Changes in hydrogen bonding and environment of tryptophan residues on helix F of bacteriorhodopsin during the photocycle: a time-resolved ultraviolet resonance Raman study

Impact of protein-chromophore interaction on the retinal excited state and photocycle of Gloeobacter rhodopsin: role of conserved tryptophan residues

The function of microbial as well as mammalian retinal proteins (aka rhodopsins) is associated with a photocycle initiated by light excitation of the retinal chromophore of the protein, covalently bound through a protonated Schiff base linkage. Although electrostatics controls chemical reactions of many organic molecules, attempt to understand its role in controlling excited state reactivity of rhodopsins and, thereby, their photocycle is scarce. Here, we investigate the effect of highly conserved tryptophan residues, between which the all-trans retinal chromophore of the protein is sandwiched in microbial rhodopsins, on the charge distribution along the retinal excited state, quantum yield and nature of the light-induced photocycle and absorption properties of Gloeobacter rhodopsin (GR). Replacement of these tryptophan residues by non-aromatic leucine (W222L and W122L) or phenylalanine (W222F) does not significantly affect the absorption maximum of the protein, while all the mutants showed higher sensitivity to photobleaching, compared to wild-type GR. Flash photolysis studies revealed lower quantum yield of trans-cis photoisomerization in W222L as well as W222F mutants relative to wild-type. The photocycle kinetics are also controlled by these tryptophan residues, resulting in altered accumulation and lifetime of the intermediates in the W222L and W222F mutants. We propose that protein-retinal interactions facilitated by conserved tryptophan residues are crucial for achieving high quantum yield of the light-induced retinal isomerization, and affect the thermal retinal re-isomerization to the resting state.

Protein dynamics of a light-driven Na+ pump rhodopsin probed using a tryptophan residue near the retinal chromophore

Direct observation of protein structural changes during ion transport in ion pumps provides valuable insights into the mechanism of ion transport. In this study, we examined structural changes in the light-driven sodium ion (Na+) pump rhodopsin KR2 on the sub-millisecond time scale, corresponding with the uptake and release of Na+. We compared the ion-pumping activities and transient absorption spectra of WT and the W215F mutant, in which the Trp215 residue located near the retinal chromophore on the cytoplasmic side was replaced with a Phe residue. Our findings indicated that atomic contacts between the bulky side chain of Trp215 and the C20 methyl group of the retinal chromophore promote relaxation of the retinal chromophore from the 13-cis to the all-trans form. Since Trp215 is conserved in other ion-pumping rhodopsins, the present results suggest that this residue commonly acts as a mechanical transducer. In addition, we measured time-resolved ultraviolet resonance Raman (UVRR) spectra to show that the environment around Trp215 becomes less hydrophobic at 1 ms after photoirradiation and recovers to the unphotolyzed state with a time constant of around 10 ms. These time scales correspond to Na+ uptake and release, suggesting evolution of a transient ion channel at the cytoplasmic side for Na+ uptake, consistent with the alternating-access model of ion pumps. The time-resolved UVRR technique has potential for application to other ion-pumping rhodopsins and could provide further insights into the mechanism of ion transport.

Contact-Mediated Retinal-Opsin Coupling Enables Proton Pumping in Gloeobacter Rhodopsin

When a chromophore embedded in a photoreceptive protein undergoes a reaction upon photoexcitation, the photoreaction triggers structural changes in the protein moiety that are necessary for the function of the protein. It is thus essential to elucidate the coupling between the chromophore and protein moiety to understand the functional mechanism for photoreceptive proteins, but the mechanism by which this coupling occurs remains poorly understood. Here, we show that nonbonded atomic contacts play an essential role in driving functionally important structural changes following photoisomerization of the chromophore in Gloeobacter rhodopsin (GR). Time-resolved ultraviolet resonance Raman spectroscopy revealed that the substitution of Trp222, which contacts with methyl groups of the retinal chromophore, with a Phe residue reduced the extent of structural change. The proton-pumping activity of the GR mutant was as small as 9% of that of the wild type. Time-resolved visible absorption and resonance Raman spectra showed that the photocycle of the mutant proceeded to the L intermediate following the all-trans to 13-cis photoisomerization step but did not result in the deprotonation of the chromophore. The present results demonstrate that the atomic contacts between the chromophore and the Trp222 side chain induce the structural changes necessary for proton transfer. The requirement for dense atomic packing in a protein structure for the efficient propagation of structural changes through a coupling mechanism is discussed.

