Time-resolved resonance Raman spectroscopy of intermediates of bacteriorhodopsin: The bK(590) intermediate

Vibrational Study of the Inward Proton Pump Xenorhodopsin NsXeR: Switch Order Determines Vectoriality

Common proton pumps, e.g. HsBR and PR, transport protons out of the cell. Xenorhodopsins (XeR) were the first discovered microbial rhodopsins which come as natural inward proton pumps. In this work we combine steady-state (cryo-)FTIR and Raman spectroscopy with time-resolved IR and UV/Vis measurements to roadmap the inward proton transport of NsXeR and pinpoint the most important mechanistic features. Through the assignment of characteristic bands of the protein backbone, the retinal chromophore, the retinal Schiff base and D220, we could follow the switching processes for proton accessibility in accordance with the isomerization / switch / transfer model. The corresponding transient IR signatures suggest that the initial assignment of D220 as the proton acceptor needs to be questioned due to the temporal mismatch of the Schiff base and D220 protonation steps. The switching events in the K-L and MCP-MEC transitions are finely tuned by changes of the protein backbone and rearrangements of the Schiff base. This finely tuned mechanism is disrupted at cryogenic temperatures, being reflected in the replacement of the previously reported long-lived intermediate GS* by an actual redshifted (O-like) intermediate.

Probing Structure and Reaction Dynamics of Proteins Using Time-Resolved Resonance Raman Spectroscopy

The mechanistic understanding of protein functions requires insight into the structural and reaction dynamics. To elucidate these processes, a variety of experimental approaches are employed. Among them, time-resolved (TR) resonance Raman (RR) is a particularly versatile tool to probe processes of proteins harboring cofactors with electronic transitions in the visible range, such as retinal or heme proteins. TR RR spectroscopy offers the advantage of simultaneously providing molecular structure and kinetic information. The various TR RR spectroscopic methods can cover a wide dynamic range down to the femtosecond time regime and have been employed in monitoring photoinduced reaction cascades, ligand binding and dissociation, electron transfer, enzymatic reactions, and protein un- and refolding. In this account, we review the achievements of TR RR spectroscopy of nearly 50 years of research in this field, which also illustrates how the role of TR RR spectroscopy in molecular life science has changed from the beginning until now. We outline the various methodological approaches and developments and point out current limitations and potential perspectives.

On the molecular mechanisms of the Schiff base deprotonation during the bacteriorhodopsin photocycle

Using optical flash photolysis and time-resolved Raman methods, we examined intermediates formed during the photocycle of bacteriorhodopsin (bR), as well as the bR color change, as a function of pH (in the 7.0-1.5 region) and as a function of the number of bound Ca(2+) ions. It is found that at a pH just below 3 or with less than two bound Ca(2+) per bR, the deprotonation (the L(550) --> M(412)) step ceases, yet the K(610) and L(550) analogues are still formed as in native bR. The lack of deprotonation in the photocycle of both acid blue and deionized blue bR and the similarity of their Raman spectra as well as of their K(610) and L(550) analogues strongly suggest that both blue samples have nearly the same retinal active site. It is suggested that in both blue species, bound cations are removed via a proton-cation exchange equilibrium, either on the cation exchange column for the deionized sample or in solution for the acid blue sample. The proton-cation exchange equilibrium is found to quantitatively account for the pH dependence of the purple-to-blue color change. The different mechanisms responsible for the large reduction ( approximately 11 units) of the pK(a) value of the protonated Schiff base (PSB) during the photocycle are discussed. The absence of the L(550) --> M(412) deprotonation process in both blue species is discussed in terms of the previously proposed cation model for the deprotonation of the PSB during the photocycle of native bR. The extent of the deprotonation and the blue-to-purple color change are found to follow the same dependence on either the pH or the amount of cations added to deionized blue bR. This observed correlation is briefly discussed.

