Time-resolved ultraviolet resonance Raman studies of protein structure: application to bacteriorhodopsin

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.

Protein Dynamics Preceding Photoisomerization of the Retinal Chromophore in Bacteriorhodopsin Revealed by Deep-UV Femtosecond Stimulated Raman Spectroscopy

Bacteriorhodopsin is a prototypical photoreceptor protein that functions as a light-driven proton pump. The retinal chromophore of bacteriorhodopsin undergoes C₁₃═C₁₄ trans-to-cis isomerization upon photoexcitation, and it has been believed to be the first event that triggers the cascaded structural changes in bacteriorhodopsin. We investigated the protein dynamics of bacteriorhodopsin using deep-ultraviolet resonance femtosecond stimulated Raman spectroscopy. It was found that the stimulated Raman signals of tryptophan and tyrosine residues exhibit significant changes within 0.2 ps after photoexcitation while they do not noticeably change during the isomerization process. This result implies that the protein environment changes first, and its change is small during isomerization. The obtained femtosecond stimulated Raman data indicate that ultrafast change is induced in the protein part by the sudden creation of the large dipole of the excited-state chromophore, providing an environment that realizes efficient and selective isomerization.

Insights into Protein Structure and Dynamics by Ultraviolet and Visible Resonance Raman Spectroscopy

Raman spectroscopy is a form of vibrational spectroscopy based on inelastic scattering of light. In resonance Raman spectroscopy, the wavelength of the incident light falls within an absorption band of a chromophore, and this overlap of excitation and absorption energy greatly enhances the Raman scattering efficiency of the absorbing species. The ability to probe vibrational spectra of select chromophores within a complex mixture of molecules makes resonance Raman spectroscopy an excellent tool for studies of biomolecules. In this Current Topic, we discuss the type of molecular insights obtained from steady-state and time-resolved resonance Raman studies of a prototypical photoactive protein, rhodopsin. We also review recent efforts in ultraviolet resonance Raman investigations of soluble and membrane-associated biomolecules, including integral membrane proteins and antimicrobial peptides. These examples illustrate that resonance Raman is a sensitive, selective, and practical method for studying the structures of biological molecules, and the molecular bonding, geometry, and environments of protein cofactors, the backbone, and side chains.

Tryptophan as a probe of photosystem I electron transfer reactions: a UV resonance Raman study

Photosystem I (PSI) is one of the two membrane-associated reaction centers involved in oxygenic photosynthesis. In photosynthesis, solar energy is converted to chemical energy in the form of a transmembrane charge separation. PSI oxidizes cytochrome c(6) or plastocyanin and reduces ferredoxin. In cyanobacterial PSI, there are 10 tryptophan residues with indole side chains located less than 10 A from the electron transfer cofactors. In this study, we apply pump-probe difference UV resonance Raman (UVRR) spectroscopy to acquire the spectrum of aromatic amino acids in cyanobacterial PSI. This UVRR technique allows the use of the tryptophan vibrational spectrum as a reporter for structural changes, which are linked to PSI electron transfer reactions. Our results show that photo-oxidation of the chlorophyll a/a' heterodimer, P(700), causes shifts in the vibrational frequencies of two or more tryptophan residues. Similar perturbations of tryptophan are observed when P(700) is chemically oxidized. The observed spectral frequencies suggest that the perturbed tryptophan side chains are only weakly or not hydrogen bonded and are located in an environment in which there is steric repulsion. The direction of the spectral shifts is consistent with an oxidation-induced increase in dielectric constant or a change in hydrogen bonding. To explain our results, the perturbation of tryptophan residues must be linked to a PSI conformational change, which is, in turn, driven by P(700) oxidation.

