Effect of iodination of the purple membrane on the photocycle of bacteriorhodopsin

Bacteriorhodopsin in the purple membrane of Halobacterium halobium is coupled to a photocycle that results in the release and uptake of protons. The role of tyrosyl residues in the photocycle of bacteriorhodopsin has been investigated by the technique of chemical modifications of these residues by iodination and nitration. The studies indicate that modification of a tyrosyl residue accelerates M₄₁₂ formation, whereas modification of another type of tyrosine residue(s) accessible from the cytoplasmic surface of the purple membrane inhibits M₄₁₂ decay. The results support the hypothesis that a reversible deprotonation of tyrosine residues prior to and after M₄₁₂ formation in the photocycle are steps in the light-driven pathway of H⁺ translocation by bacteriorhodopsin.     

Effects of the crystalline structure of purple membrane on the kinetics and energetics of the bacteriorhodopsin photocycle.

Time-resolved difference spectra were measured for Triton X-100 solubilized bacteriorhodopsin monomers between 100 ns and 100 ms after photoexcitation. The results are consistent with the general scheme K in equilibrium L in equilibrium M1 in equilibrium M2 in equilibrium N in equilibrium O----BR proposed previously for purple membranes [Váró, G., & Lanyi, J.K. (1990) Biochemistry 29, 2241-2250]. The rate constants which involve proton release or uptake, i.e., kLM1, kNO, and kON, were significantly higher in the monomeric protein than in purple membrane; the other steps were less affected. Analysis of the temperature dependencies of the rate constants between 5 and 30 degrees C yielded the enthalpies and entropies of activation for all steps except the two absent back-reactions. Comparison of these with data for purple membranes [Váró, G., & Lanyi, J.K. (1991) Biochemistry 30, 5016-5022] shows that the crystalline structure affects the energetics of the photocycle. In bacteriorhodopsin immobilized by the lattice of the purple membrane, the entropy changes leading to all transition states are more positive. Thus, the forward reactions proceed with less conformational hindrance. However, the thermal (enthalpic) barriers are higher. These effects are particularly pronounced for the M1----M2 and O----BR reactions. Large changes of the enthalpy and entropy levels of intermediates in the M2----BR reaction segment, but not in the K----M1 segment, upon solubilization of the protein are consistent with our earlier proposal that major protein conformational changes occur in the photocycle and they begin with the M1----M2 reaction.     

Electron diffraction analysis of the M412 intermediate of bacteriorhodopsin.

High resolution electron diffraction data have been recorded for glucose-embedded purple membrane specimens in which bacteriorhodopsin (bR) has been trapped by cooling slowly to below--100 degrees C under continuous illumination. Thin films (OD approximately 0.7) of glucose-embedded membranes, prepared as a control, showed virtually 100% conversion to the M state, and stacks of such thin film specimens gave very similar x-ray diffraction patterns in the bR568 and the M412 state in most experiments. To be certain that any measured differences in diffraction intensity would be real, two independent sets of electron diffraction intensities were recorded for near-equatorial, i.e. (hkO), reflections. Little correlation was indeed observed between these two sets for delta F values at low resolution (15-5.0 A, 49 reflections), but the correlation coefficient is approximately 0.3 at high resolution (5.0-3.3 A, 218 reflections). Thus, while most of the measured difference is error, the mean delta F and the correlation coefficient can be used to estimate the smaller, true delta F due to structural changes occurring in the M state. The magnitude of this estimated true mean delta F is equal to what would be produced if approximately five to seven nonhydrogen atoms were moved to structurally uncorrelated (i.e., new) positions in the M state. Movements of a few amino acid side chains, and repositioning of atoms of the retinal group and the associated lysine side chain after trans-cis isomerization, are the most probable causes of the observed intensity changes in the M state.(ABSTRACT TRUNCATED AT 250 WORDS)     

Polarized Fourier transform infrared (FTIR) difference spectroscopy of the M412 intermediate in the bacteriorhodopsin photocycle

The possibility that light-induced protein conformational changes accompany the formation of the M₄₁₂ species in the bacteriorhodopsin photocycle is investigated by polarized Fourier transform infrared (FTIR) spectroscopy on oriented films of purple membrane. From the light-induced FTIR dichroism changes, it is estimated that: (i) the CO stretching vibration at 1762 cm⁻¹, which has been assigned to a protonated Asp carboxyl group in M₄₁₂ [(1985) Biochemistry 24, 400-407], is oriented at (θ = 35 ± 5° from the normal to the membrane plane; (ii) the limit for the change in the average tilt angle of the α-helices after photoconversion is less than 2°. The latter observation excludes the large variations in the protein conformation during the M⁴¹² formation proposed by Draheim and Cassim [(1985) Biophys. J. 47, 497-507].     