Early picosecond events in the photocycle of bacteriorhodopsin

The primary processes of the photochemical cycle of light-adapted bacteriorhodopsin (BR) were studied by various experimental techniques with a time resolution of 5 x 10(-13) s. The following results were obtained. (a) After optical excitation the first excited singlet state S(1) of bacteriorhodopsin is observed via its fluorescence and absorption properties. The population of the excited singlet state decays with a lifetime tau(1) of approximately 0.7 ps (430 +/- 50 fs) (52). (b) With the same time constant the first ground-state intermediate J builds up. Its absorption spectrum is red-shifted relative to the spectrum of BR by approximately 30 nm. (c) The second photoproduct K, which appears with a time constant of tau(2) = 5 ps shows a red-shift of 20 nm, relative to the peak of BR. Its absorption remains constant for the observation time of 300 ps. (d) Upon suspending bacteriorhodopsin in D(2)O and deuterating the retinal Schiff base at its nitrogen (lysine 216), the same photoproducts J and K are observed. The relaxation time constants tau(1) and tau(2) remain unchanged upon deuteration within the experimental accuracy of 20%.

Transmembrane location of retinal in purple membrane: fluorescence energy transfer in maximally packed donor-acceptor systems

Transmembrane location of the retinal chromophore in the purple membrane of Halobacterium halobium was investigated in three different systems in which excitation energy transfer between the chromophore and external dye molecules condensed on the membrane surfaces was observed. In system ii, the energy donor was the retinal chromophore converted in situ to a fluorescent derivative. The fluorescent membranes were embedded in solid cobalt-EDTA, which served as energy acceptors. System iii was similar to system ii, except that the acceptors were tris(2,2'-bipyridyl)ruthenium(II) complex in solid form. The positively charged ruthenium complex had a radius of 0.7 nm, whereas the cobalt complex in system ii was smaller (radius approximately 0.4 nm) and negatively charged. System iv was stacked sheets of native purple membrane with interspersed ruthenium complex; energy transfer from the luminescent ruthenuim complex to the native retinal chromophore was observed. The energy transfer rates in these three systems, and in two additional systems already described (Kouyama, T., K. Kinosita, Jr., and A. Ikegami, 1983, J. Mol. Biol., 165:91-107), were all consistent with a location of the retinal chromophore at a depth of 1.0 +/- 0.3 nm from a surface of the purple membrane. All the analyses in the present work involved an assumption that contacts between the external dye molecules and membrane surfaces were maximal; the depth values obtained cannot be underestimates. The chromophore therefore must be outside the middle one-third of the thickness, approximately 4.5 nm, of the purple membrane.

Subpicosecond resonance Raman spectra of the early intermediates in the photocycle of bacteriorhodopsin

The resonance Raman spectra are presented for the species formed during the photocycle of bacteriorhodopsin (bR) on a timescale of 800-900 fs. In the ethylenic stretch region two intermediates were found with frequencies of 1,510 and 1,518 cm(-1), corresponding to species with optical absorption maxima at 660 and 625 nm, respectively. This leads to the assignment of the 1,518 cm(-1) band to the J(625) intermediate. In the fingerprint region, the appearance of a vibration at 1,195 cm(-1) strongly suggests that the isomerization indeed has taken place in a time less than the pulsewidth of our laser. This supports the previous proposals made on the basis of the optical spectra. The spectra are compared with those observed in tens of picoseconds up to nanoseconds.

Nanosecond retinal structure changes in K-590 during the room-temperature bacteriorhodopsin photocycle: picosecond time-resolved coherent anti-stokes Raman spectroscopy