Construction of a subnanosecond time-resolved, high-resolution ultraviolet resonance Raman measurement system and its application to reveal the dynamic structures of proteins

A subnanosecond time-resolved ultraviolet (UV) resonance Raman system has been developed to study protein structural dynamics. The system is based on a 1 kHz Nd:YLF-pumped Ti:Sapphire regenerative amplifier with harmonic generation that can deliver visible (412, 440, 458, and 488 nm) and UV (206, 220, 229, and 244 nm) pulses. A subnanosecond (0.2 ns) tunable near-infrared pulse from a custom-made Ti:Sapphire oscillator is used to seed the regenerative amplifier. A narrow linewidth of the subnanosecond pulse offers the advantage of high resolution of UV resonance Raman spectra, which is critical to obtain site-specific information on protein structures. By combination with a 1 m single spectrograph equipped with a 3600 grooves/mm holographic grating and a custom-made prism prefilter, the present system achieves excellent spectral (<10 cm(-1)) and frequency (approximately 1 cm(-1)) resolutions with a relatively high temporal resolution (<0.5 ns). We also report the application of this system to two heme proteins, hemoglobin A and CooA, with the 440 nm pump and 220 nm probe wavelengths. For hemoglobin A, a structural change during the transition to the earliest intermediate upon CO photodissociation is successfully observed, specifically, nanosecond cleavage of the A-E interhelical hydrogen bonds within each subunit at Trpalpha14 and Trpbeta15 residues. For CooA, on the other hand, rapid structural distortion (<0.5 ns) by CO photodissociation and nanosecond structural relaxation following CO geminate recombination are observed through the Raman bands of Phe and Trp residues located near the heme. These results demonstrate the high potential of this instrument to detect local protein motions subsequent to photoreactions in their active sites.

Factors influencing the energetics of electron and proton transfers in proteins. What can be learned from calculations

A protein structure should provide the information needed to understand its observed properties. Significant progress has been made in developing accurate calculations of acid/base and oxidation/reduction reactions in proteins. Current methods and their strengths and weaknesses are discussed. The distribution and calculated ionization states in a survey of proteins is described, showing that a significant minority of acidic and basic residues are buried in the protein and that most of these remain ionized. The electrochemistry of heme and quinones are considered. Proton transfers in bacteriorhodopsin and coupled electron and proton transfers in photosynthetic reaction centers, 5-coordinate heme binding proteins and cytochrome c oxidase are highlighted as systems where calculations have provided insight into the reaction mechanism.

Raman structural markers of tryptophan and histidine side chains in proteins

The Raman spectrum of a protein contains a wealth of information on the structure and interaction of the protein. To extract the structural information from the Raman spectrum, it is necessary to identify and interpret the marker bands that reflect the structure and interaction in the protein. Recently, new Raman structural markers have been proposed for the tryptophan and histidine side chains by examining the spectra-structure correlations of model compounds. Raman structural markers are now available for the conformation, hydrogen bonding, hydrophobic interaction, and cation-pi interaction of the indole ring of Trp. For His, protonation, tautomerism, and metal coordination of the imidazole ring can be studied by using Raman markers. The high-resolution X-ray crystal structures of proteins provide the basis for testing and modifying the Raman structural markers of Trp and His. The structures derived from Raman spectra are generally consistent with the X-ray crystal structures, giving support for the applicability of most Raman structural makers. Possible modifications and limitations to some marker bands are also discussed.

Picosecond dynamics of G-protein coupled receptor activation in rhodopsin from time-resolved UV resonance Raman spectroscopy

The protein response to retinal chromophore isomerization in the visual pigment rhodopsin is studied using picosecond time-resolved UV resonance Raman spectroscopy. High signal-to-noise Raman spectra are obtained using a 1 kHz Ti:Sapphire laser apparatus that provides <3 ps visible (466 nm) pump and UV (233 nm) probe pulses. When there is no time delay between the pump and probe events, tryptophan modes W18, W16, and W3 exhibit decreased Raman scattering intensity. At longer pump-probe time delays of +5 and +20 ps, both tryptophan (W18, W16, W3, and W1) and tyrosine (Y1 + 2xY16a, Y7a, Y8a) peak intensities drop by up to 3%. These intensity changes are attributed to decreased hydrophobicity in the microenvironment near at least one tryptophan and one tyrosine residue that likely arise from weakened interaction with the beta-ionone ring of the chromophore following cis-to-trans isomerization. Examination of the crystal structure suggests that W265 and Y268 are responsible for these signals. These UV Raman spectral changes are nearly identical to those observed for the rhodopsin-to-Meta I transition, implying that impulsively driven protein motion by the isomerizing chromophore during the 200 fs primary transition drives key structural changes that lead to protein activation.

