The pH dependence of the subpicosecond retinal photoisomerization process in bacteriorhodopsin: evidence for parallel photocycles

Existence of two substates in the O intermediate of the bacteriorhodopsin photocycle

The proton pumping cycle of bacteriorhodopsin (bR) is initiated when the retinal chromophore with the 13-trans configuration is photo-isomerized into the 13-cis configuration. To understand the recovery processes of the initial retinal configuration that occur in the late stage of the photocycle, we have performed a comprehensive analysis of absorption kinetics data collected at various pH levels and at different salt concentrations. The result of analysis revealed the following features of the late stages of the trans photocycle. i) Two substates occur in the O intermediate. ii) The visible absorption band of the first substate (O1) appears at a much shorter wavelength than that of the late substate (O2). iii) O1 is in rapid equilibrium with the preceding state (N), but O1 becomes less stable than N when an ionizable residue (X₁) with a pKa value of 6.5 (in 2 M KCl) is deprotonated. iv) At a low pH and at a low salt concentration, the decay time constant of O2 is longer than those of the preceding states, but the relationship between these time constants is altered when the medium pH or the salt concentration is increased. On the basis of the present observations and previous studies on the structure of the chromophore in O, we suspect that the retinal chromophore in O1 takes on a distorted 13-cis configuration and the O1-to-O2 transition is accompanied by cis-to-trans isomerization about C13C14 bond.

A Unified View on Varied Ultrafast Dynamics of the Primary Process in Microbial Rhodopsins

All-trans to 13-cis photoisomerization of the protonated retinal Schiff base (PRSB) chromophore is the primary step that triggers various biological functions of microbial rhodopsins. While this ultrafast primary process has been extensively studied, it has been recognized that the relevant excited-state relaxation dynamics differ significantly from one rhodopsin to another. To elucidate the origin of the complicated ultrafast dynamics of the primary process in microbial rhodopsins, we studied the excited-state dynamics of proteorhodopsin, its D97N mutant, and bacteriorhodopsin by femtosecond time-resolved absorption (TA) spectroscopy in a wide pH range. The TA data showed that their excited-state relaxation dynamics drastically change when pH approaches the pK_a of the counterion residue of the PRSB chromophore in the ground state. This result reveals that the varied excited-state relaxation dynamics in different rhodopsins mainly originate from the difference of the ground-state heterogeneity (i.e., protonation/deprotonation of the PRSB counterion).

Intermediate spectra and photocycle kinetics of the Asp96 --> asn mutant bacteriorhodopsin determined by singular value decomposition with self-modeling

Singular value decomposition with self-modeling is applied to resolve the intermediate spectra and kinetics of the Asp96 --> Asn mutant bacteriorhodopsin. The search for the difference spectra of the intermediates is performed in eigenvector space on the stoichiometric plane. The analysis of data at pH values ranging from 4 to 8 and temperatures between 5 and 25 degrees C reveals significant, early partial recovery of the initial state after photoexcitation. The derived spectra are not biased by assumed photocycles. The intermediate spectra derived in the initial step differ from spectra determined in prior analyses, which results in intermediate concentrations with improved stoichiometric properties. Increasingly more accurate photocycles follow with increasing assumed complexity, of which parallel models are favored, consistent with recent, independent experimental evidence.

Kinetic and thermodynamic study of the bacteriorhodopsin photocycle over a wide pH range

The photocycle of bacteriorhodopsin and its thermodynamic parameters were studied in the pH range of 4.5-9. Measurements were performed at five different wavelengths (410, 500, 570, 610, and 650 nm), in the time interval 300 ns to 0.5 s, at six temperatures between 5 and 30 degreesC. Data were fitted to different photocycle models. The sequential model with reversible reactions gave a good fit, and the linear character of the Eyring plots was fulfilled. The parallel model with unidirectional reactions gave a poor fit, and the Eyring plot of the rate constants did not follow the expected linear behavior. When a parallel model with reversible reactions, which has twice as many free parameters as the sequential model, was considered, the quality of the fit did not improve and the Eyring plots were not linear. The sequential model was used to determine the thermodynamic activation parameters (activation enthalpy, entropy, and free energy) of the transitions and the free energy levels of the intermediates. pH dependence of the parameters revealed details of the transitions between the intermediates: the transitions M1 to M2 and N to O disclosed a large entropy increase, which could be interpreted as a loosening of the protein structure. The pH dependence of the energy levels explains the disappearance of intermediate O at high pH. A hypothesis is proposed to interpret the relation between the observed pKa of the photocycle energetics and the role of several amino acids in the protein.

Electric signals during the bacteriorhodopsin photocycle, determined over a wide pH range

From the electric signals measured after photoexcitation, the electrogenicity of the photocycle intermediates of bacteriorhodopsin were determined in a pH range of 4.5-9. Current measurements and absorption kinetic signals at five wavelengths were recorded in the time interval from 300 ns to 0.5 s. To fit the data, the model containing sequential intermediates connected by reversible first-order reactions was used. The electrogenicities were calculated from the integral of the current signal, by using the time-dependent concentrations of the intermediates, obtained from the fits. Almost all of the calculated electrogenicities were pH independent, suggesting that the charge motions occur inside the protein. Only the N intermediate exhibited pH-dependent electrogenicity, implying that the protonation of Asp96, from the intracellular part of the protein, is not from a well-determined proton donor. The calculated electrogenicities gave good approximations of all of the details of the measured electric signals.

The photocycle of bacteriorhodopsin at high pH and ionic strength. I. Effects of pH and buffer on the absorption kinetics

A fitting analysis resolved the kinetics in the microsecond to second time range of the absorption changes in the bacteriorhodopsin photocycle at pH = 8.0-9.5 in 3 M KCl into seven exponential components. The time constants and/or amplitudes of all components are strongly pH-dependent. In the pH range studied, the logarithms of the pH-dependent time constants varied linearly with pH. The maximum absolute value of the corresponding slopes was 0.4, in contrast with the theoretically expected value of 1 for unidirectional reactions coupled directly to proton exchange with the bulk phase. This indicates that the extracted macroscopic rate constants are not identical to the microscopic rate constants for the elementary photocycle reaction steps. Unexpected differences were found in the kinetic parameters in CHES and borate buffers.

Reorientations in the bacteriorhodopsin photoscycle are pH dependent

Chromophore reorientations during the bacteriorhodopsin photocycle in the purple membrane of Halobacterium salinarium have been detected by time-resolved linear dichroism measurements of the optical anisotropy over the pH range from 4 to 10 and at ionic strengths from 10 mM to 1 M. The results show that reorientations in the L and M states of bacteriorhodopsin are pH dependent, reaching their largest amplitude when the membrane is at pH 6-8. Reorientations on the millisecond time scale of unexcited spectator proteins in the native purple membrane also depend on pH, consistent with the suggestion that spectator reorientations are triggered by reorientation of the photoexcited protein. The results imply that a group with a PK(a) of 5 to 6 enables reorientations, and that the deprotonation of a site at pH values above 9 restricts reorientational motion. This suggests that reorientations in M may be correlated with proton release.