Femtosecond spectroscopy of acidified and neutral bacteriorhodopsin

Kobayashi, Takayoshi; Terauchi, Mamoru; Kouyama, Tsutomu; Yoshizawa, M.; Taiji, Makoto

doi:10.1117/12.57310

Cited by 28 publications

(60 citation statements)

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“…It is seen that the placement of retinal inside the protein reduces the isomerization barrier governing the thermal isomerization of retinal around two (C 13 -C 14 , C 15 -N) double bonds, by about 20 kcal/mol. This result is in agreement with the common notion that the protein environment enhances the isomerizational transformations of in situ retinal [71,72]. However, the question arises whether the standard classical electrostatic models with their pairwise additive potentials describe the chromophore-protein interactions properly, or if the polarizing effect of the environment must be included.…”

supporting

confidence: 79%

“…It has been observed that modification of protein groups in the vicinity of the retinal Schiff base shifts considerably the bR absorption spectrum [69] and affects drastically the rates of both thermally- [70] and photo- [71,72] activated isomerization processes in bR. The experiments imply that the protein environment plays a crucial role in determining the physico-chemical properties of…”

Section: Quantum Chemistry Of In Situ Retinalmentioning

confidence: 90%

“…It has been observed that modification of protein groups in the vicinity of the retinal Schiff base shifts considerably the bR absorption spectrum [69] and affects drastically the rates of both thermally- [70] and photo- [71,72] [75,76,77]. At present, there exist a number of ab initio as well as semi-empirical techniques which try to account for the realistic atomic structure and charge distribution of the environment via explicit incorporation of protein (or solution) point charges in the electronic Hamiltonian of the quantum chemically treated substrate [78,79,80,81,82,83].…”

Section: Quantum Chemistry Of In Situ Retinalmentioning

confidence: 99%

See 2 more Smart Citations

Quantum Chemistry of in situ Retinal: Study of the Spectral Properties and Dark Adaptation of Bacteriorhodopsin

Logunov

Schulten

1996

Quantum Mechanical Simulation Methods for Studying Biological Systems

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1A combination of molecular dynamics and quantum chemistry techniques have been employed to study the electronic excitation and conformational potential surface of retinal in the binding site of bacteriorhodopsin (bR). The CASSCF(6,9)/6-31G level of ab initio calculations (within Gaussian92) has been used for the treatment of both the ground (S0) and excited (S1) states of retinal. Charges of all atoms in the protein are represented by spherical Gaussians and explicitly included in the electronic Hamiltonian of retinal. Spectral properties have been analyzed for the native bR pigment as well as for its D85N mutant.The calculated relative shift in the absorption maxima between the two pigments is in better agreement with experiment than the computed absolute parameters of the absorption line shapes. The dark adaptation processes in bacteriorhodopsin (which involves rotation around the 13-14 and the 15-N retinal double bonds) has been modelled by following the pre-defined reaction coordinate. Our simulations support the notion that the isomerization process is catalyzed by the protonation of an aspartic acid (Asp85) side group of bacteriorhodopsin. 2 IntroductionBacteriorhodopsin (bR) spans the cell membrane of Halobacterium halobium and functions as a light-driven proton pump. bR contains seven α-helices which enclose the prosthetic group, all-trans retinal, bound via a protonated Schiff base linkage to Lys-216. Figure 1a shows the chemical structure of retinal and its conventional numbering scheme. The bR structure is presented in Fig. 2a. Retinal absorbs light and undergoes a photoisomerization process; the thermal reversal of this reaction is coupled to transfer of a proton from the cytoplasmic side (top in Fig. 2a) to the extracellular side (bottom in Fig. 2a) of the protein.Recent reviews that discuss the structure and function of bR are [1,2,3,4,5,6,7]. Figure 1 here Bacteriorhodopsin accomplishes its function through a cyclic process initiated by absorption of a photon. This photon triggers an isomerization of retinal, which proceeds then through several intermediate states identified by their absorption spectra. An accepted kinetic scheme for this cycle is an unbranched series of intermediates, shown in Fig. 3. Photoisomerization occurs in the bR 568 → J 625 transition. During the L 550 → M 412 transition the Schiff base proton is transferred to Asp-85 and, subsequently, to the outside of the cell [8,9,10,11,12,13]. During the M 412 → N 520 transition, a proton is transferred to the Schiff base from Asp-96, which then takes up a proton from the cytoplasmic environment [13]. The reaction cycle is completed as the protein returns to bR 568 via the O 640 intermediate. Figure 2 here When bR is allowed to equilibrate in the dark, it converts within an hour to a 2:1 mixture containing 13-cis retinal and all-trans retinal bR [14]. The protein containing the 13-cis retinal isomer of bRis referred to as the dark adapted (DA) pigment of bR, bR 548 , which absorbs at 548 nm. bR 548 contains, actually, retinal in a 1...