Molecular dynamics study of the M412 intermediate of bacteriorhodopsin.

Molecular dynamics simulations have been carried out to study the M412 intermediate of bacteriorhodopsin's (bR) photocycle. The simulations start from two simulated structures for the L550 intermediate of the photocycle, one involving a 13-cis retinal with strong torsions, the other a 13,14-dicis retinal, from which the M412 intermediate is initiated through proton transfer to Asp-85. The simulations are based on a refined structure of bR568 obtained through all-atom molecular dynamics simulations and placement of 16 waters inside the protein. The structures of the L550 intermediates were obtained through simulated photoisomerization and subsequent molecular dynamics, and simulated annealing. Our simulations reveal that the M412 intermediate actually comprises a series of conformations involving 1) a motion of retinal; 2) protein conformational changes; and 3) diffusion and reconfiguration of water in the space between the retinal Schiff base nitrogen and the Asp-96 side group. (1) turns the retinal Schiff base nitrogen from an early orientation toward Asp-85 to a late orientation toward Asp-96; (2) disconnects the hydrogen bond network between retinal and Asp-85 and tilts the helix F of bR, enlarging bR's cytoplasmic channel; (3) adds two water molecules to the three water molecules existing in the cytoplasmic channel at the bR568 stage and forms a proton conduction pathway. The conformational change (2) of the protein involves a 60 degrees bent of the cytoplasmic side of helix F and is induced through a break of a hydrogen bond between Tyr-185 and a water-side group complex in the counterion region.     

Structure of an early intermediate in the M-state phase of the bacteriorhodopsin photocycle.

The structure of an early M-intermediate of the wild-type bacteriorhodopsin photocycle formed by actinic illumination at 230 K has been determined by x-ray crystallography to a resolution of 2.0 A. Three-dimensional crystals were trapped by illuminating with actinic light at 230 K, followed by quenching in liquid nitrogen. Amide I, amide II, and other infrared absorption bands, recorded from single bacteriorhodopsin crystals, confirm that the M-substate formed represents a structure that occurs early after deprotonation of the Schiff base. Rotation about the retinal C13-C14 double bond appears to be complete, but a relatively large torsion angle of 26 degrees is still seen for the C14-C15 bond. The intramolecular stress associated with the isomerization of retinal and the subsequent deprotonation of the Schiff base generates numerous small but experimentally measurable structural changes within the protein. Many of the residues that are displaced during the formation of the late M (M(N)) substate formed by three-dimensional crystals of the D96N mutant (Luecke et al., 1999b) are positioned, in early M, between their resting-state locations and the ones which they will adopt at the end of the M phase. The relatively small magnitude of atomic displacements observed in this intermediate, and the well-defined positions adopted by nearly all of the atoms in the structure, may make the formation of this structure favorable to model (simulate) by molecular dynamics.     

Photoreaction of N560 intermediate in the photocycle of bacteriorhodopsin.

Sophisticated measurements were made on the nanosecond time-resolved absorbance change of the purple membrane of Halobacterium halobium under cw background light irradiation (440-800 nm, 11-441 mW/cm2). A red-shifted transient species R660 (KN, Q) was found in alkaline conditions (pH > 9.3). Background light intensity effect shows that (i) R660 is photochemically formed from N560 intermediate which is accumulated under background light irradiation because of the elongated lifetime in alkaline suspension, and that (ii) the slow decaying M412 is not photochemically formed from N560 but from bR568.     

Pressure effects on the photocycle of purple membrane

We studied the effects of hydrostatic pressure on the kinetics of the photocycle of purple membrane from Halobacterium halobium. The data were interpreted in terms of a unidirectional and unbranched model. We found that all of the distinct processes of the photocycle are retarded by pressure, with the earlier, fast processes showing less sensitivity to pressure than the later, slow processes. The qualitative similarity of these results with the effects of solvent viscosity on the photocycle kinetics suggests that the primary effects of pressure on the kinetics are via the intrinsic viscosity of the membrane and not via activation volumes. There is a strong quantitative correlation between the pressure effects and the solvent viscosity effects, further supporting this interpretation. We observed a monotonic decrease in the positive absorbance change signal at 640 nm near the end of the photocycle as the pressure is increased. This signal is usually ascribed to the O intermediate, and we interpreted our finding, along with evidence from other experiments, to mean that an ionizable group or groups, such as carboxylic acids, are undissociated and uncharged in O.     

Structural characterization of the L-to-M transition of the bacteriorhodopsin photocycle.

