Ultrashort Processes of Native Phytochrome: Femtosecond Kinetics of the Far-Red-Absorbing Form Pfr

Optical control of ultrafast structural dynamics in a fluorescent protein

The photoisomerization reaction of a fluorescent protein chromophore occurs on the ultrafast timescale. The structural dynamics that result from femtosecond optical excitation have contributions from vibrational and electronic processes and from reaction dynamics that involve the crossing through a conical intersection. The creation and progression of the ultrafast structural dynamics strongly depends on optical and molecular parameters. When using X-ray crystallography as a probe of ultrafast dynamics, the origin of the observed nuclear motions is not known. Now, high-resolution pump-probe X-ray crystallography reveals complex sub-ångström, ultrafast motions and hydrogen-bonding rearrangements in the active site of a fluorescent protein. However, we demonstrate that the measured motions are not part of the photoisomerization reaction but instead arise from impulsively driven coherent vibrational processes in the electronic ground state. A coherent-control experiment using a two-colour and two-pulse optical excitation strongly amplifies the X-ray crystallographic difference density, while it fully depletes the photoisomerization process. A coherent control mechanism was tested and confirmed the wave packets assignment.

Bacteriophytochrome Photoisomerization Proceeds Homogeneously Despite Heterogeneity in Ground State

Phytochromes are red/far-red photoreceptors that are widely distributed in plants and prokaryotes. Ultrafast photoisomerization of a double bond in a biliverdin cofactor or other linear tetrapyrrole drives their photoactivity, but their photodynamics are only partially understood. Multiexponential dynamics were observed in previous ultrafast spectroscopic studies and were attributed to heterogeneous populations of the pigment-protein complex. In this work, two-dimensional photon echo spectroscopy was applied to study dynamics of the bacteriophytochromes RpBphP2 and PaBphP. Two-dimensional photon echo spectroscopy can simultaneously resolve inhomogeneity in ensembles and fast dynamics by correlating pump wavelength with the emitted signal wavelength. The distribution of absorption and emission energies within the same state indicates an ensemble of heterogeneous protein environments that are spectroscopically distinct. However, the lifetimes of the dynamics are uniform across the ensemble, suggesting a homogeneous model involving sequential intermediates for the initial photodynamics of isomerization.

Heterogeneous photodynamics of the pfr state in the cyanobacterial phytochrome Cph1

Femtosecond photodynamics of the P_fr form of the red/far-red phytochrome N-terminal PAS-GAF-PHY photosensory core module of the cyanobacterial phytochrome Cph1 (termed Cph1Δ) from Synechocystis were resolved with visible broadband transient absorption spectroscopy. Multiphasic generation dynamics via global target analysis revealed parallel evolution of two pathways with distinct excited- and ground-state kinetics. These measurements resolved two subpopulations: a majority subpopulation with fast excited-state decay and slower ground-state dynamics, corresponding to previous descriptions of P_fr dynamics, and a minority subpopulation with slower excited-state decay and faster ground-state primary dynamics. Both excited-state subpopulations generated the isomerized, red-shifted Lumi-F_f photoproduct (715 nm); subsequent ground-state evolution to a blue-shifted Meta-F_r population (635 nm) proceeded on 3 ps and 1.5 ns time scales for the two subpopulations. Meta-F_r was spectrally similar to a recently described photoinactive fluorescent subpopulation of P_r (^FluorP_r). Thus, the reverse P_fr to P_r photoconversion of Cph1Δ involves minor structural deformation of Meta-F_r to generate the fluorescent, photochemically refractory form of P_r, with slower subsequent equilibration with the photoactive P_r subpopulation (^PhotoP_r).

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.

Femtobiology

Functions of biologically active molecules are frequently initiated by elementary chemical reactions such as energy and electron transfer, cis-trans isomerizations, and proton transfer. The nature of these reactions generally makes them very fast and efficient, occurring on picosecond and femtosecond timescales. Ultrafast spectroscopy has played an important role in the study of a number of biological processes and has provided unique information about several of nature's responses to light. Here I review the current understanding of light-energy collection and conversion in photosynthesis, the function of carotenoid molecules in photosynthesis, and the primary light-initiated reactions of the photoreceptors rhodopsin, bacteriorhodopsin, photoactive yellow protein, phytochrome, and a new type of blue-light receptor based on flavin chromophores.