Nature of the chromophore binding site of bacteriorhodopsin: the potential role of Arg82 as a principal counterion

The nature of the chromophore binding site of light-adapted bacteriorhodopsin is analyzed by using modified neglect of differential overlap with partial single and double configuration interaction (MNDO-PSDCI) molecular orbital theory to interpret previously reported linear and nonlinear optical spectroscopic measurements. We conclude that in the absence of divalent metal cations in close interaction with Asp85 and Asp212, a positively charged amino acid must be present in the same vicinity. We find that models in which Arg82 is pointed upward into the chromophore binding site and directly stabilizes Asp85 and Asp212 are successful in rationalizing the observed one-photon and two-photon properties. We conclude further that a water molecule is strongly hydrogen bonded to the chromophore imine proton. The chromophore "1Bu*+" and "1Ag*-" states, despite extensive mixing, exhibit significantly different configurational character. The lowest-lying "1Bu*+" state is dominated by single excitations, whereas the second-excited "1Ag*-" state is dominated by double excitations. We can rule out the possibility of a negatively charged binding site, because such a site would produce a lowest-lying "1Ag*-" state, which is contrary to experimental observation. The possibility that Arg82 migrates toward the extracellular surface during the photocycle is examined.

Bacteriorhodopsin

Bacteriorhodopsin is a seven-transmembrane helical protein that contains all-trans retinal. In this light-driven pump, a reaction cycle initiated by photoisomerization to 13-cis causes translocation of a proton across the membrane. Local changes in the geometry of the protonated Schiff base and the proton acceptor Asp85, and the proton conductivities of the half channels that lead from this active site to the two membrane surfaces, interact so as to allow timely proton transfers that result in proton release on the extracellular side and proton uptake on the cytoplasmic one. The details of the steps in this photocycle, and the underlying principles that ensure unidirectionality of the movement of a proton across the protein, provide strong clues to how ion pumps function.

Infrared spectroscopic identification of the C-O stretching vibration associated with the tyrosyl Z. and D. radicals In photosystem II

Photosystem II (PSII) is a multisubunit complex, which catalyzes the photo-induced oxidation of water and reduction of plastoquinone. Difference Fourier-transform infrared (FT-IR) spectroscopy can be used to obtain information about the structural changes accompanying oxidation of the redox-active tyrosines, D and Z, in PSII. The focus of our work is the assignment of the 1478 cm-1 vibration, which is observable in difference infrared spectra associated with these tyrosyl radicals. The first set of FT-IR experiments is performed with continuous illumination. Use of cyanobacterial strains, in which isotopomers of tyrosine have been incorporated, supports the assignment of a positive 1478/1477 cm-1 mode to the C-O stretching vibration of the tyrosyl radicals. In negative controls, the intensity of this spectral feature decreases. The negative controls involve the use of inhibitors or site-directed mutants, in which the oxidation of Z or D is eliminated, respectively. The assignment of the 1478/1477 cm-1 mode is also based on control EPR and fluorescence measurements, which demonstrate that no detectable Fe+2QA- signal is generated under FT-IR experimental conditions. Additionally, the difference infrared spectrum, associated with formation of the S2QA- state, argues against the assignment of the positive 1478 cm-1 line to the C-O vibration of QA-. In the second set of FT-IR experiments, single turnover flashes are employed, and infrared difference spectra are recorded as a function of time after photoexcitation. Comparison to kinetic transients generated in control EPR experiments shows that the decay of the 1477 cm-1 line precisely parallels the decay of the D. EPR signal. Taken together, these two experimental approaches strongly support the assignment of a component of the 1478/1477 cm-1 vibrational lines to the C-O stretching modes of tyrosyl radicals in PSII. Possible reasons for the apparently contradictory results of Hienerwadel et al. (1996) Biochemistry 35, 15,447-15,460 and Hienerwadel et al. (1997) Biochemistry 36, 14,705-14,711 are discussed. Copyright 1998 Elsevier Science B.V. All rights reserved.