A conserved Trp residue in HwBR contributes to its unique tolerance toward acidic environments

Bacteriorhodopsin (BR) is a light-driven outward proton pump found mainly in halophilic archaea. A BR from an archaeon Haloquadratum walsbyi (HwBR) was found to pump protons under more acidic conditions compared with most known BR proteins. The atomic structural study on HwBR unveiled that a pair of hydrogen bonds between the BC and FG loop in its periplasmic region may be a factor in such improved pumping capability. Here, we further investigated the retinal-binding pocket of HwBR and found that Trp94 contributes to the higher acid tolerance. Through single mutations in a BR from Halobacterium salinarum and HwBR, we examined the conserved tryptophan residues in the retinal-binding pocket. Among these residues of HwBR, mutagenesis at Trp94 facing the periplasmic region caused the most significant disruption to optical stability and proton-pumping capability under acidic conditions. The other tryptophan residues of HwBR exerted little impact on both maximum absorption wavelength and pH-dependent proton pumping. Our findings suggest that the residues from Trp94 to the hydrogen bonds at the BC loop confer both optical stability and functionality on the overall protein in low-pH environments.

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.

Photoinduced transformation of UVR8 monitored by vibrational and fluorescence spectroscopy

Tryptophan residues at the dimer interface of the plant photoreceptor UVR8 promote monomerisation after UV-B absorption via a so far unknown mechanism. Using FTIR spectroscopy we assign light-induced structural transitions of UVR8 mainly to amino acid side chains without major transformations of the secondary structure of the physiologically relevant C-terminal extension. Additionally, we assign the monomerisation associated increase and red shift of the UVR8 tryptophan emission to a photoinduced rearrangement of tryptophan side chains and a relocation of the aspartic acid residues D96 and D107, respectively. By illumination dependent emission spectroscopy we furthermore determined the quantum yield of photoinduced monomerisation to 20 ± 8%.

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.

A set of engineered Escherichia coli expression strains for selective isotope and reactivity labeling of amino acid side chains and flavin cofactors

Biological reactions are facilitated by delicate molecular interactions between proteins, cofactors and substrates. To study and understand their dynamic interactions researchers have to take great care not to influence or distort the object of study. As a non-invasive alternative to a site-directed mutagenesis approach, selective isotope labeling in combination with vibrational spectroscopy may be employed to directly identify structural transitions in wild type proteins. Here we present a set of customized Escherichia coli expression strains, suitable for replacing both the flavin cofactor and/or selective amino acids with isotope enriched or chemically modified substrates. For flavin labeling we report optimized auxotrophic strains with significantly enhanced flavin uptake properties. Labeled protein biosynthesis using these strains was achieved in optimized cultivation procedures using high cell density fermentation. Finally, we demonstrate how this approach is used for a clear assignment of vibrational spectroscopic difference signals of apoprotein and cofactor of a flavin containing photoreceptor of the BLUF (Blue Light receptors Using FAD) family.

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.

