yields on an ultrafast time scale. This is relevant for energy storage using bio-molecular machines (9, 32). Recently, Prokhorenko et al. showed that the isomerization yield of retinal in bR could be manipulated in a low intensity, biologically relevant regime through the use of phase and amplitude shaped optical fields (25). Modifications of as much as Ϯ20% were observed compared with unshaped pulses capable of exciting an equal number of molecules. Yet the ultimate yields remain small as photon flux was restricted to excite Ϸ0.3% of the chromophores in the excitation volume. In a different experiment, Vogt et al. used much higher intensity, shorter wavelength pump pulses to excite bR and a shaped 800-nm dump pulse to study the evolution of the molecule on the excited state PES (30). They found that the excited population is transferred most effectively back to t...

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“…[1][2][3][4][5][6][7] Another example is bacteriorhodopsin, which undergoes an ultrafast photoisomerization reaction of the protonated Schiff base of retinal (PSBR) from the all-trans form to the 13-cis for after light illumination. [8][9][10][11][12][13][14][15][16][17][18][19][20] As a result, the photocycle is triggered and a proton is transported from the cytoplasmic side to the extracellular side across the purple membrane of Halobacterium salinarum. The rhodopsin molecule contains the protonated Schiff base of retinal as well as the bacteriorhodopsin molecule.…”

Section: Introductionmentioning

confidence: 99%

Stress tensor analysis of the protein quake of photoactive yellow protein

Koike¹,

Kawaguchi²,

Yamato³

2008

Phys. Chem. Chem. Phys.

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Immediately after photon absorption, the photoenergy is converted to local stress energy via the ultrafast photoisomerization reaction of the p-coumaric acid (pCA) chromophore in a small water-soluble blue light receptor, photoactive yellow protein (PYP), derived from the halophilic bacterium, Halorhodospira halophila. A series of conformational changes are then induced, which are intimately related with the relaxation process on the energy landscape of PYP. In order to understand the signaling function of PYP in atomic detail, the characterization of the physical mechanism of the protein quake of PYP is important, as is the atomic description of the series of conformational changes associated with the photocycle. Here, we report a theoretical/computational study for the analysis of the intramolecular stress tensor for the dark state and three intermediate states, pR, pB1 and pB2, of PYP. As a result, we found that the magnitude of the stress released during the change from the pR to the pB1 state is significantly large at the hydroxyl oxygen atom of Tyr42, suggesting that this atom is the focus of the protein quake of PYP. This is consistent with previous experimental observations.

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Temperature Dependence of Femtosecond Excited State Dynamics of Bacteriorhodopsin Analyzed by the Fourier Transform of Optical Absorption Spectra

Cited by 14 publications

References 12 publications

Deuterium Substitution Effect on the Excited-State Dynamics of Rhodopsin

Deuterium Substitution Effect on the Excited-State Dynamics of Rhodopsin

Control of retinal isomerization in bacteriorhodopsin in the high-intensity regime

Stress tensor analysis of the protein quake of photoactive yellow protein

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