Low-Frequency Vibrations and Their Role in Ultrafast Photoisomerization Reaction Dynamics of Photoactive Yellow Protein

Tracking Ultrafast Structural Dynamics by Time-Domain Raman Spectroscopy

In traditional Raman spectroscopy, narrow-band light is irradiated on a sample, and its inelastic scattering, i.e., Raman scattering, is detected. The energy difference between the Raman scattering and the incident light corresponds to the vibrational energy of the molecule, providing the Raman spectrum that contains rich information about the molecular-level properties of the materials. On the other hand, by using ultrashort optical pulses, it is possible to induce Raman-active coherent nuclear motion of the molecule and to observe the molecular vibration in real time. Moreover, this time-domain Raman measurement can be combined with femtosecond photoexcitation, triggering chemical changes, which enables tracking ultrafast structural dynamics in a form of “time-resolved” time-domain Raman spectroscopy, also known as time-resolved impulsive stimulated Raman spectroscopy. With the advent of stable, ultrashort laser pulse sources, time-resolved impulsive stimulated Raman spectroscopy now realizes high sensitivity and a wide detection frequency window from THz to 3000 cm^–1, and has seen success in unveiling the molecular mechanisms underlying the efficient functions of complex molecular systems. In this Perspective, we overview the present status of time-domain Raman spectroscopy, particularly focusing on its application to the study of femtosecond structural dynamics. We first explain the principle and a brief history of time-domain Raman spectroscopy and then describe the apparatus and recent applications to the femtosecond dynamics of complex molecular systems, including proteins, molecular assemblies, and functional materials. We also discuss future directions for time-domain Raman spectroscopy, which has reached a status allowing a wide range of applications.

Unveiling coupled electronic and vibrational motions of chromophores in condensed phases

The quest for capturing molecular movies of functional systems has motivated scientists and engineers for decades. A fundamental understanding of electronic and nuclear motions, two principal components of the molecular Schrödinger equation, has the potential to enable the de novo rational design for targeted functionalities of molecular machines. We discuss the development and application of a relatively new structural dynamics technique, femtosecond stimulated Raman spectroscopy with broadly tunable laser pulses from the UV to near-IR region, in tracking the coupled electronic and vibrational motions of organic chromophores in solution and protein environments. Such light-sensitive moieties hold broad interest and significance in gaining fundamental knowledge about the intramolecular and intermolecular Hamiltonian and developing effective strategies to control macroscopic properties. Inspired by recent experimental and theoretical advances, we focus on the in situ characterization and spectroscopy-guided tuning of photoacidity, excited state proton transfer pathways, emission color, and internal conversion via a conical intersection.

Elucidating the Molecular Mechanism of Ultrafast Pfr-State Photoisomerization in Bathy Bacteriophytochrome PaBphP

Bacteriophytochromes are photoreceptors that regulate various physiological processes induced by photoisomerization in a linear tetrapyrrole chromophore upon red/far-red light absorption. Here, we investigate the photoinduced Pfr-state isomerization mechanism of a bathy bacteriophytochrome from Pseudomonas aeruginosa combining femtosecond-resolved fluorescence and absorption methods. We observed initial coherent oscillation motions in the first 1 ps with low-frequency modes below 60 cm^-1, then a bifurcation of the wavepacket with the distinct excited-state lifetimes in a few picoseconds, and finally chromophore-protein coupled ground-state conformational evolution on nanosecond time scales. Together with systematic mutational studies, we revealed the critical roles of hydrogen bonds in tuning the photoisomerization dynamics. These results provide a clear molecular picture of the Pfr-state photoisomerization, a mechanism likely applicable to the other phytochromes.

