Ultrafast excited-state isomerization in phytochrome revealed by femtosecond stimulated Raman spectroscopy

Dynamic inhomogeneity in the photodynamics of cyanobacterial phytochrome Cph1

Phytochromes are widespread red/far-red photosensory proteins well known as critical regulators of photomorphogenesis in plants. It is often assumed that natural selection would have optimized the light sensing efficiency of phytochromes to minimize nonproductive photochemical deexcitation pathways. Surprisingly, the quantum efficiency for the forward P_r-to-P_fr photoconversion of phytochromes seldom exceeds 15%, a value very much lower than that of animal rhodopsins. Exploiting ultrafast excitation wavelength- and temperature-dependent transient absorption spectroscopy, we resolve multiple pathways within the ultrafast photodynamics of the N-terminal PAS-GAF-PHY photosensory core module of cyanobacterial phytochrome Cph1 (termed Cph1Δ) that are primarily responsible for the overall low quantum efficiency. This inhomogeneity primarily reflects a long-lived fluorescent subpopulation that exists in equilibrium with a spectrally distinct, photoactive subpopulation. The fluorescent subpopulation is favored at elevated temperatures, resulting in anomalous excited-state dynamics (slower kinetics at higher temperatures). The spectral and kinetic behavior of the fluorescent subpopulation strongly resembles that of the photochemically compromised and highly fluorescent Y₁₇₆H variant of Cph1Δ. We present an integrated, heterogeneous model for Cph1Δ that is based on the observed transient and static spectroscopic signals. Understanding the molecular basis for this dynamic inhomogeneity holds potential for rational design of efficient phytochrome-based fluorescent and photoswitchable probes.

Tyrosine 263 in cyanobacterial phytochrome Cph1 optimizes photochemistry at the prelumi-R→lumi-R step

We report a low-temperature fluorescence spectroscopy study of the PAS-GAF-PHY sensory module of Cph1 phytochrome, its Y263F mutant (both with known 3D structures) as well as Y263H and Y263S to connect their photochemical parameters with intramolecular interactions. None of the holoproteins showed photochemical activity at low temperature, and the activation barriers for the Pr→lumi-R photoreaction (2.5-3.1 kJ mol(-1)) and fluorescence quantum yields (0.29-0.42) were similar. The effect of the mutations on Pr→Pfr photoconversion efficiency (ΦPr→Pfr) was observed primarily at the prelumi-R S0 bifurcation point corresponding to the conical intersection of the energy surfaces at which the molecule relaxes to form lumi-R or Pr, lowering ΦPr→Pfr from 0.13 in the wild type to 0.05-0.07 in the mutants. We suggest that the Ea activation barrier in the Pr* S1 excited state might correspond to the D-ring (C19) carbonyl - H290 hydrogen bond or possibly to the hindrance caused by the C13(1) /C17(1) methyl groups of the C and D rings. The critical role of the tyrosine hydroxyl group can be at the prelumi-R bifurcation point to optimize the yield of the photoprocess and energy storage in the form of lumi-R for subsequent rearrangement processes culminating in Pfr formation.

Non-classicality of the molecular vibrations assisting exciton energy transfer at room temperature

Advancing the debate on quantum effects in light-initiated reactions in biology requires clear identification of non-classical features that these processes can exhibit and utilize. Here we show that in prototype dimers present in a variety of photosynthetic antennae, efficient vibration-assisted energy transfer in the sub-picosecond timescale and at room temperature can manifest and benefit from non-classical fluctuations of collective pigment motions. Non-classicality of initially thermalized vibrations is induced via coherent exciton-vibration interactions and is unambiguously indicated by negativities in the phase-space quasi-probability distribution of the effective collective mode coupled to the electronic dynamics. These quantum effects can be prompted upon incoherent input of excitation. Our results therefore suggest that investigation of the non-classical properties of vibrational motions assisting excitation and charge transport, photoreception and chemical sensing processes could be a touchstone for revealing a role for non-trivial quantum phenomena in biology.