Structural intermediates occurring in the photocycle of wild-type bacteriorhodopsin are trapped by illuminating hydrated, glucose-embedded purple membrane at 170 K, 220 K, 230 K, and 240 K. We characterize light-induced changes in protein conformation by electron diffraction difference Fourier maps, and relate these to previous work on photocycle intermediates by infrared (FTIR) spectroscopy. Samples illuminated at 170 K are confirmed by FTIR spectroscopy to be in the L state; a difference Fourier projection map shows no structural change within the 0.35-nm resolution limit of our data. Difference maps obtained with samples illuminated at 220 K, 230 K, and 240 K, respectively, reveal a progressively larger structural response in helix F when the protein is still in the M state, as judged by the FTIR spectra. Consistent with previous structural studies, an adjustment in the position or in the degree of ordering of helix G accompanies this motion. The model of the photocycle emerging from this and previous studies is that bacteriorhodopsin experiences minimal change in protein structure until a proton is transferred from the Schiff base to Asp85. The M intermediate then undergoes a conformational evolution that opens a hydrated "half-channel," allowing the subsequent reprotonation of the Schiff base by Asp96.     

Electrooptical measurements on purple membrane containing bacteriorhodopsin mutants.

Electrooptical measurements on purple membrane containing the wild-type and 10 different bacteriorhodopsin mutants have shown that the direction of the permanent electric dipole moment of all these membranes reverses at different pH values in the range 3.2-6.4. The induced dipole moment and the retinal angle exhibit an increased value at these pHs. The results demonstrate that the bacteriorhodopsin protein makes an important contribution to the electrooptical properties of the purple membrane.     

Effects of electric field on the photocycle of bacteriorhodopsin

The photoconversion of bacteriorhodopsin and the effects of an applied electric field (5 · 10⁷ V · m^?1) were studied in dry films of purple membranes from Halobacterium halobium. The electric field was found to cause at least two different effects: (1) it blocks in part the formation of the batho-bacteriorhodopsin (K), most probably due to electrically-induced dark transition of some bacteriorhodopsin molecules into the photochemically inactive form; (2) it decreases the rate of the intermediate M decay, the rise time of the M formation being unaffected by electric field. The observed phenomena may suggest a feedback control mechanism for the regulation of the bacteriorhodopsin photocycle in purple membranes.     

The projection structure of the low temperature K intermediate of the bacteriorhodopsin photocycle determined by electron diffraction

Bacteriorhodopsin (bR) is an integral membrane protein which absorbs visible light and pumps protons across the cell membrane of Halobacterium salinarium. bR is one of the few membrane-bound pumps whose structure is known at atomic resolution. Changes in the protein structure of bR are a crucial element in the mechanism of proton pumping and can be followed by a variety of spectroscopic, and diffraction methods. A number of intermediates in the photocycle have been identified spectroscopically and a number of laboratories have been successful in reporting the structural changes taking place in the later stages of the photocycle over the millisecond time-scale using diffraction techniques. These studies have revealed significant changes in the protein structure, possibly involving changes in flexibility and/or movement of helices. Earlier intermediates which arise and decay on the picosecond to microsecond time-scale have proven more difficult to trap. Here, we report for the first time the successful trapping and diffraction analysis of bR in a low temperature state resembling the very early intermediate, K. We have calculated a projection difference map to 3.5 A resolution. The map reveals no significant structural changes in the molecule, despite having a very low background noise level. This does not rule out the possibility of movements in a direction perpendicular to the plane of the membrane. However, the data are consistent with other evidence that significant structural changes do not occur in the protein itself.     

Surface pH controls purple-to-blue transition of bacteriorhodopsin. A theoretical model of purple membrane surface.

We have developed a surface model of purple membrane and applied it in an analysis of the purple-to-blue color change of bacteriorhodopsin which is induced by acidification or deionization. The model is based on dissociation and double layer theory and the known membrane structure. We calculated surface pH, ion concentrations, charge density, and potential as a function of bulk pH and concentration of mono- and divalent cations. At low salt concentrations, the surface pH is significantly lower than the bulk pH and it becomes independent of bulk pH in the deionized membrane suspension. Using an experimental acid titration curve for neutral, lipid-depleted membrane, we converted surface pH into absorption values. The calculated bacteriohodopsin color changes for acidification of purple, and titrations of deionized blue membrane with cations or base agree well with experimental results. No chemical binding is required to reproduce the experimental curves. Surface charge and potential changes in acid, base and cation titrations are calculated and their relation to the color change is discussed. Consistent with structural data, 10 primary phosphate and two basic surface groups per bacteriorhodopsin are sufficient to obtain good agreement between all calculated and experimental curves. The results provide a theoretical basis for our earlier conclusion that the purple-to-blue transition must be attributed to surface phenomena and not to cation binding at specific sites in the protein.     

