Isomerization In Bacteriorhodopsin Research Articles

Retinal isomerization in bacteriorhodopsin captured by a femtosecond X-ray laser

Retinal isomerization in bacteriorhodopsin captured by a femtosecond X-ray laser

Retinal isomerization in bacteriorhodopsin captured by a femtosecond x-ray laser.

Ultrafast isomerization of retinal is the primary step in photoresponsive biological functions including vision in humans and ion transport across bacterial membranes. We used an x-ray laser to study the subpicosecond structural dynamics of retinal isomerization in the light-driven proton pump bacteriorhodopsin. A series of structural snapshots with near-atomic spatial resolution and temporal resolution in the femtosecond regime show how the excited all-trans retinal samples conformational states within the protein binding pocket before passing through a twisted geometry and emerging in the 13-cis conformation. Our findings suggest ultrafast collective motions of aspartic acid residues and functional water molecules in the proximity of the retinal Schiff base as a key facet of this stereoselective and efficient photochemical reaction.

2P281 固体NMRを用いた圧力誘起によるバクテリオロドプシン中レチナールの異性化機構の解析(光生物-視覚・光受容,第48回日本生物物理学会年会)

2P281 固体NMRを用いた圧力誘起によるバクテリオロドプシン中レチナールの異性化機構の解析(光生物-視覚・光受容,第48回日本生物物理学会年会)

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

A learning algorithm was used to manipulate optical pulse shapes and optimize retinal isomerization in bacteriorhodopsin, for excitation levels up to 1.8 x 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.

1P-215 固体NMRによるバクテリオロドプシンの圧力によって誘起されるレチナール異性化機構の解析(光生物-視覚・光受容,第47回日本生物物理学会年会)

1P-215 固体NMRによるバクテリオロドプシンの圧力によって誘起されるレチナール異性化機構の解析(光生物-視覚・光受容,第47回日本生物物理学会年会)

On the mechanism of weak-field coherent control of retinal isomerization in bacteriorhodopsin

Experimental studies of the short time reaction dynamics controlling the chemical branching ratio provide direct evidence for the mechanism of coherent control of the retinal photoisomerization in bacteriorhodopsin in the weak-field limit with respect to the previous report [V. Prokhorenko, A. Nagy, S. Waschuk, L. Brown, R. Birge, R. Miller, Science 313 (2006) 1257]. The phase sensitivity of the reaction dynamics is directly revealed using time- and frequency-resolved pump–probe measurements. The high degree of control of the reaction branching ratio is theoretically explained through a combination of spectral amplitude shaping and phase-dependent coupling to selectively excite vibrations most strongly coupled to the reaction coordinate. Coherent control in this context must involve reaction dynamics that occur on time scales comparable to electronic and vibrational decoherence time scales.

Comment on "Coherent Control of Retinal Isomerization in Bacteriorhodopsin"

Prokhorenko et al. (Research Articles, 1 September 2006, p. 1257) reported that, in the weak-field regime, the efficiency of retinal isomerization in bacteriorhodopsin can be controlled by modulating the spectral phase of the photoexcitation pulse. However, in the linear excitation regime, the signal measured in an experiment involving a time-invariant, stationary process can be shown to be independent of the pulse spectral phase.

Response to Comment on "Coherent Control of Retinal Isomerization in Bacteriorhodopsin"

Joffre attempts to show that the linear response of any quantum system to an external perturbation is phase insensitive, but he uses incorrect mathematical assumptions, misinterprets the time invariance principle, and ignores causality. We argue that the opposite case—an explicit phase dependence for a signal measured in the linear excitation regime—can equally be shown using Joffre's approach and assumptions.

Femtosecond pump–shaped-dump quantum control of retinal isomerization in bacteriorhodopsin

We experimentally demonstrate molecular quantum control on the photoisomerization of retinal in bacteriorhodopsin with pump and shaped-dump femtosecond laser pulses. The objective is a reversion of regular control schemes for optimal excitation in which the pump pulse is shaped. Instead, we seek optimal de-excitation with a shaped-dump pulse. The pump–shaped-dump–probe scheme allows control of molecular systems away from the initial Franck–Condon window in regions of the potential-energy landscape where the decisive reaction step occurs. In addition, this method has the potential to provide information on wave packet evolution and underlying potential-energy surfaces.