Active and silent chromophore isoforms for phytochrome Pr photoisomerization: An alternative evolutionary strategy to optimize photoreaction quantum yields

Photoisomerization of a protein bound chromophore is the basis of light sensing of many photoreceptors. We tracked Z-to-E photoisomerization of Cph1 phytochrome chromophore PCB in the Pr form in real-time. Two different phycocyanobilin (PCB) ground state geometries with different ring D orientations have been identified. The pre-twisted and hydrogen bonded PCB(a) geometry exhibits a time constant of 30 ps and a quantum yield of photoproduct formation of 29%, about six times slower and ten times higher than that for the non-hydrogen bonded PCB(b) geometry. This new mechanism of pre-twisting the chromophore by protein-cofactor interaction optimizes yields of slow photoreactions and provides a scaffold for photoreceptor engineering.

Multiple hydrogen bonding in excited states of aminopyrazine in methanol solution: time-dependent density functional theory study

Aminopyrazine (AP) and AP-methanol complexes have been theoretically studied by using density functional theory (DFT) and time-dependent density functional theory (TDDFT). The excited-state hydrogen bonds are discussed in detail. In the ground state the intermolecular multiple hydrogen bonds can be formed between AP molecule and protic solvents. The AP monomer and hydrogen-bonded complex of AP with one methanol are photoexcited initially to the S2 state, and then transferred to the S1 state via internal conversion. However the complex of AP with two methanol molecules is directly excited to the S1 state. From the calculated electronic excited energies and simulated absorption spectra, we find that the intermolecular hydrogen bonds are strengthened in the electronic excited states. The strengthening is confirmed by the optimized excited-state geometries. The photochemical processes in the electronic excited states are significantly influenced by the excited-state hydrogen bond strengthening.

Optimally shaped narrowband picosecond pulses for femtosecond stimulated Raman spectroscopy

A comparison between a Fabry-Pérot etalon filter and a conventional grating filter for producing the picosecond (ps) Raman pump pulses for femtosecond stimulated Raman spectroscopy (FSRS) is presented. It is shown that for pulses of equal energy the etalon filter produces Raman signals twice as large as that of the grating filter while suppressing the electronically resonant background signal. The time asymmetric profile of the etalon-generated pulse is shown to be responsible for both of these observations. A theoretical discussion is presented which quantitatively supports this hypothesis. It is concluded that etalons are the ideal method for the generation of narrowband ps pulses for FSRS because of the optical simplicity, efficiency, improved FSRS intensity and reduced backgrounds.

Unraveling the Primary Isomerization Dynamics in Cyanobacterial Phytochrome Cph1 with Multi-pulse Manipulations

The ultrafast mechanisms underlying the initial photoisomerization (Pr → Lumi-R) in the forward reaction of the cyanobacterial photoreceptor Cph1 were explored with multipulse pump-dump-probe transient spectroscopy. A recently postulated multi-population model was used to fit the transient pump-dump-probe and dump-induced depletion signals. We observed dump-induced depletion of the Lumi-R photoproduct, demonstrating that photoisomerization occurs via evolution on both the excited- and ground-state electronic surfaces. Excited-state equilibrium was not observed, as shown via the absence of a dump-induced excited-state "Le Châtelier redistribution" of excited-state populations. The importance of incorporating the inhomogeneous dynamics of Cph1 in interpreting measured transient data is discussed.

Early time excited-state structural evolution of pyranine in methanol revealed by femtosecond stimulated Raman spectroscopy