Fifth-order time-domain Raman spectroscopy of photoactive yellow protein for visualizing vibrational coupling in its excited state

We report fifth-order time-domain Raman spectroscopy of photoactive yellow protein (PYP), with the aim to visualize vibrational coupling in its excited state. After the ultrashort actinic pump pulse prepared the vibrational coherence and population in the excited state, the evolving vibrational structure was tracked by time-resolved impulsive stimulated Raman spectroscopy using sub-7-fs pulses. The obtained fifth-order time-domain Raman data were translated to a two-dimensional (2D) frequency-frequency correlation map, which visualizes the correlation between low- and high-frequency vibrational modes of the excited state. The 2D map of PYP reveals a cross peak, indicating the coupling between the phenolic C─O stretch mode of the chromophore and the low-frequency modes (~160 cm^-1), assignable to the intermolecular motions involving the surrounding hydrogen-bonded amino acids. The unveiled coupling suggests the importance of the low-frequency vibrational motion in the primary photoreaction of PYP, highlighting the unique capability of this spectroscopic approach for studying ultrafast reaction dynamics.

Excitation-Wavelength-Dependent Photocycle Initiation Dynamics Resolve Heterogeneity in the Photoactive Yellow Protein from Halorhodospira halophila

Photoactive yellow proteins (PYPs) make up a diverse class of blue-light-absorbing bacterial photoreceptors. Electronic excitation of the p-coumaric acid chromophore covalently bound within PYP results in triphasic quenching kinetics; however, the molecular basis of this behavior remains unresolved. Here we explore this question by examining the excitation-wavelength dependence of the photodynamics of the PYP from Halorhodospira halophila via a combined experimental and computational approach. The fluorescence quantum yield, steady-state fluorescence emission maximum, and cryotrapping spectra are demonstrated to depend on excitation wavelength. We also compare the femtosecond photodynamics in PYP at two excitation wavelengths (435 and 475 nm) with a dual-excitation-wavelength-interleaved pump-probe technique. Multicompartment global analysis of these data demonstrates that the excited-state photochemistry of PYP depends subtly, but convincingly, on excitation wavelength with similar kinetics with distinctly different spectral features, including a shifted ground-state beach and altered stimulated emission oscillator strengths and peak positions. Three models involving multiple excited states, vibrationally enhanced barrier crossing, and inhomogeneity are proposed to interpret the observed excitation-wavelength dependence of the data. Conformational heterogeneity was identified as the most probable model, which was supported with molecular mechanics simulations that identified two levels of inhomogeneity involving the orientation of the R52 residue and different hydrogen bonding networks with the p-coumaric acid chromophore. Quantum calculations were used to confirm that these inhomogeneities track to altered spectral properties consistent with the experimental results.

Probing the early stages of photoreception in photoactive yellow protein with ultrafast time-domain Raman spectroscopy

Unveiling the nuclear motions of photoreceptor proteins in action is a crucial goal in protein science in order to understand their elaborate mechanisms and how they achieve optimal selectivity and efficiency. Previous studies have provided detailed information on the structures of intermediates that appear during the later stages (>ns) of such photoreception cycles, yet the initial events immediately after photoabsorption remain unclear because of experimental challenges in monitoring nuclear rearrangements on ultrafast timescales, including protein-specific low-frequency motions. Using time-domain Raman probing with sub-7-fs pulses, we obtain snapshot vibrational spectra of photoactive yellow protein and a mutant with high sensitivity, providing insights into the key responses that drive photoreception. Our data show a drastic intensity drop of the excited-state marker band at 135 cm^-1 within a few hundred femtoseconds, suggesting a rapid weakening of the hydrogen bond that anchors the chromophore. We also track formation of the first ground-state intermediate over the first few picoseconds and fully characterize its vibrational structure, revealing a substantially-twisted cis conformation.