Coherent Control of Retinal Isomerization in Bacteriorhodopsin

Optical control of the primary step of photoisomerization of the retinal molecule in bacteriorhodopsin from the all-trans to the 13-cis state was demonstrated under weak field conditions (where only 1 of 300 retinal molecules absorbs a photon during the excitation cycle) that are relevant to understanding biological processes. By modulating the phases and amplitudes of the spectral components in the photoexcitation pulse, we showed that the absolute quantity of 13-cis retinal formed upon excitation can be enhanced or suppressed by +/-20% of the yield observed using a short transform-limited pulse having the same actinic energy. The shaped pulses were shown to be phase-sensitive at intensities too low to access different higher electronic states, and so these pulses apparently steer the isomerization through constructive and destructive interference effects, a mechanism supported by observed signatures of vibrational coherence. These results show that the wave properties of matter can be observed and even manipulated in a system as large and complex as a protein.

1P425 Structure analysis of Tyr residues with retinal isomerization in bacteriorhodopsin by solid state NMR(17. Light driven system,Poster Session,Abstract,Meeting Program of EABS &BSJ 2006)

1P425 Structure analysis of Tyr residues with retinal isomerization in bacteriorhodopsin by solid state NMR(17. Light driven system,Poster Session,Abstract,Meeting Program of EABS &BSJ 2006)

Primary events in the bacteriorhodopsin photocycle: Torsional vibrational dephasing in the first excited electronic state

A new model of the primary events of the bacteriorhodopsin (BR) photocycle is derived from the analysis of vibrational spectroscopic data obtained from native BR (BR-570) and three artificial BR pigments containing structurally modified retinals with carbon rings bridging specific C–C and C C bonds (BR6.11, BR6.9, and BR5.12). Vibrational spectra from the ground-states and from picosecond intermediates appearing in the respective photo-reactions are measured by coherent anti-Stokes Raman spectroscopy (CARS). Special attention is given to an analysis of the time-dependent bandwidth changes in vibrational bands assigned to the C C stretching and hydrogen-out-of-plane (HOOP) modes. The bandwidth analysis reveals an intramolecular, vibrational dephasing mechanism in the lowest-energy electronic excited state, involving a coupling between out-of-plane motion along the retinal backbone and C C stretching modes. The mode-selective coupling plays a significant role as a precursor to the all- trans → 13- cis isomerization in BR and accounts for primary events in the BR photocycle not previously demonstrated.

Retinal isomerization in bacteriorhodopsin is controlled by specific chromophore-protein interactions. A study with noncovalent artificial pigments.

It has previously been shown that, in mutants lacking the Lys-216 residue, protonated Schiff bases of retinal occupy noncovalently the bacteriorhodopsin (bR) binding site. Moreover, the retinal-Lys-216 covalent bond is not a prerequisite for initiating the photochemical and proton pump activity of the pigment. In the present work, various Schiff bases of aromatic polyene chromophores were incubated with bacterioopsin to give noncovalent pigments that retain the Lys-216 residue in the binding site. It was observed that the pigment's absorption was considerably red-shifted relative to the corresponding protonated Schiff bases (PSB) in solution and was sensitive to Schiff base linkage substitution. Their PSB pK(a) is considerably elevated, similarly to those of related covalently bound pigments. However, the characteristic low-pH purple to blue transition is not observed, but rather a chromophore release from the binding site takes place that is characterized by a pK(a) of approximately 6 (sensitive to the specific complex). It is suggested that, in variance with native bR, in these complexes Asp-85 is protonated and Asp-212 serves as the sole negatively charged counterion. In contrast to the bound analogues, no photocycle could be detected. It is suggested that a specific retinal-protein geometrical arrangement in the binding site is a prerequisite for achieving the selective retinal photoisomerization.