To understand chemical reactivity of molecules in condensed phase in real time, a structural dynamics technique capable of monitoring molecular conformational motions on their intrinsic time scales, typically on femtoseconds to picoseconds, is needed. We have studied a strong photoacid pyranine (8-hydroxypyrene-1,3,6-trisulfonic acid, HPTS, pK(a)* ≈ 0) in pure methanol and observed that excited-state proton transfer (ESPT) is absent, in sharp contrast with our previous work on HPTS in aqueous solutions wherein ESPT prevails following photoexcitation. Two transient vibrational marker bands at ~1477 (1454) and 1532 (1528) cm(-1) appear in CH3OH (CD3OD), respectively, rising within the instrument response time of ~140 fs and decaying with 390-470 (490-1400) fs and ~200 ps time constants in CH3OH (CD3OD). We attribute the mode onset to small-scale coherent proton motion along the pre-existing H-bonding chain between HPTS and methanol, and the two decay stages to the low-frequency skeletal motion-modulated Franck-Condon relaxation within ~1 ps and subsequent rotational diffusion of H-bonding partners in solution before fluorescence. The early time kinetic isotope effect (KIE) of ~3 upon methanol deuteration argues active proton motions particularly within the first few picoseconds when coherent skeletal motions are underdamped. Pronounced quantum beats are observed for high-frequency modes consisting of strong phenolic COH rocking (1532 cm(-1)) or H-out-of-plane wagging motions (952 cm(-1)) due to anharmonic coupling to coherent low-frequency modes impulsively excited at ca. 96, 120, and 168 cm(-1). The vivid illustration of atomic motions of HPTS in varying H-bonding geometry with neighboring methanol molecules unravels the multidimensional energy relaxation pathways immediately following photoexcitation, and provides compelling evidence that, in lieu of ESPT, the photoacidity of HPTS promptly activates characteristic low-frequency skeletal motions to search phase space mainly concerning the phenolic end and to efficiently dissipate vibrational energy via skeletal deformation and proton shuttling motions within the intermediate, relatively confined excited-state HPTS-methanol complex on a solvent-dependent dynamic potential energy surface.

Ultrafast red light activation of Synechocystis phytochrome Cph1 triggers major structural change to form the Pfr signalling-competent state

Phytochromes are dimeric photoreceptors that regulate a range of responses in plants and microorganisms through interconversion of red light-absorbing (Pr) and far-red light-absorbing (Pfr) states. Photoconversion between these states is initiated by light-driven isomerization of a bilin cofactor, which triggers protein structural change. The extent of this change, and how light-driven structural changes in the N-terminal photosensory region are transmitted to the C-terminal regulatory domain to initiate the signalling cascade, is unknown. We have used pulsed electron-electron double resonance (PELDOR) spectroscopy to identify multiple structural transitions in a phytochrome from Synechocystis sp. PCC6803 (Cph1) by measuring distances between nitroxide labels introduced into the protein. We show that monomers in the Cph1 dimer are aligned in a parallel ‘head-to-head’ arrangement and that photoconversion between the Pr and Pfr forms involves conformational change in both the N- and C-terminal domains of the protein. Cryo-trapping and kinetic measurements were used to probe the extent and temporal properties of protein motions for individual steps during photoconversion of Cph1. Formation of the primary photoproduct Lumi-R is not affected by changes in solvent viscosity and dielectric constant. Lumi-R formation occurs at cryogenic temperatures, consistent with their being no major structural reorganization of Cph1 during primary photoproduct formation. All remaining steps in the formation of the Pfr state are affected by solvent viscosity and dielectric constant and occur only at elevated temperatures, implying involvement of a series of long-range solvent-coupled conformational changes in Cph1. We show that signalling is achieved through ultrafast photoisomerization where localized structural change in the GAF domain is transmitted and amplified to cause larger-scale and slower conformational change in the PHY and histidine kinase domains. This hierarchy of timescales and extent of structural change orientates the histidine kinase domain to elicit the desired light-activated biological response.