Communication maps of vibrational energy transport through Photoactive Yellow Protein

We calculate communication maps for Photoactive Yellow Protein (PYP) from the purple phototropic eubacterium Halorhodospira halophile and use them to elucidate energy transfer pathways from the chromophore through the rest of the protein in the ground and excited state. The calculations reveal that in PYP excess energy from the chromophore flows mainly to regions of the surrounding residues that hydrogen bond to the chromophore. In addition, quantum mechanics/molecular mechanics and molecular dynamics (MD) simulations of the dielectric response of the protein and solvent environment due to charge rearrangement on the chromophore following photoexcitation are also presented, with both approaches yielding similar time constants for the response. Results of MD simulations indicate that the residues hydrogen bonding to the chromophore make the largest contribution to the response.

Photoisomerisation quantum yield and non-linear cross-sections with femtosecond excitation of the photoactive yellow protein

The quantum yield of photoisomerisation of the photoactive yellow protein (PYP) strongly depends on peak power and wavelength with femtosecond optical excitation. Using systematic power titrations and addition of second order dispersion resulting in 140, 300 and 600 fs pulse durations, the one and multi-photon cross-sections at 400, 450 and 490 nm have been assessed from transient absorption spectroscopy and additionally the Z-scan technique. Applying a target model that incorporates photoselection theory, estimates for the cross-sections for stimulated emission and absorption of the first excited state, the amount of ultrafast internal conversion and the underlying species associated dynamics have been determined. The final quantum yields for photoisomerisation were found to be 0.06, 0.14-0.19 and 0.02 for excitation wavelengths 400, 450 and 490 nm and found to increase with increasing pulse durations. Transient absorption measurements and Z-scan measurements at 450 nm, coinciding with the maximum wavelength of the ground state absorption, indicate that the photochemical quantum yield is intrinsically limited by an ultrafast internal conversion reaction as well as by stimulated emission cross-section. With excitation at 400 nm photoisomerisation quantum yield is further significantly limited by competing multi-photon excitation into excited state absorption at 385 nm previously proposed to result in photoionisation. With excitation at 490 nm the photoisomerisation quantum yield is predominantly limited further by the significantly higher stimulated emission cross-section compared to ground state cross-section as well as multi-photon processes. In addition to photoionisation, a second product of multi-photon excitation is identified and characterised by an induced absorption at 500 nm and a time constant of 2 ps for relaxation. With power densities up to 138 GW cm(-2) the measurements have not provided indication for coherent multi-photon absorption of PYP. In the saturation regime with 450 nm excitation, the limit for the photoisomerisation quantum yield was found to be 0.14-0.19 and the excited state absorption cross-section 6.1 × 10(-17) cm(2) or 0.36 times the ground state cross-section of 1.68 × 10(-16) cm(2) per molecule. This places a fundamental restriction on the maximum populations and sample penetration that may be achieved for instance in femtosecond pump-probe experiments with molecular crystals of PYP.

Photochemistry of fac-[Re(bpy)(CO)3Cl]

The photochemistry of fac-[Re(bpy)(CO)₃Cl] (1 a; bpy=2,2′-bipyridine) initiated by irradiation using <330 nm light has been investigated. Isomerization proceeded in THF to give the corresponding mer-isomer 1 b. However, in the presence of a small amount of MeCN, the main product was the CO-ligand-substituted complex (OC-6-24)-[Re(bpy)(CO)₂Cl(MeCN)] (2 c; bpy=2,2′-bipyridine). In MeCN, two isomers, 2 c and its (OC-6-34) form (2 a), were produced. Only 2 c thermally isomerized to produce the (OC-6-44) form 2 b. A detailed investigation led to the conclusion that both 1 b and 2 c are produced by a dissociative mechanism, whereas 2 a forms by an associative mechanism. A comparison of the ultrafast transient UV-visible absorption, emission, and IR spectra of 1 a acquired by excitation using higher-energy light (e.g., 270 nm) and lower-energy light (e.g., 400 nm) gave detailed information about the excited states, intermediates, and kinetics of the photochemical reactions and photophysical processes of 1 a. Irradiation of 1 a using the higher-energy light resulted in the generation of the higher singlet excited state with τ≤25 fs, from which intersystem crossing proceeded to give the higher triplet state (³HES(1)). In THF, ³HES(1) was competitively converted to both the triplet ligand field (³LF) and metal-to-ligand charge transfer (³mLCT) with lifetimes of 200 fs, in which the former is a reactive state that converts to [Re(bpy)(CO)₂Cl(thf)]⁺ (1 c) within 10 ps by means of a dissociative mechanism. Re-coordination of CO to 1 c gives both 1 a and 1 b. In MeCN, irradiation of 1 a by using high-energy light gives the coordinatively unsaturated complex, which rapidly converted to 2 c. A seven-coordinate complex is also produced within several hundred femtoseconds, which is converted to 2 a within several hundred picoseconds.