Time-resolved vibrational spectra are used to elucidate the structural changes in the retinal chromophore within the K-590 intermediate that precedes the formation of the L-550 intermediate in the room-temperature (RT) bacteriorhodopsin (BR) photocycle. Measured by picosecond time-resolved coherent anti-Stokes Raman scattering (PTR/CARS), these vibrational data are recorded within the 750 cm-1 to 1720 cm-1 spectral region and with time delays of 50-260 ns after the RT/BR photocycle is optically initiated by pulsed (< 3 ps, 1.75 nJ) excitation. Although K-590 remains structurally unchanged throughout the 50-ps to 1-ns time interval, distinct structural changes do appear over the 1-ns to 260-ns period. Specifically, comparisons of the 50-ps PTR/CARS spectra with those recorded with time delays of 1 ns to 260 ns reveal 1) three types of changes in the hydrogen-out-of-plane (HOOP) region: the appearance of a strong, new feature at 984 cm-1; intensity decreases for the bands at 957 cm-1, 952 cm-1, and 939 cm-1; and small changes intensity and/or frequency of bands at 855 cm-1 and 805 cm-1; and 2) two types of changes in the C-C stretching region: the intensity increase in the band at 1196 cm-1 and small intensity changes and/or frequency shifts for bands at 1300 cm-1 and 1362 cm-1. No changes are observed in the C = C stretching region, and no bands assignable to the Schiff base stretching mode (C = NH+) mode are found in any of the PTR/CARS spectra assignable to K-590. These PTR/CARS data are used, together with vibrational mode assignments derived from previous work, to characterize the retinal structural changes in K-590 as it evolves from its 3.5-ps formation (ps/K-590) through the nanosecond time regime (ns/K-590) that precedes the formation of L-550. The PTR/CARS data suggest that changes in the torsional modes near the C14-C15 = N bonds are directly associated with the appearance of ns/K-590, and perhaps with the KL intermediate proposed in earlier studies. These vibrational data can be primarily interpreted in terms of the degree of twisting of the C14-C15 retinal bond. Such twisting may be accompanied by changes in the adjacent protein. Other smaller, but nonetheless clear, spectral changes indicate that alterations along the retinal polyene chain also occur. The changes in the retinal structure are preliminary to the deprotonation of the Schiff base nitrogen during the formation of M-412. The time constant for the ps/ns K-590 transformation is estimated from the amplitude change of four vibrational bands in the HOOP region to be 40-70 ns.

Picosecond dynamics of bacteriorhodopsin, probed by time-resolved infrared spectroscopy

The photoinduced reaction cycle of bacteriorhodopsin (BR) has been studied by means of a recently developed picosecond infrared spectroscopic method at ambient temperature. BR - K difference spectra between 1560 and 1700 cm-1 have been recorded at delay times from 100 ps to 14 ns. The spectrum remains unchanged during this period. The negative difference OD band at 1660 cm-1 indicates the peptide backbone responds within 50 ps. A survey in the region of carboxylic side chain absorption around 1740 cm-1 reveals that perturbations of those groups, present in low-temperature FTIR spectra, are not observable within 10 ns, suggesting a slow conformational change.

Applications of ultrafast laser spectroscopy for the study of biological systems

The discovery of mode-locked laser operation now nearly two decades ago has started a development which enables researchers to probe the dynamics of ultrafast physical and chemical processes at the molecular level on shorter and shorter time scales. Naturally the first applications were in the fields of photophysics and photochemistry where it was then possible for the first time to probe electronic and vibrational relaxation processes on a sub-nanosecond timescale. The development went from lasers producing pulses of many picoseconds to the shortest pulses which are at present just a few femtoseconds long. Soon after their discovery ultrashort pulses were applied also to biological systems which has revealed a wealth of information contributing to our understanding of a broadrange of biological processes on the molecular level.It is the aim of this review to discuss the recent advances and point out some future trends in the study of ultrafast processes in biological systems using laser techniques. The emphasis will be mainly on new results obtained during the last 5 or 6 years. The term ultrafast means that I shall restrict myself to sub-nanosecond processes with a few exceptions.

The opsin family of proteins

Images

Determination of retinal chromophore structure in bacteriorhodopsin with resonance Raman spectroscopy