Red/green cyanobacteriochromes: sensors of color and power

Phytochromes are red/far-red photoreceptors using cysteine-linked linear tetrapyrrole (bilin) chromophores to regulate biological responses to light. Light absorption triggers photoisomerization of the bilin between the 15Z and 15E photostates. The related cyanobacteriochromes (CBCRs) extend the photosensory range of the phytochrome superfamily to shorter wavelengths of visible light. Several subfamilies of CBCRs have been described. Representatives of one such subfamily, including AnPixJ and NpR6012g4, exhibit red/green photocycles in which the 15Z photostate is red-absorbing like that of phytochrome but the 15E photoproduct is instead green-absorbing. Using recombinant expression of individual CBCR domains in Escherichia coli, we fully survey the red/green subfamily from the cyanobacterium Nostoc punctiforme. In addition to 14 new photoswitching CBCRs, one apparently photochemically inactive protein exhibiting intense red fluorescence was observed. We describe a novel orange/green photocycle in one of these CBCRs, NpF2164g7. Dark reversion varied in this panel of CBCRs; some examples were stable as the 15E photoproduct for days, while others reverted to the 15Z dark state in minutes or even seconds. In the case of NpF2164g7, dark reversion was so rapid that reverse photoconversion of the green-absorbing photoproduct was not significant in restoring the dark state, resulting in a broadband response to light. Our results demonstrate that red/green CBCRs can thus act as sensors for the color or intensity of the ambient light environment.

Ultrafast E to Z photoisomerization dynamics of the Cph1 phytochrome

Femtosecond photodynamics of the reverse ( 15E Pfr→ 15Z Pr) reaction of the red/far-red phytochrome Cph1 from Synechocystis were resolved with visible broadband transient absorption spectroscopy. Multi-phasic dynamics were resolved and separated via global target analysis into a fast-decaying (260 fs) excited-state population that bifurcates to generate the isomerized Lumi-F primary photoproduct and a non-isomerizing vibrationally excited ground state that relaxes back into the 15E Pfr ground state on a 2.8-ps time scale. Relaxation on a 1-ms timescale results in the loss of red absorbing region, but not blue region, of Lumi-F, which indicates that formation of 15Z Pr occurs on slower timescales.

Ultrafast conformational dynamics of pyranine during excited state proton transfer in aqueous solution revealed by femtosecond stimulated Raman spectroscopy

Proton transfer reaction plays an essential role in a myriad of chemical and biological processes, and to reveal the choreography of the proton motion intra- and intermolecularly, a spectroscopic technique capable of capturing molecular structural snapshots on the intrinsic time scale of proton transfer motions is needed. The photoacid pyranine (8-hydroxypyrene-1,3,6-trisulfonic acid, HPTS) serves as a paradigm case to dissect excited state proton transfer (ESPT) events in aqueous solution, triggered precisely by photoexcitation. We have used femtosecond stimulated Raman spectroscopy (FSRS) to yield novel insights into the ultrafast conformational dynamics of photoexcited HPTS in complex with water and acetate molecules. Marker bands attributed to the deprotonated form of HPTS (1139 cm(-1), ∼220 fs rise) appear earlier and faster than the monomer acetic acid peak (864 cm(-1), ∼530 fs rise), indicating that water molecules actively participate in the ESPT chain. Several key low-frequency modes at 106, 150, 195, and 321 cm(-1) have been identified to facilitate ESPT at different stages from 300 fs, 1 ps, to 6 ps and beyond, having distinctive dynamics contributing through hydrogen bonds with 0, 1, and more intervening water molecules. The time-resolved FSRS spectroscopy renders a direct approach to observe the reactive coupling between the vibrational degrees of freedom of photoexcited HPTS in action, therefore revealing the anharmonicity matrix both within HPTS and between HPTS and the neighboring acceptor molecules. The observed excited state conformational dynamics are along the ESPT multidimensional reaction coordinate and are responsible for the photoacidity of HPTS in aqueous solution.

Solid-state NMR spectroscopic study of chromophore-protein interactions in the Pr ground state of plant phytochrome A

Despite extensive study, the molecular structure of the chromophore-binding pocket of phytochrome A (phyA), the principal photoreceptor controlling photomorphogenesis in plants, has not yet been successfully resolved. Here, we report a series of two-dimensional (2-D) magic-angle spinning solid-state NMR experiments on the recombinant N-terminal, 65-kDa PAS-GAF-PHY light-sensing module of phytochrome A3 from oat (Avena sativa), assembled with uniformly 13C- and 15N-labeled phycocyanobilin (u-[13C,15N]-PCB-As.phyA3). The Pr state of this protein was studied regarding the electronic structure of the chromophore and its interactions with the proximal amino acids. Using 2-D 13C-13C and 1H-15N experiments, a complete set of 13C and 15N assignments for the chromophore were obtained. Also, a large number of 1H-13C distance restraints between the chromophore and its binding pocket were revealed by interfacial heteronuclear correlation spectroscopy. 13C doublings of the chromophore A-ring region and the C-ring carboxylate moiety, together with the observation of two Pr isoforms, Pr-I and Pr-II, demonstrate the local mobility of the chromophore and the plasticity of its protein environment. It appears that the interactions and dynamics in the binding pocket of phyA in the Pr state are remarkably similar to those of cyanobacterial phytochrome (Cph1). The N-terminus of the region modeled (residues 56-66 of phyA) is highly mobile. Differences in the regulatory processes involved in plant and Cph1 phytochromes are discussed.