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supporting

confidence: 79%

“…It has been observed that modification of protein groups in the vicinity of the retinal Schiff base shifts considerably the bR absorption spectrum [69] and affects drastically the rates of both thermally- [70] and photo- [71,72] activated isomerization processes in bR. The experiments imply that the protein environment plays a crucial role in determining the physico-chemical properties of…”

Section: Quantum Chemistry Of In Situ Retinalmentioning

confidence: 90%

“…It has been observed that modification of protein groups in the vicinity of the retinal Schiff base shifts considerably the bR absorption spectrum [69] and affects drastically the rates of both thermally- [70] and photo- [71,72] [75,76,77]. At present, there exist a number of ab initio as well as semi-empirical techniques which try to account for the realistic atomic structure and charge distribution of the environment via explicit incorporation of protein (or solution) point charges in the electronic Hamiltonian of the quantum chemically treated substrate [78,79,80,81,82,83].…”

Section: Quantum Chemistry Of In Situ Retinalmentioning

confidence: 99%

See 1 more Smart Citation

Quantum Chemistry of in situ Retinal: Study of the Spectral Properties and Dark Adaptation of Bacteriorhodopsin

Logunov

Schulten

1996

Quantum Mechanical Simulation Methods for Studying Biological Systems

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“…The transient spectra for the wild type bR obtained in our experiment ( Figure 2) are similar to those measured previously. 16 …”

Section: Resultsmentioning

confidence: 97%

Photoisomerization Quantum Yield and Apparent Energy Content of the K Intermediate in the Photocycles of Bacteriorhodopsin, Its Mutants D85N, R82Q, and D212N, and Deionized Blue Bacteriorhodopsin

et al. 1996

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The quantum yield of photoisomerization and the energy content of the K intermediate in the photocycle of bacteriorhodopsin and its mutants D85N, R82Q, and D212N and deionized blue bR were measured. Transient optical absorption and photoacoustic spectroscopy with excitation using 400 fs laser pulse were combined to obtain results. The spectroscopic characteristics of the excited state, the J and K intermediates in the photocycle of the mutants, and deionized blue bR were determined. The presence of both 13-cis and all-trans isomers in the ground state of light-adapted D85N, R82Q, and D212N and deionized blue bR makes extraction of the quantum yield for each isomer difficult. Thus, only average values of the quantum yield for these samples were determined. The replacement of charged groups in the vicinity of the retinal Schiff base was found to decrease the rate of the photoisomerization by up to 30 times, but with no signficant change in either the apparent quantum yield of the photoisomerization or the energy stored in the K intermediate. The results are discussed in terms of the different models for the excited and ground state potential surfaces of the retinal configuration in bacteriorhodopsin.

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“…Figure 1 illustrates the complicated spectroscopic information in fs time-resolved absorption spectra of BR, including both visible region and near-infrared region. Wavelength zone below 500 nm is the characteristic absorption band (CAB) of I 460 [8,[27][28][29] ; the bleaching band at 530-610 nm corresponds to the depletion of the ground-state molecules of all-trans retinal; the wavelength range between 600 and 700 nm is the CABs of J 625 and K 590 [28,29] The negative signal above 700 nm is the stimulated emission from the excited-state BR (BR*). The spectra of these intermediates are superposed severely and this consequently messes up the dynamics process of every intermediate.…”

Section: Femtosecond Absorption Spectroscopymentioning

confidence: 99%

Ultrafast isomerization dynamics of retinal in bacteriorhodopsin as revealed by femtosecond absorption spectroscopy

Zhong

et al. 2008

Sci. Bull.

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Femtosecond spectroscopy of acidified and neutral bacteriorhodopsin

Cited by 28 publications

References 0 publications

Quantum Chemistry of in situ Retinal: Study of the Spectral Properties and Dark Adaptation of Bacteriorhodopsin

Quantum Chemistry of in situ Retinal: Study of the Spectral Properties and Dark Adaptation of Bacteriorhodopsin

Photoisomerization Quantum Yield and Apparent Energy Content of the K Intermediate in the Photocycles of Bacteriorhodopsin, Its Mutants D85N, R82Q, and D212N, and Deionized Blue Bacteriorhodopsin

Ultrafast isomerization dynamics of retinal in bacteriorhodopsin as revealed by femtosecond absorption spectroscopy

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