Fourier transform infrared double-flash experiments resolve bacteriorhodopsin's M1 to M2 transition

The orientation of the central proton-binding site, the protonated Schiff base, away from the proton release side to the proton uptake side is crucial for the directionality of the proton pump bacteriorhodopsin. It has been proposed that this movement, called the reprotonation switch, takes place in the M1 to M2 transition. To resolve the molecular events in this M1 to M2 transition, we performed double-flash experiments. In these experiments a first pulse initiates the photocycle and a second pulse selectively drives bR molecules in the M intermediate back into the BR ground state. For short delay times between initiating and resetting pulses, most of the M molecules being reset are in the M1 intermediate, and for longer delay times most of the reset M molecules are in the M2 intermediate. The BR-M1 and BR-M2 difference spectra are monitored with nanosecond step-scan Fourier transform infrared spectroscopy. Because the Schiff base reprotonation rate is kM1 = 0.8 x 10(7) s(-1) in the light-induced M1 back-reaction and kM2 = 0.36 x 10(7) s(-1) in the M2 back-reaction, the two different M intermediates represent two different proton accessibility configurations of the Schiff base. The results show only a minute movement of one or two peptide bonds in the M1 to M2 transition that changes the interaction of the Schiff base with Y185. This backbone movement is distinct from the larger one in the subsequent M to N transition. No evidence of a chromophore isomerization is seen in the M1 to M2 transition. Furthermore, the results show time-resolved reprotonation of the Schiff base from D85 in the M photo-back-reaction, instead of from D96, as in the conventional cycle.

Bacteriorhodopsin: a paradigm for proton pumps?

Recent studies of the photochemistry of wild type and mutant bacteriorhodopsins, their proton release and uptake kinetics, and their X-ray diffraction structure have suggested a hypothesis for the way energy is coupled in this light-driven proton pump. The first and critical step in converting light energy to a vectorial proton potential is the transfer of the Schiff base proton to D85 which causes dissociation of the Schiff base-counterion complex. Removal of this primarily coulombic interaction destabilizes the protein structure, and results in transition to an alternative conformation in which the two proton conduction pathways between the active site and the membrane surfaces are reorganized. Recovery of the initial charge state of the Schiff base and D85 must therefore occur through a series of unidirectional proton transfers that create a transmembrane electrochemical proton gradient. Passage of the transported proton through the two peripheral protein domains appears to utilize hydrogen bonded networks containing aspartate, arginine and bound water. This kind of mutual interaction between the active site and the protein conformation that determines the conductive pathways to the two membrane surfaces may have relevance to ion pumps in general.