The physical chemistry of the enigmatic phospholipid diacylglycerol pyrophosphate

Phosphatidic acid (PA) is a lipid second messenger that is formed transiently in plants in response to different stress conditions, and plays a role in recruiting protein targets, ultimately enabling an adequate response. Intriguingly, this increase in PA concentration in plants is generally followed by an increase in the phospholipid diacylglycerolpyrophosphate (DGPP), via turnover of PA. Although DGPP has been shown to induce stress-related responses in plants, it is unclear to date what its molecular function is and how it exerts its effect. Here, we describe the physicochemical properties, i.e., effective molecular shape and charge, of DGPP. We find that unlike PA, which imparts a negative curvature stress to a (phospho)lipid bilayer, DGPP stabilizes the bilayer phase of phosphatidylethanolamine (PE), similar to the effect of phosphatidylcholine (PC). DGPP thus has zero curvature. The pKa(2) of the phosphomonoester of DGPP is 7.44 ± 0.02 in a PC bilayer, compared to a pKa(2) of 7.9 for PA. Replacement of half of the PC with PE decreases the pKa(2) of DGPP to 6.71 ± 0.02, similar to the behavior previously described for PA and summarized in the electrostatic-hydrogen bond switch model. Implications for the potential function of DGPP in biomembranes are discussed.

Conformational homogeneity and excited-state isomerization dynamics of the bilin chromophore in phytochrome Cph1 from resonance Raman intensities

The ground-state structure and excited-state isomerization dynamics of the P(r) and P(fr) forms of phytochrome Cph1 are investigated using resonance Raman intensity analysis. Electronic absorption and stimulated resonance Raman spectra of P(r) and P(fr) are presented; vibronic analysis of the Raman intensities and absorption spectra reveals that both conformers exist as a single, homogeneous population of molecules in the ground state. The homogeneous and inhomogeneous contributions to the overall electronic broadening are determined, and it is found that the broadening is largely homogeneous in nature, pointing to fast excited-state decay. Franck-Condon displacements derived from the Raman intensity analysis reveal the initial atomic motions in the excited state, including the highly displaced, nontotally symmetric torsional and C(15)-H HOOP modes that appear because of symmetry-reducing distortions about the C(14)-C(15) and C(15)=C(16) bonds. P(fr) is especially well primed for ultrafast isomerization and torsional Franck-Condon analysis predicts a <200 fs P(fr) → P(r) isomerization. This time is significantly faster than the observed 700 fs reaction time, indicating that the P(fr) S(1) surface has a D-ring rotational barrier caused by steric interactions with the protein.

Femtosecond stimulated Raman spectroscopy using a scanning multichannel technique

A scanning multichannel technique (SMT) has been implemented in femtosecond stimulated Raman spectroscopy (FSRS). By combining several FSRS spectra detected at slightly different positions of the spectrograph via SMT, we have eliminated the systematic noise patterns ("fixed pattern noise") due to the variation in sensitivity and noise characteristics of the individual charge-coupled device (CCD) pixels. In nonresonant FSRS, solvent subtraction can effectively remove the systematic noise pattern even without SMT. However, in the case of resonant FSRS, we show that a similar solvent subtraction procedure is ineffective at removing the noise patterns without SMT. Application of SMT results in averaged FSRS spectra with improved signal-to-noise ratios that approach the shot-noise limit.