Clean sub-8-fs pulses at 400 nm generated by a hollow fiber compressor for ultraviolet ultrafast pump-probe spectroscopy

Clean 7.5 fs pulses at 400 nm with less than 3% energy in tiny satellite pulses were obtained by spectral broadening in a hollow fiber and dispersive compensating using a prism pair together with a deformable mirror system. As an example, this stable and clean pulse was used to study the ultrafast pump-probe spectroscopy of photoactive yellow protein. Moreover, the self-diffraction signal shows a smoothed and broadened laser spectrum and is expected to have a further clean laser pulse, which makes it more useful in the ultrafast pump-probe spectroscopy in the future.

Coherent ultrafast torsional motion and isomerization of a biomimetic dipolar photoswitch

Femtosecond fluorescence up-conversion, UV-Vis and IR transient absorption spectroscopy are used to study the photo-isomerization dynamics of a new type of zwitterionic photoswitch based on a N-alkylated indanylidene pyrroline Schiff base framework (ZW-NAIP). The system is biomimetic, as it mimics the photophysics of retinal, in coupling excited state charge translocation and isomerization. While the fluorescence lifetime is 140 fs, excited state absorption persists over 230 fs in the form of a vibrational wavepacket according to twisting of the isomerizing double bond. After a short "dark" time window in the UV-visible spectra, which we associate with the passage through a conical intersection (CI), the wavepacket appears on the ground state potential energy surface, as evidenced by the transient mid-IR data. This allows for a precise timing of the photoreaction all the way from the initial Franck-Condon region, through the CI and into both ground state isomers, until incoherent vibrational relaxation dominates the dynamics. The photo-reaction dynamics remarkably follow those observed for retinal in rhodopsin, with the additional benefit that in ZW-NAIP the conformational change reverses the zwitterion dipole moment direction. Last, the pronounced low-frequency coherences make these molecules ideal systems for investigating wavepacket dynamics in the vicinity of a CI and for coherent control experiments.

Coherent oscillations in ultrafast fluorescence of photoactive yellow protein

The ultrafast photoinduced dynamics of photoactive yellow protein in aqueous solution were studied at room temperature by femtosecond fluorescence spectroscopy using an optical Kerr-gate technique. Coherent oscillations of the wave packet were directly observed in the two-dimensional time-energy map of ultrafast fluorescence with 180 fs time resolution and 5 nm spectral resolution. The two-dimensional map revealed that four or more oscillatory components exist within the broad bandwidth of the fluorescence spectrum, each of which is restricted in the respective narrow spectral region. Typical frequencies of the oscillatory modes are 50 and 120 cm(-1). In the landscape on the map, the oscillatory components were recognized as the ridges which were winding and descending with time. The amplitude of the oscillatory and winding behaviors is a few hundred cm(-1), which is the same order as the frequencies of the oscillations. The mean spectral positions of the oscillatory components in the two-dimensional map are well explained by considering the vibrational energies of intramolecular modes in the electronic ground state of the chromophore. The entire view of the wave packet oscillations and broadening in the electronic excited state, accompanied by fluorescence transitions to the vibrational sublevels belonging to the electronic ground state, was obtained.