Tryptophan 171 in Pharaonis phoborhodopsin (sensory rhodopsin II) interacts with the chromophore retinal and its substitution with alanine or threonine slowed down the decay of M- and O-intermediate

Pharaonis phoborhodopsin (ppR), also called pharaonis sensory rhodopsin II, NpSRII, is a photoreceptor for the photophobic response of Natronomonas pharaonis. Tryptophan 182 (W182) of bacteriorhodopsin (bR) is near the chromophore retinal and has been suggested to interact with retinal during the photoreaction and also to be involved in the hydrogen-bonding network around the retinal. W182 of bR is conserved in ppR as tryptophan 171 (W171). To elucidate whether W171 of ppR interacts with retinal during the photoreaction and/or is involved in the hydrogen-bonding network as in bR, we formed W171-substituted mutants of ppR, W171A and W171T. Our low-temperature spectroscopic study has revealed that the substitution of W171 to Ala or Thr resulted in the stabilization of M- and O-intermediates. The stability of M and absorption spectral changes during the M-decay were different depending on the substituted residue. These findings suggest that W171 in ppR interacts with retinal and the degree of the interaction depends on the substituted residues, which might be rate determining in the M-decay. In addition, the involvement of W171 in the hydrogen-bonding network is suggested by the O-decay. We also found that glycerol slowed the decay of M and not of O.

Electrostatic and steric interactions determine bacteriorhodopsin single-molecule biomechanics

Bacteriorhodopsin (bR) is a haloarchaeal membrane protein that converts the energy of single photons into large structural changes to directionally pump protons across purple membrane. This is achieved by a complex combination of local dynamic interactions controlling bR biomechanics at the submolecular level, producing efficient amplification of the retinal photoisomerization. Using single molecule force spectroscopy at different salt concentrations, we show that tryptophan (Trp) residues use steric specific interactions to create a rigid scaffold in bR extracellular region and are responsible for the main unfolding barriers. This scaffold, which encloses the retinal, controls bR local mechanical properties and anchors the protein into the membrane. Furthermore, the stable Trp-based network allows ion binding to two specific sites on the extracellular loops (BC and FG), which are involved in proton release and lateral transport. In contrast, the cytoplasmic side of bR is mainly governed by relatively weak nonspecific electrostatic interactions that provide the flexibility necessary for large cytoplasmic structural rearrangements during the photocycle. The presence of an extracellular Trp-based network tightly enclosing the retinal seems common to most haloarchaeal rhodopsins, and could be relevant to their exceptional efficiency.

Steady-state and transient ultraviolet resonance Raman spectrometer for the 193-270 nm spectral region

We describe a state-of-the-art tunable ultraviolet (UV) Raman spectrometer for the 193-270 nm spectral region. This instrument allows for steady-state and transient UV Raman measurements. We utilize a 5 kHz Ti-sapphire continuously tunable laser (approximately 20 ns pulse width) between 193 nm and 240 nm for steady-state measurements. For transient Raman measurements we utilize one Coherent Infinity YAG laser to generate nanosecond infrared (IR) pump laser pulses to generate a temperature jump (T-jump) and a second Coherent Infinity YAG laser that is frequency tripled and Raman shifted into the deep UV (204 nm) for transient UV Raman excitation. Numerous other UV excitation frequencies can be utilized for selective excitation of chromophoric groups for transient Raman measurements. We constructed a subtractive dispersion double monochromator to minimize stray light. We utilize a new charge-coupled device (CCD) camera that responds efficiently to UV light, as opposed to the previous CCD and photodiode detectors, which required intensifiers for detecting UV light. For the T-jump measurements we use a second camera to simultaneously acquire the Raman spectra of the water stretching bands (2500-4000 cm(-1)) whose band-shape and frequency report the sample temperature.

Theoretical framework for octopus rhodopsin crystallization

Bacteriorhodopsin (bR) is presently a classical example of membrane protein crystallization. We are comparing the structure of bR with the homology model of octopus rhodopsin (octR), which is similar in topology to bR and as highly ordered in its native membranes as bR in purple membranes. Such comparison provides insights for optimization of present octR experimentation both for crystallization and for application in nanobiotechnology in a manner similar to bR, and possibly even superior in optical computation.

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.