Second-chance forward isomerization dynamics of the red/green cyanobacteriochrome NpR6012g4 from Nostoc punctiforme

The primary ultrafast Z-to-E isomerization photodynamics of the phytochrome-related cyanobacteriochrome NpR6012g4 from Nostoc punctiforme was studied by transient absorption pump-dump-probe spectroscopy. A 2 ps dump pulse resonant with the stimulated emission band depleted 21% of the excited-state population, while the initial photoproduct Lumi-R was depleted by only 11%. We observed a red-shifted ground-state intermediate (GSI) that we assign to a metastable state that failed to isomerize fully. Multicomponent global analysis implicates the generation of additional Lumi-R from the GSI via crossing over the ground-state thermal barrier for full isomerization, explaining the discrepancy between excited-state and Lumi-R depletion by the dump pulse. This second-chance ground-state dynamics provides a plausible explanation for the unusually high quantum yield of 40% for the primary isomerization step in the forward reaction of NpR6012g4.

Femtosecond photodynamics of the red/green cyanobacteriochrome NpR6012g4 from Nostoc punctiforme. 2. reverse dynamics

Phytochromes are red/far-red photosensory proteins that utilize photoisomerization of a linear tetrapyrrole (bilin) chromophore to photoconvert reversibly between red- and far-red-absorbing forms (P(r) and P(fr), respectively). Cyanobacteriochromes (CBCRs) are related photosensory proteins with more diverse spectral sensitivity. The mechanisms that underlie this spectral diversity have not yet been fully elucidated. One of the main CBCR subfamilies photoconverts between a red-absorbing 15Z ground state, like the familiar P(r) state of phytochromes, and a green-absorbing photoproduct ((15E)P(g)). We have previously used the red/green CBCR NpR6012g4 from the cyanobacterium Nostoc punctiforme to examine ultrafast photodynamics of the forward photoreaction. Here, we examine the reverse reaction. Using excitation-interleaved transient absorption spectroscopy with broadband detection and multicomponent global analysis, we observed multiphasic excited-state dynamics. Interleaved excitation allowed us to identify wavelength-dependent shifts in the ground-state bleach that equilibrated on a 200 ps time scale, indicating ground-state heterogeneity. Compared to the previously studied forward reaction, the reverse reaction has much faster excited-state decay time constants and significantly higher photoproduct yield. This work thus demonstrates striking differences between the forward and reverse reactions of NpR6012g4 and provides clear evidence of ground-state heterogeneity in the phytochrome superfamily.

Structure-guided engineering enhances a phytochrome-based infrared fluorescent protein

Phytochrome is a multidomain dimeric red light photoreceptor that utilizes a chromophore-binding domain (CBD), a PHY domain, and an output module to induce cellular changes in response to light. A promising biotechnology tool emerged when a structure-based substitution at Asp-207 was shown to be an infrared fluorophore that uses a biologically available tetrapyrrole chromophore. We report multiple crystal structures of this D207H variant of the Deinococcus radiodurans CBD, in which His-207 is observed to form a hydrogen bond with either the tetrapyrrole A-ring oxygen or the Tyr-263 hydroxyl. Based on the implications of this duality for fluorescence properties, Y263F was introduced and shown to have stronger fluorescence than the original D207H template. Our structures are consistent with the model that the Y263F change prevents a red light-induced far-red light absorbing phytochrome chromophore configuration. With the goal of decreasing size and thereby facilitating use as a fluorescent tag in vivo, we also engineered a monomeric form of the CBD. Unexpectedly, photoconversion was observed in the monomer despite the lack of a PHY domain. This observation underscores an interplay between dimerization and the photochemical properties of phytochrome and suggests that the monomeric CBD could be used for further studies of the photocycle. The D207H substitution on its own in the monomer did not result in fluorescence, whereas Y263F did. Combined, the D207H and Y263F substitutions in the monomeric CBD lead to the brightest of our variants, designated Wisconsin infrared phytofluor (Wi-Phy).