Anharmonic Vibrational Calculations Modeling the Raman Spectra of Intermediates in the Photoactive Yellow Protein (PYP) Photocycle

The role of anharmonic effects in the vibrational spectroscopy of the dark state and two major chromophore intermediates of the photoactive yellow protein (PYP) photocycle is examined via ab initio vibrational self-consistent field (VSCF) calculations and time-resolved resonance Raman spectroscopy. For the first time, anharmonicity is considered explicitly in calculating the vibrational spectra of an ensemble consisting of the PYP chromophore surrounded by model compounds used as mimics of the important active-site residues. Predictions of vibrational frequencies on an ab initio corrected semiempirical potential energy surface show remarkable agreement with experimental frequencies for all three states, thus shedding light on the potential along the reaction path. For example, calculated frequencies for vibrational modes of the red-shifted intermediate, PYPL, exhibit an overall average error of 0.82% from experiment. Upon analysis of anharmonicity patterns in the PYP modes we observe a decrease in anharmonicity in the C8-C9 stretching mode nu29 (trans-cis isomerization marker mode) with the onset of the cis configuration in PYPL. This can be attributed to the loss of the hydrogen-bonding character of the adjacent C9-O2 to the methylamine (Cys69 backbone). For several of the modes, the anharmonicity is mostly due to mode-mode coupling, while for others it is mostly intrinsic. This study shows the importance of the inclusion of anharmonicity in theoretical spectroscopic calculations, and the sensitivity of experiments to anharmonicity. The characterization of protein active-site residues by small molecular mimics provides an acceptable chemical structural representation for biomolecular spectroscopy calculations.

Vibrational assignment of the 4-hydroxycinnamyl chromophore in photoactive yellow protein

Photoactive yellow protein (PYP) is a bacterial photoreceptor containing a 4-hydroxycinnamyl chromophore. We report the Raman spectra for the dark state of PYP whose chromophore is isotopically labeled with 13C at the carbonyl carbon atom or at the ring carbon atoms. Spectra have been also measured with PYP in D2O where the exchangeable protons are deuterated. Most of the observed Raman bands are assigned on the basis of the observed isotope shifts and normal mode calculations using a density functional theory. We discuss the implication for the analysis of the infrared spectra of PYP. The comprehensive assignment provides a satisfactory framework for future investigations of the photocycle mechanism in PYP by vibrational spectroscopy.

Ultrafast light-induced response of photoactive yellow protein chromophore analogues

The fluorescence decays of several analogues of the photoactive yellow protein (PYP) chromophore in aqueous solution have been measured by femtosecond fluorescence up-conversion and the corresponding time-resolved fluorescence spectra have been reconstructed. The native chromophore of PYP is a thioester derivative of p-coumaric acid in its trans deprotonated form. Fluorescence kinetics are reported for a thioester phenyl analogue and for two analogues where the thioester group has been changed to amide and carboxylate groups. The kinetics are compared to those we previously reported for the analogues bearing ketone and ester groups. The fluorescence decays of the full series are found to lie in the 1-10 ps range depending on the electron-acceptor character of the substituent, in good agreement with the excited-state relaxation kinetics extracted from transient absorption measurements. Steady-state photolysis is also examined and found to depend strongly on the nature of the substituent. While it has been shown that the ultrafast light-induced response of the chromophore in PYP is controlled by the properties of the protein nanospace, the present results demonstrate that, in solution, the relaxation dynamics and pathway of the chromophore is controlled by its electron donor-acceptor structure: structures of stronger electron donor-acceptor character lead to faster decays and less photoisomerisation.