The analysis of the vibrational spectrum of the retinal chromophore in bacteriorhodopsin with isotopic derivatives provides a powerful "structural dictionary" for the translation of vibrational frequencies and intensities into structural information. Of importance for the proton-pumping mechanism is the unambiguous determination of the configuration about the C13=C14 and C=N bonds, and the protonation state of the Schiff base nitrogen. Vibrational studies have shown that in light-adapted BR568 the Schiff base nitrogen is protonated and both the C13=C14 and C=N bonds are in a trans geometry. The formation of K625 involves the photochemical isomerization about only the C13=C14 bond which displaces the Schiff base proton into a different protein environment. Subsequent Schiff base deprotonation produces the M412 intermediate. Thermal reisomerization of the C13=C14 bond and reprotonation of the Schiff base occur in the M412------O640 transition, resetting the proton-pumping mechanism. The vibrational spectra can also be used to examine the conformation about the C--C single bonds. The frequency of the C14--C15 stretching vibration in BR568, K625, L550 and O640 argues that the C14--C15 conformation in these intermediates is s-trans. Conformational distortions of the chromophore have been identified in K625 and O640 through the observation of intense hydrogen out-of-plane wagging vibrations in the Raman spectra (see Fig. 2). These two intermediates are the direct products of chromophore isomerization. Thus it appears that following isomerization in a tight protein binding pocket, the chromophore cannot easily relax to a planar geometry. The analogous observation of intense hydrogen out-of-plane modes in the primary photoproduct in vision (Eyring et al., 1982) suggests that this may be a general phenomenon in protein-bound isomerizations. Future resonance Raman studies should provide even more details on how bacterio-opsin and retinal act in concert to produce an efficient light-energy convertor. Important unresolved questions involve the mechanism by which the protein catalyzes deprotonation of the L550 intermediate and the mechanism of the thermal conversion of M412 back to BR568. Also, it has been shown that under conditions of high ionic strength and/or low light intensity two protons are pumped per photocycle (Kuschmitz & Hess, 1981). How might this be accomplished?(ABSTRACT TRUNCATED AT 400 WORDS)

Investigation of the primary photochemistry of bacteriorhodopsin by low-temperature Fourier-transform infrared spectroscopy

The method of Fourier-transform infrared difference spectroscopy was applied to investigate the transition at 77K of bacteriorhodopsin in its light-adapted form to K6(10), the first intermediate which is stable at low temperature. In addition to unmodified bacteriorhodopsin, bacteriorhodopsin in 2H2O and bacteriorhodopsin containing [15-2H]retinal was used. The results show that major rearrangements occur in the Schiff base in this transition. It is not possible to identify a C = N stretching vibration of the Schiff base in K6(10). The identification of an N-H bending vibration in K6(10) shows that the nitrogen of the previous Schiff base still has a proton attached. The fingerprint region exhibits very unusual features for K6(10) and bears no similarity to protonated retinylidene Schiff base model compounds of any isomeric composition. Therefore, no conclusions on the isomeric state of the retinal in K6(10) can be drawn. The spectra show that the terminal part of the retinal is predominantly reflected in the difference spectra. This indicates that the most polar part of the retinal is located near the Schiff base. We have evidence for protein molecular changes occurring in this transition at 77K.

Fourier transform infrared difference spectroscopy of bacteriorhodopsin and its photoproducts

Fourier transform infrared difference spectroscopy has been used to obtain the vibrational modes in the chromophore and apoprotein that change in intensity or position between light-adapted bacteriorhodopsin and the K and M intermediates in its photocycle and between dark-adapted and light-adapted bacteriorhodopsin. Our infrared measurements provide independent verification of resonance Raman results that in light-adapted bacteriorhodopsin the protein-chromophore linkage is a protonated Schiff base and in the M state the Schiff base is unprotonated. Although we cannot unambiguously identify the Schiff base stretching frequency in the K state, the most likely interpretation of deuterium shifts of the chromophore hydrogen out-of-plane vibrations is that the Schiff base in K is protonated. The intensity of the hydrogen out-of-plane vibrations in the K state compared with the intensities of those in light-adapted and dark-adapted bacteriorhodopsin shows that the conformation of the chromophore in K is considerably distorted. In addition, we find evidence that the conformation of the protein changes during the photocycle.