A stopped-flow apparatus for infrared spectroscopy of aqueous solutions

IR spectroscopy has been widely applied in the study of photo-activated biological processes such as photosynthesis, but has not been applied to the study of reacting systems which require rapid mixing of aqueous solutions. This has been due in part to the high pressure needed to make an aqueous solution flow rapidly through the 50 microns optical pathlength between the plates in an IR cuvette suitable for use with 2H2O and the high viscosity of the concentrated protein solutions required to generate measurable IR signals. An apparatus, based largely on conventional stopped-flow technology, is described which achieves mixing well within the time-resolved performance (approximately 40 ms) of modern Fourier-transform IR (FTIR) spectrometers, since the dead time of the mixing device is approximately 15 ms. It has proved possible to achieve efficient mixing by using a simple six-jet mixing device. This is probably at least in part because of the high back pressure which develops when aqueous fluid is passed rapidly through the short pathlength of the cuvette and which promotes turbulent flow. Several examples of measurements of the deacylation of acylchymotrypsins are provided which demonstrate the operation of the apparatus in conjunction with a spectrometer capable of scanning at four scans/s. For cinnamoyl-chymotrypsin, isotope-edited spectra have been obtained which show somewhat lower resolution than is achieved by conventional scanning methods, since some smoothing has to be applied to the spectra. Difference spectra of the acylation of chymotrypsin by glycylglycine p-nitrophenyl ester have been obtained by averaging ten stopped-flow shots and show good signal-to-noise ratio without smoothing. It is predicted that this apparatus is likely to find a variety of applications in the study of enzyme-catalysed reactions, since the spectra are relatively rich in structural information, and isotope editing greatly enhances the interpretability of the spectra.

Proton translocation mechanism and energetics in the light-driven pump bacteriorhodopsin

In spite of many still unsolved problems, the mechanism and energetics of the light-driven proton transport are now basically understood. Energy captured during photoexcitation, and retained in the form of bond rotations and strains of the retinal, is transformed into directed changes in the pKa values of vectorially arranged proton transfer groups. The framework for the spatial and temporal organization of these changes is provided by the protein near the retinal Schiff base. The transport is completed by proton transfer among three essential groups in three domains lying roughly parallel with the membrane plane (Fig. 1): (a) the anionic D85 that is included in a complex of residues on the extracellular side containing also R82, D212, Y57 and bound water; (b) the protonated Schiff base; and (c) the protonated D96 that is included in a complex of residues on the cytoplasmic side containing also R227, T46, S226, and bound water. Other neighboring polar groups and water bound elsewhere which play a role in the transport do so either by further influencing the pKa values of the three protonable groups, or by providing passive pathways for proton transfer. The Schiff base proton, destabilized after photoexcitation, is transferred to the low pKa group D85 located on the extracellular side. The access of the deprotonated Schiff base then changes to the cytoplasmic side (the 'reprotonation switch') and its proton affinity increases. Finally, the proton of the high pKa group D96, with access to the cytoplasmic side, is destabilized by a protein conformational change through rearrangement of R227, T46, S226 and bound water, and becomes transferred to the Schiff base. As shown schematically in Fig. 3, these internal events are coupled to proton release and uptake at the two aqueous surfaces. The charge of the extracellular hydrogen-bonded complex is redistributed upon protonation of D85, and if the pH is above the pKa of the complex a proton is released to the bulk. After reprotonation of the Schiff base the pKa of the cytoplasmic hydrogen-bonded complex is raised well above the pH, and D96 regains a proton from the bulk. If the pH is lower than the pKa of the extracellular complex the proton release is delayed until the end of the photocycle. In either sequence there is net transfer of a proton from the cytoplasmic to the extracellular phase. The transfer of excess free energy from the chromophore to the protein, and finally to the transported proton, is described by a characteristic thermodynamic cycle.(ABSTRACT TRUNCATED AT 400 WORDS)

A difference Fourier-transform infrared study of two redox-active tyrosine residues in photosystem II

Photosystem II, the photosynthetic water-oxidizing complex, contains two redox-active tyrosine residues. Although current models suggest that these tyrosines are located in symmetric positions in the reaction center, there are functional differences between them. To elucidate those structural factors that give rise to this functional asymmetry, we have used difference Fourier-transform infrared spectroscopy to obtain the vibrational difference spectrum associated with the oxidation of each of these redox-active residues. Isotopic labeling was employed to definitively assign vibrational lines to the redox-active tyrosines. This work has shown that the vibrational spectra of the two redox-active species are significantly different from each other. This result suggests that the structure of the redox-active residue helps to determine its role in electron transfer in the reaction center.