Binding, tuning and mechanical function of the 4-hydroxy-cinnamic acid chromophore in photoactive yellow protein

The bacterial photoreceptor protein photoactive yellow protein (PYP) covalently binds the chromophore 4-hydroxy coumaric acid, tuning (spectral) characteristics of this cofactor. Here, we study this binding and tuning using a combination of pointmutations and chromophore analogs. In all photosensor proteins studied to date the covalent linkage of the chromophore to the apoprotein is dispensable for light-induced catalytic activation. We analyzed the functional importance of the covalent linkage using an isosteric chromophore-protein variant in which the cysteine is replaced by a glycine residue and the chromophore by thiomethyl-p-coumaric acid (TMpCA). The model compound TMpCA is shown to weakly complex with the C69G protein. This non-covalent binding results in considerable tuning of both the pKa and the color of the chromophore. The photoactivity of this system, however, was strongly impaired, making PYP the first known photosensor protein in which the covalent linkage of the chromophore is of paramount importance for the functional activity of the protein in vitro. We also studied the influence of chromophore analogs on the color and photocycle of PYP, not only in WT, but especially in the E46Q mutant, to test if effects from both chromophore and protein modifications are additive. When the E46Q protein binds the sinapinic acid chromophore, the color of the protein is effectively changed from yellow to orange. The altered charge distribution in this protein also results in a changed pKa value for chromophore protonation, and a strongly impaired photocycle. Both findings extend our knowledge of the photochemistry of PYP for signal generation.

Development of simultaneous frequency- and time-resolved coherent anti-Stokes Raman scattering for ultrafast detection of molecular Raman spectra

The development of a time-resolved coherent anti-Stokes Raman scattering (CARS) variant for use as a probe of excited electronic state Raman-active modes following excitation with an ultrafast pump pulse is detailed. Application of this technique involves a combination of broadband fs-time scale pulses and a narrowband pulse of ps duration that allows multiplexed detection of the CARS signal, permitting direct observation of molecular Raman frequencies and intensities with time resolution dictated by the broadband pulses. Thus, this nonlinear optical probe, designated fs/ps CARS, is suitable for observation of Raman spectral evolution following excitation with a pump pulse. Because of the spatial separation of the CARS output signal relative to the three input beams inherent in a folded BOXCARS arrangement, this technique is particularly amenable to probing low-frequency vibrational modes, which play a significant role in accepting vibrational energy during intramolecular vibrational energy redistribution within electronically excited states. Additionally, this spatial separation allows discrimination against strong fluorescence signal, as demonstrated in the case of rhodamine 6G.

Structural changes during the photocycle of photoactive yellow protein monitored by ultraviolet resonance raman spectra of tyrosine and tryptophan

Photoactive yellow protein (PYP) is a bacterial blue light photoreceptor, and photoexcitation of dark-state PYP (PYP(dark)) triggers a photocycle that involves several intermediate states. We report the ultraviolet resonance Raman spectra of PYP with 225-250 nm excitations and investigate protein structural changes accompanying the formation of the putative signaling state denoted PYP(M). The PYP(M)-PYP(dark) difference spectra show several features of tyrosine and tryptophan, indicating environmental changes for these amino acid residues. The tyrosine difference signals show small upshifts with intensity changes in Y8a and Y9a bands. Although there are five tyrosine residues in PYP, Tyr42 and Tyr118 are suggested to be responsible for the difference signals on the basis of a global fitting analysis of the difference spectra at different excitation wavelengths and the crystal structure of PYP(dark). A further experiment on the Thr50-->Val mutant supports environmental changes in Tyr42. The observed upshift of the Y8a band suggests a weaker or broken hydrogen bond between Tyr42 and the chromophore in PYP(M). In addition, a reorientation of the OH group in Tyr42 is suggested from the upshift of the Y9a band. For tryptophan, the Raman bands of W3, W16, and W18 modes diminish in intensity upon formation of PYP(M). The loss of intensities is attributable to an exposure of tryptophan in PYP(M). PYP contains only one tryptophan (Trp119) that is located more than 10 A from the active site. Thus the observed changes are indicative of global conformational changes in protein during the transition from PYP(dark) to PYP(M). These results are in line with the currently proposed photocycle mechanism of PYP.