Temperature-scan cryocrystallography reveals reaction intermediates in bacteriophytochrome

Light is a fundamental signal that regulates important physiological processes such as development and circadian rhythm in living organisms. Phytochromes form a major family of photoreceptors responsible for red light perception in plants, fungi and bacteria. They undergo reversible photoconversion between red-absorbing (Pr) and far-red-absorbing (Pfr) states, thereby ultimately converting a light signal into a distinct biological signal that mediates subsequent cellular responses. Several structures of microbial phytochromes have been determined in their dark-adapted Pr or Pfr states. However, the structural nature of initial photochemical events has not been characterized by crystallography. Here we report the crystal structures of three intermediates in the photoreaction of Pseudomonas aeruginosa bacteriophytochrome (PaBphP). We used cryotrapping crystallography to capture intermediates, and followed structural changes by scanning the temperature at which the photoreaction proceeded. Light-induced conformational changes in PaBphP originate in ring D of the biliverdin (BV) chromophore, and E-to-Z isomerization about the C(15) = C(16) double bond between rings C and D is the initial photochemical event. As the chromophore relaxes, the twist of the C(15) methine bridge about its two dihedral angles is reversed. Structural changes extend further to rings B and A, and to the surrounding protein regions. These data indicate that absorption of a photon by the Pfr state of PaBphP converts a light signal into a structural signal via twisting and untwisting of the methine bridges in the linear tetrapyrrole within the confined protein cavity.

Fluorescence quantum yield and photochemistry of bacteriophytochrome constructs

Bacteriophytochromes (Bphs) are red-light photoreceptor proteins with a photosensory core that consists of three distinct domains, PAS, GAF and PHY, and covalently binds biliverdin (BV) to a conserved cysteine in the PAS domain. In a recent development, PAS-GAF variants were engineered for use as a near-infrared fluorescent marker in mammalian tissues (Tsien and co-workers, Science, 2009, 324, 804-807). Here, we report the fluorescence quantum yield and photochemistry of two highly-related Bphs from Rps. palustris, RpBphP2 (P2) and RpBphP3 (P3) with distinct photoconversion and fluorescence properties. We applied ultrafast spectroscopy to wild type P3 and P2 PAS-GAF proteins and their P3 D216A, Y272F and P2 D202A PAS-GAF-PHY mutant proteins. In these mutants hydrogen-bond interactions between a conserved aspartate (Asp) which connects the BV chromophore with the PHY domains are disrupted. The excited-state lifetime of the truncated P3 and P2 PAS-GAF proteins was significantly longer than in their PAS-GAF-PHY counterparts that constitute the full photosensory core. Mutation of the conserved Asp to Ala in the PAS-GAF-PHY protein had a similar but larger effect. The fluorescence quantum yields of the P3 D216A and Y272F mutants were 0.066, higher than that of wild type P3 (0.043) and similar to the engineered Bph of Tsien and co-workers. We conclude that elimination of a key hydrogen-bond interaction between Asp and a conserved Arg in the PHY domain is responsible for the excited-state lifetime increase in all Bph variants studied here. H/D exchange resulted in a 1.4-1.7 fold increase of excited-state lifetime. The results support a reaction model in which deactivation of the BV chromophore proceeds via excited-state proton transfer from the BV pyrrole nitrogens to the backbone of the conserved Asp or to a bound water. This work may aid in rational structure- and mechanism-based conversion of constructs based on P3 and other BPhs into efficient near-IR, deep tissue, fluorescent markers.

Surface-Enhanced Femtosecond Stimulated Raman Spectroscopy

Surface-enhanced Raman spectroscopy (SERS) and femtosecond stimulated Raman spectroscopy (FSRS) have revolutionized the Raman spectroscopy field. SERS provides spectroscopic detection of single molecules, and FSRS enables the acquisition of Raman spectra on the ultrafast time scale of molecular motion. Here, we present the first successful combination of these two techniques, demonstrating surface-enhanced femtosecond stimulated Raman spectroscopy (SE-FSRS) using gold nanoantennas with embedded reporter molecules. Using a picosecond Raman and femtosecond probe pulse, the time- and ensemble-averaged enhancement factor is estimated to be in the range of 10(4)-10(6). We report the line shapes, power dependence, and magnitude of the SE-FSRS signal and discuss contributions to sample degradation on the minute time scale. With these first successful proof-of-principle experiments, time-resolved SE-FSRS techniques can now be rationally attempted with the goals of investigating the dynamics of plasmonic materials as well as examining the contributions of environmental heterogeneities by probing more homogeneous molecular subsets.