Subpicosecond midinfrared spectroscopy of the Pfr reaction of phytochrome Agp1 from Agrobacterium tumefaciens

Phytochromes are light-sensing pigments found in plants and bacteria. For the first time, the P(fr) photoreaction of a phytochrome has been subject to ultrafast infrared vibrational spectroscopy. Three time constants of 0.3 ps, 1.3 ps, and 4.0 ps were derived from the kinetics of structurally specific marker bands of the biliverdin chromophore of Agp1-BV from Agrobacterium tumefaciens after excitation at 765 nm. VIS-pump-VIS-probe experiments yield time constants of 0.44 ps and 3.3 ps for the underlying electronic-state dynamics. A reaction scheme is proposed including two kinetic steps on the S(1) excited-state surface and the cooling of a vibrationally hot P(fr) ground state. It is concluded that the upper limit of the E-Z isomerization of the C(15) = C(16) methine bridge is given by the intermediate time constant of 1.3 ps. The reaction scheme is reminiscent of that of the corresponding P(r) reaction of Agp1-BV as published earlier.

Ultrafast dynamics of phytochrome from the cyanobacterium synechocystis, reconstituted with phycocyanobilin and phycoerythrobilin

Femtosecond time-resolved transient absorption spectroscopy was employed to characterize for the first time the primary photoisomerization dynamics of a bacterial phytochrome system in the two thermally stable states of the photocycle. The 85-kDa phytochrome Cph1 from the cyanobacterium Synechocystis PCC 6803 expressed in Escherichia coli was reconstituted with phycocyanobilin (Cph1-PCB) and phycoerythrobilin (Cph1-PEB). The red-light-absorbing form Pr of Cph1-PCB shows an approximately 150 fs relaxation in the S(1) state after photoexcitation at 650 nm. The subsequent Z-E isomerization between rings C and D of the linear tetrapyrrole-chromophore is best described by a distribution of rate constants with the first moment at (16 ps)(-1). Excitation at 615 nm leads to a slightly broadened distribution. The reverse E-Z isomerization, starting from the far-red-absorbing form Pfr, is characterized by two shorter time constants of 0.54 and 3.2 ps. In the case of Cph1-PEB, double-bond isomerization does not take place, and the excited-state lifetime extends into the nanosecond regime. Besides a stimulated emission rise time between 40 and 150 fs, no fast relaxation processes are observed. This suggests that the chromophore-protein interaction along rings A, B, and C does not contribute much to the picosecond dynamics observed in Cph1-PCB but rather the region around ring D near the isomerizing C(15) [double bond] C(16) double bond. The primary reaction dynamics of Cph1-PCB at ambient temperature is found to exhibit very similar features as those described for plant type A phytochrome, i.e., a relatively slow Pr, and a fast Pfr, photoreaction. This suggests that the initial reactions were established already before evolution of plant phytochromes began.

FTIR studies of phytochrome photoreactions reveal the C=O bands of the chromophore: consequences for its protonation states, conformation, and protein interaction

The molecular changes of phytochrome during red --> far-red and reverse photoreactions have been monitored by static infrared difference spectroscopy using the recombinant 65 kDa N-terminal fragment assembled with a chromophore chemically modified at ring D or with a chromophore isotopically labeled with (18)O at the carbonyl group of ring A. This allows the identification of the C=O stretching vibrations of rings D and A. We exclude the formation of an iminoether in Pfr. The positions of both these modes show that the chromophore always remains protonated. The upshift of the C=O stretch of ring D in the first photoproducts is explained by a twisted methine bridge connecting rings C and D. The changes in the vibrational pattern during the red --> far-red conversion show that the backreaction is not just the reversal of the forward reaction. The infrared difference spectra of the fragment deviate very little from those of the full-length protein. The differences which are related to the lack of the C-terminal half of the protein constituting the signaling domain are possibly important for the understanding of the signaling mechanism.