Infrared evidence that the Schiff base of bacteriorhodopsin is protonated: bR570 and K intermediates

It is possible, by using Fourier-transform infrared (FTIR) difference spectroscopy, to detect the conformational changes occurring in both the protein and the chromophore of bacteriorhodopsin during the photocycle. In contrast to Raman spectroscopy, a laser is unnecessary and hence the problem of a perturbing probe beam is eliminated. Furthermore, the relatively high signal-to-noise ratio obtainable with FTIR enables measurements to be made in minutes over a large spectral range. In the study reported in this paper, we used this method to examine the state of protonation of the retinylidene Schiff base in light-adapted bR570 and in K, the first intermediate in the photocycle. Resonance Raman spectroscopy provides evidence that bR570 is protonated, but these results have been questioned on the basis of theoretical and experimental grounds. FTIR difference spectral changes in the bR570-to-K transition clearly indicate that bR570 contains a protonated Schiff base. In contrast, the K intermediate displays a Schiff base that is altered but still is associated to some degree with a proton. Because the low-temperature FTIR difference spectrum of bR570 and K is similar to the recently reported low-temperature resonance Raman spectra of bR570 and K [Braiman, M. & Mathies, R. (1982) Proc. Natl. Acad. Sci. USA 79, 403-407], we can assign most, but not all, vibrational changes in the bR570-to-K transition to the chromophore. These results are consistent with a simple model of the first step in the photocycle which involves a movement of the Schiff base proton away from a counterion.

Resonance Raman spectra of bacteriorhodopsin's primary photoproduct: evidence for a distorted 13-cis retinal chromophore

We have obtained the resonance Raman spectrum of bacteriorhodopsin's primary photoproduct K with a novel low-temperature spinning sample technique. Purple membrane at 77 K is illuminated with spatially separated actinic (pump) and probe laser beams. The 514-nm pump beam produces a photostationary steady-state mixture of bacteriorhodopsin and K. This mixture is then rotated through the red (676 nm) probe beam, which selectively enhances the Raman scattering from K. The essential advantage of our successive pump-and-probe technique is that it prevents the fluorescence excited by the pump beam from masking the red probe Raman scattering. K exhibits strong Raman lines at 1516, 1294, 1194, 1012, 957, and 811 cm-1. The effects of C15 deuteration on K's fingerprint lines correlate well with those seen in 13-cis model compounds, indicating that K has a 13-cis chromophore. However, the presence of unusually strong "low-wavenumber" lines at 811 and 957 cm-1, attributable to hydrogen out-of-plane wags, indicates that the protein holds the chromophore in a distorted conformation after trans leads to cis isomerization.

Resonance Raman study of the primary photochemistry of bacteriorhodopsin

Resonance Raman multicomponent spectra of the light-adapted form of bacteriorhodopsin, bRLA568, and its first photoproduct, K628, have been obtained at liquid nitrogen temperatures. The spectra of both bRLA568 and K628 could be obtained with the known sample compositions under our irradiating conditions and computer subtraction techniques. In agreement with previous results, we find that both bRLA568 and K628 contain chromophores linked to the apoprotein by protonated Schiff bases of retinal. Neither pigment form, suspended in H2O or 2H2O, compares closely to the spectral features of all-trans and 13-cis protonated and deuterated model chromophores, respectively. The data are consistent with other results, suggesting that a chromophore isomerization takes place in the bRLA568-to-K628 phototransition. However, the exact structure of the in situ chromophore would appear not to involve simple trans-to-13-cis structures found in solution.

Time-resolved protein fluorescence studies of intermediates in the photochemical cycle of bacteriorhodopsin

The photolysis-induced changes in the protein fluorescence intensity (at 320 nm) during the proton-pumping cycle of bacteriorhodopsin were examined by a delayed two-pulse technique in the time range 1 microsecond-20 msec at room temperature. No detectable change in the protein fluorescence intensity was observed on the earliest time scale within the lifetime of the intermediate K590, when retinal apparently undergoes the largest structural changes. The time dependence of the relative changes in fluorescence intensity did, however, display a close correlation with the population of the L550 and M412 intermediates. From a computer numerical fit of the data, with available published kinetic parameters, the protein fluorescence quantum yields of the K590, L550, and M412 intermediates are found to be 1.0, 0.92, and 0.80 of that for native bR570, respectively. The probable mechanisms of the observed fluorescence quenching during the photochemical cycle are qualitatively discussed.