Initial photoinduced dynamics of the photoactive yellow protein

The photoactive yellow protein (PYP) is the photoreceptor protein responsible for initiating the blue-light repellent response of the Halorhodospira halophila bacterium. Optical excitation of the intrinsic chromophore in PYP, p-coumaric acid, leads to the initiation of a photocycle that comprises several distinct intermediates. The dynamical processes responsible for the initiation of the PYP photocycle have been explored with several time-resolved techniques, which include ultrafast electronic and vibrational spectroscopies. Ultrafast electronic spectroscopies, such as pump-visible probe, pump-dump-visible probe, and fluorescence upconversion, are useful in identifying the timescales and connectivity of the transient intermediates, while ultrafast vibrational spectroscopies link these intermediates to dynamic structures. Herein, we present the use of these techniques for exploring the initial dynamics of PYP, and show how these techniques provide the basis for understanding the complex relationship between protein and chromophore, which ultimately results in biological function.

Solvent Effect on the Excited-State Dynamics of Analogues of the Photoactive Yellow Protein Chromophore

We previously reported that two analogues of the Photoactive Yellow Protein chromophore, trans-p-hydroxycinnamic acid (pCA(2-)) and its amide derivative (pCM-) in their deprotonated forms, undergo a trans-cis photoisomerization whereas the thioester derivative, trans-p-hydroxythiophenyl cinnamate (pCT-), does not. pCT- is also the only one to exhibit a short-lived intermediate on its excited-state deactivation pathway. We here further stress the existence of two different relaxation mechanisms for these molecules and examine the reaction coordinates involved. We looked at the effect of the solvent properties (viscosity, polarity, solvation dynamics) on their excited-state relaxation dynamics, probed by ultrafast transient absorption spectroscopy. Sensitivity to the solvent properties is found to be larger for pCT- than for pCA(2-) and pCM-. This difference is considered to reveal that either the relaxation pathway or the reaction coordinate is different for these two classes of analogues. It is also found to be correlated to the electron donor-acceptor character of the molecule. We attribute the excited-state deactivation of analogues bearing a weaker acceptor group, pCA(2-) and pCM-, to a stilbene-like photoisomerization mechanism with the concerted rotation of the ethylenic bond and one adjacent single bond. For pCT-, which contains a stronger acceptor group, we consider a photoisomerization mechanism mainly involving the single torsion of the ethylenic bond. The excited-state deactivation of pCT- would lead to the formation of a ground-state intermediate at the "perp" geometry, which would return to the initial trans conformation without net isomerization.

Primary steps of the photoactive yellow protein: isolated chromophore dynamics and protein directed function

The cycle of the photoactive yellow protein (PYP) has been extensively studied, but the dynamics of the isolated chromophore responsible for transduction is unknown. Here, we present real-time observation of the dynamics of the negatively charged chromophore and detection of intermediates along the path of trans-to-cis isomerization using femtosecond mass selection/electron detachment techniques. The results show that the role of the protein environment is not in the first step of double-bond twisting (barrier crossing) but in directing efficient conversion to the cis-structure and in impeding radical formation within the protein.

Resonance Raman Evidence for Two Conformations Involved in the L Intermediate of Photoactive Yellow Protein

The blue light receptor photoactive yellow protein (PYP) displays a photocycle that involves several intermediate states. Here we report resonance Raman spectroscopic investigations of the short-lived red-shifted intermediate denoted PYP(L). We have found that the Raman bands of the carbonyl C=O stretching mode nu(11) as well as the C=C stretching mode nu(13) for the chromophore can be resolved into two peaks, and the ratio of the two components varies as a function of pH with pK(a) approximately 6. The isotope effects on the resonance Raman spectra have confirmed a deprotonated cis-chromophore for the two components. The results indicate the presence of two conformations in the active site of PYP(L). The normal coordinate calculations based on the density functional theory provide a structural model for the two conformations, where the low pH form is possibly an active structure for the protonation reaction generating a following intermediate in the photocycle.