Modelling multi-pulse population dynamics from ultrafast spectroscopy

Current advanced laser, optics and electronics technology allows sensitive recording of molecular dynamics, from single resonance to multi-colour and multi-pulse experiments. Extracting the occurring (bio-) physical relevant pathways via global analysis of experimental data requires a systematic investigation of connectivity schemes. Here we present a Matlab-based toolbox for this purpose. The toolbox has a graphical user interface which facilitates the application of different reaction models to the data to generate the coupled differential equations. Any time-dependent dataset can be analysed to extract time-independent correlations of the observables by using gradient or direct search methods. Specific capabilities (i.e. chirp and instrument response function) for the analysis of ultrafast pump-probe spectroscopic data are included. The inclusion of an extra pulse that interacts with a transient phase can help to disentangle complex interdependent pathways. The modelling of pathways is therefore extended by new theory (which is included in the toolbox) that describes the finite bleach (orientation) effect of single and multiple intense polarised femtosecond pulses on an ensemble of randomly oriented particles in the presence of population decay. For instance, the generally assumed flat-top multimode beam profile is adapted to a more realistic Gaussian shape, exposing the need for several corrections for accurate anisotropy measurements. In addition, the (selective) excitation (photoselection) and anisotropy of populations that interact with single or multiple intense polarised laser pulses is demonstrated as function of power density and beam profile. Using example values of real world experiments it is calculated to what extent this effectively orients the ensemble of particles. Finally, the implementation includes the interaction with multiple pulses in addition to depth averaging in optically dense samples. In summary, we show that mathematical modelling is essential to model and resolve the details of physical behaviour of populations in ultrafast spectroscopy such as pump-probe, pump-dump-probe and pump-repump-probe experiments.

Two ground state isoforms and a chromophore D-ring photoflip triggering extensive intramolecular changes in a canonical phytochrome

Phytochrome photoreceptors mediate light responses in plants and in many microorganisms. Here we report studies using (1)H-(13)C magic-angle spinning NMR spectroscopy of the sensor module of cyanobacterial phytochrome Cph1. Two isoforms of the red-light absorbing Pr ground state are identified. Conclusive evidence that photoisomerization occurs at the C15-methine bridge leading to a β-facial disposition of the ring D is presented. In the far-red-light absorbing Pfr state, strong hydrogen-bonding interactions of the D-ring carbonyl group to Tyr-263 and of N24 to Asp-207 hold the chromophore in a tensed conformation. Signaling is triggered when Asp-207 is released from its salt bridge to Arg-472, probably inducing conformational changes in the tongue region. A second signal route is initiated by partner swapping of the B-ring propionate between Arg-254 and Arg-222.

Multichromatic control of gene expression in Escherichia coli

Light is a powerful tool for manipulating living cells because it can be applied with high resolution across space and over time. We previously constructed a red light-sensitive Escherichia coli transcription system based on a chimera between the red/far-red switchable cyanobacterial phytochrome Cph1 and the E. coli EnvZ/OmpR two-component signaling pathway. Here, we report the development of a green light-inducible transcription system in E. coli based on a recently discovered green/red photoswitchable two-component system from cyanobacteria. We demonstrate that the transcriptional output is proportional to the intensity of green light applied and that the green sensor is orthogonal to the red sensor at intensities of 532-nm light less than 0.01 W/m(2). Expression of both sensors in a single cell allows two-color optical control of transcription both in batch culture and in patterns across a lawn of engineered cells. Because each sensor functions as a photoreversible switch, this system should allow the spatial and temporal control of the expression of multiple genes through different combinations of light wavelengths. This feature aids precision single-cell and population-level studies in systems and synthetic biology.