Characterization of a conical intersection between the ground and first excited state for a retinal analog

Ab initio complete active space SCF calculations have been carried out to investigate the first excited electronic state of a retinal protonated Schiff base analog: all-trans-3,7-dimethylnona-2,4,6,8-tetraenmethylimminium cation. This model of the retinal chromophore in bacteriorhodopsin includes five conjugated double bonds as well as both pertinent backbone methyl groups. The excited state minimum that is relevant for isomerization in bacteriorhodopsin is investigated and is found to be in very close proximity to a Jahn–Teller conical intersection. The two (global) coordinates that are most effective in promoting efficient internal conversion back to the ground electronic state (by lifting the degeneracy between the ground and first excited state) are identified and discussed, and the distribution of the positive charge in the retinal analog as a function of these two coordinates is investigated.

Vibrational relaxation during the retinal isomerization in Bacteriorhodopsin

Femtosecond time-resolved optical pump–infrared probe spectroscopy was employed to characterize the ethylenic (CC)-stretch vibrational dynamics (1498–1542 cm −1) of the retinal chromophore in Bacteriorhodopsin (BR) during the initial, all-trans to 13-cis isomerization. The early branching reaction was observed, i.e. formation of the ground-state 13-cis product, K, and partial recovery of the all-trans educt state BR 570. The BR 570 recovery occurs within 2 ps and thus is faster than K-formation (3–4 ps). The IR transients are described in terms of a kinetic model involving vibrational precursors for K and for the recovering BR 570, respectively.

Free-energy simulations of the retinal cis --> trans isomerization in bacteriorhodopsin.

Free-energy profiles for ground-state cis --> trans isomerization of retinal in vacuum, in solution, and in the protein bacteriorhodopsin are calculated using free-energy simulations. The free-energy barriers in the protein were 9 kcal/mol for ionized Asp85 and 14 kcal/mol for neutral Asp85, significantly lower than those found in solution (18 kcal/mol) or vacuum (19 kcal/mol). Therefore, bacteriorhodopsin can be said to act as a catalyst in the isomerization. The barrier in the protein is due mainly to stabilization of the transition state through favorable nonbonded interactions with the protein part of the system, with internal strain and interactions with solvent playing minor roles. The protonated Asp85 simulation models the behavior of the system in the N --> O transition. Our calculated 14 kcal/mol barrier and 4-ms relaxation time for this process are in excellent agreement with experimentally measured values of 12 kcal/mol and 5 ms, respectively. The ionized Asp85 simulation models two hypothetical processes: the N --> O transition with a proton removed from Asp85 and the initial BR568 --> L transition on the ground-state energy surface. The cis-trans isomerization barrier in this system is 9 kcal/mol, the lowest of all the studied cases. The presence of the charged carboxylate group in the ionized Asp85 system leads to strong stabilization of the transition state by interactions with the surroundings and changes the distance between Asp85 and the Schiff base proton compared to the corresponding distance in the neutral Asp85 system. This suggests that the protonation of Asp85 plays an important role in regulating access to the Schiff base proton. For both Asp85 ionization states the calculated cis-trans free-energy difference was close to 0, indicating that the protein can accommodate both retinal isomers equally well. The computed negligible difference between the N and O free-energy levels is in accord with experimental data.

Evidence for light-induced 13-cis , 14-s-cis isomerization in bacteriorhodopsin obtained by FTIR difference spectroscopy using isotopically labelled retinals

We have obtained by Fourier transformed infra-red (FTIR)-spectroscopy BR-K, BR-L and BR-M difference spectra of bacteriorhodopsin regenerated with isotopically labelled retinals. Thereby, we are able to assign reliably the C(14)-C(15) and C=N stretching vibrations of the various intermediates. The lower C(14)-C(15) stretching vibration frequency in L as compared with 13-cis protonated Schiff base model compounds indicates a 13-cis, 14-s-cis configuration of the retinal in this species. The unusually low C=N stretching vibration in K at 1615 cm indicates less stabilization of the positive charge at the Schiff base by the protein environment. Based on these results, a mechanism is suggested by which the stored light energy is transformed into proton transfers.