Photoacoustic spectroscopy of purple membrane fragments. Evidence for disorder during photocycle

A strong band at 412 nm has been observed in the photoacoustic spectrum of partially dried purple membrane, peaking sharply at a modulation frequency of about 70 Hz. This may be explained in terms of a disorder-order transition.     

The effect of antibiotics on the photocycle and protoncycle of purple membrane suspensions.

The interrelation was studied between the phototransient absorbing maximally at 412 nm (M412) and light-induced proton release under steady-state conditions in aqueous suspensions of 'purple membrane' derived from Halobacterium halobium. The decay of M412 was slowed down by the simultaneous application of the ionophoric antibiotics valinomycin and beauvericin. The former had only slight activity alone and the latter was effective only in conjunction with valinomycin. The steady-state concentration of M412 which was formed on illumination was a direct function of the concentration of valinomycin. Maximum stabilization of M412 was obtained when the valinomycin was approximately equimolar with the bacteriorhodopsin. Addition of salts to the medium increased the number of protons released per molecule of M412 without affecting the level of M412 which was produced by continuous illumination. The effectiveness of the salts in this respect depended on the nature of the cation. Ca2+ and their antagonists La3+ and ruthenium red were found to have especially high affinity for the system. The extent of light-induced acidification could not be enhanced by increasing the pH of the medium from 6.5 to 7.8. The possible mechanism of action of the ionophores and of the cations on the photocycle and on the proton cycle is discussed.     

Studies on the temperature effect on bacteriorhodopsin of purple and blue membrane by fluorescence and absorption spectroscopy

Fluorescence and absorption spectra were used to study the temperature effect on theconformation of bacteriorhodopsin (bR) in the blue and purple membranes (termed as bRb and bRprespectively).The maximum emission wavelengths of tryptophan fluorescence in both proteins at roomtemperature are 340 nm,and the fluorescence quantum yield of bRb is about 1.4 fold higher than that of bRp.As temperature increases,the tryptophan fluorescence of bRb decreases,while the tryptophan fluorescenceof bRp increases.The binding study of extrinsic fluorescent probe bis-ANS indicated that the probe can bindonly to bRb,but not to bRp.These results suggest that significant structural difference existed between bRband bRp.It was also found that both kinds of bR are highly thermal stable.The maximum wavelength of theprotein fluorescence emission only shifted from 340 nm to 346 nm at 100℃.More interestingly,as tempera-ture increased,the characteristic absorption peak of bRb at 605 nm decreased and a new absorption peak at380 nm formed.The transition occurred at a narrow temperature range (65℃-70℃).These facts indicatedthat an intermediate can be induced by high temperature.This phenomenon has not been reported before.     

Temperature and pH sensitivity of the O640 intermediate of the bacteriorhodopsin photocycle

The temperature and pH dependencies of the O₆₄₀ intermediate of the photocycle of bacteriorhodopsin (bR) were investigated by flash photolysis and T-jump experiments. The maximal concentration of the O₆₄₀ intermediate was found to be dependent on the temperature, which is described by a sigmoidal relationship. With increasing pH the midpoint of the sigmoidal curves shifts to higher temperatures. The Van't Hoff equation provides enthalpy and entropy values of the observed states. These results indicate that, in the investigated temperature (0-60°C) and pH (pH 4.0-10.0) range, the sequence of the principal intermediates in the pathway “M-N-O-bR” does not change. The observations of the O₆₄₀ intermediate at pH < 8.0 and of the N₅₅₀ intermediate at pH > 8.0 are most probably due only to changes of the intrinsic rate constants of the bR photocycle, not to a different mechanism.     

Thermal equilibration between the M and N intermediates in the photocycle of bacteriorhodopsin.

The stages in the photocycle of bacteriorhodopsin (BR) involving the M and N intermediates are investigated using a double pulse excitation method. A first (cycling) pulse at 532 nm is followed, with an appropriate time delay, by a second pulse (337, 406, 446, or 470 nm) which induces the M-->BR back-photoreaction. After depletion by the second pulse a repopulation of M in the millisecond range is observed which is interpreted in terms of a thermal N-->M relaxation. It is thus concluded that a (thermal) M<-->N equilibrium accounts for the biphasic decay of M in the BR photocycle. Other models for this stage of the light-driven proton-pump are therefore unnecessary.     

Location of the carboxyl terminus of bacteriorhodopsin in purple membrane.

Purple membrane samples have been prepared by trypsin digestion to have either 10 or 21 residues removed from the carboxyl terminus of the proteins. Electron diffraction of single membranes and x-ray diffraction of unoriented membrane pellets have been carried out on both these specimens and on native purple membranes. the main conclusion from this work is that the carboxyl terminus is almost entirely disordered, being free to take up many positions, and that its removal does not affect the packing in the crystal. The low resolution x-ray diffraction difference map may also suggest the approximate location of the carboxyl terminus.