First steps in the phytochrome phototransformation: a comparative femtosecond study on the forward (Pr --> Pfr) and back reaction (Pfr --> Pr)

The primary light-induced events in the reversible Pr right harpoon over left harpoon Pfr phototransformation are investigated by femtosecond absorption spectroscopy using a pump-probe technique. After the selective electronic excitation of Pr and Pfr with pulses at 610 and 730 nm, respectively, the transient absorption spectra were measured as a function of the delay time and subjected to a global fit analysis. As a result of this analysis, the decay-associated spectra of the kinetic components involved in the formation of the first photoproducts in the forward and back reaction are obtained. These spectra provide a more detailed understanding of the primary stages in the light-induced transformations. In addition, the influence of the solvent viscosity on the initial reaction steps was studied. In each direction of reaction, a short-lifetime component is found to be strongly viscosity-dependent, indicating that the primary photochemistry encompasses intramolecular motions of the chromophore or its proximal amino acid side chains. H-D exchange has no significant effect on the kinetics of the initial photoprocesses. This suggests that the isomerization reaction in both directions is not accompanied by a rate-limiting proton transfer.

Probing the photoreaction mechanism of phytochrome through analysis of resonance Raman vibrational spectra of recombinant analogues

Resonance Raman spectra of native and recombinant analogues of oat phytochrome have been obtained and analyzed in conjunction with normal mode calculations. On the basis of frequency shifts observed upon methine bridge deuteration and vinyl and C(15)-methine bridge saturation of the chromophore, intense Raman lines at 805 and 814 cm(-)(1) in P(r) and P(fr), respectively, are assigned as C(15)-hydrogen out-of-plane (HOOP) wags, lines at 665 cm(-)(1) in P(r) and at 672 and 654 cm(-)(1) in P(fr) are assigned as coupled C=C and C-C torsions and in-plane ring twisting modes, and modes at approximately 1300 cm(-)(1) in P(r) are coupled N-H and C-H rocking modes. The empirical assignments and normal mode calculations support proposals that the chromophore structures in P(r) and P(fr) are C(15)-Z,syn and C(15)-E,anti, respectively. The intensities of the C(15)-hydrogen out-of-plane, C=C and C-C torsional, and in-plane ring modes in both P(r) and P(fr) suggest that the initial photochemistry involves simultaneous bond rotations at the C(15)-methine bridge coupled to C(15)-H wagging and D-ring rotation. The strong nonbonded interactions of the C- and D-ring methyl groups in the C(15)-E,anti P(fr) chromophore structure indicated by the intense 814 cm(-1) C(15) HOOP mode suggest that the excited state of P(fr) and its photoproduct states are strongly coupled.

Kinetics of chromium(V) formation and reduction in fronds of the duckweed Spirodela polyrhiza--a low frequency EPR study

The uptake of chromate by the duckweed Spirodela polyrhiza was investigated with atomic absorption spectroscopy and the reduction of Cr(VI) to Cr(V) was measured using low frequency EPR spectroscopy. The biphasic kinetics of the uptake was fitted to parameters of a proposed kinetic model. Another model was developed to simulate chromate reduction. The first step of chromate reduction was found to be much faster than the uptake of Cr(VI) from the free space. Most probably, this step occurs already in the cell wall or on the cell membrane surface. Further reduction of Cr(V) to Cr(III) was estimated to be slower. The disappearance of the Cr(V) signal, following transfer of the plants into a Cr-free solution, lasted several tens of hours; the kinetics was mono- or biexponential depending on the length of Cr loading. The rate constants for Cr reduction in living plants were determined for the first time.

Elementary processes of photoperception by phytochrome A for high-irradiance response of hypocotyl elongation in Arabidopsis

Elementary processes of photoperception by phytochrome A (PhyA) for the high-irradiance response (HIR) of hypocotyl elongation in Arabidopsis were examined using a newly designed irradiator with LED. The effect of continuous irradiation with far-red (FR) light could be replaced by intermittent irradiation with FR light pulses if given at intervals of 3 min or less for 24 h. In this response, the Bunsen-Roscoe law of reciprocity held in each FR light pulse. Therefore, we determined the action spectrum for the response by intermittent irradiation using phyB and phyAphyB double mutants. The resultant action spectrum correlated well with the absorption spectrum of PhyA in far-red-absorbing phytochrome (Pfr). Intermittent irradiation with 550 to 667 nm of light alone had no significant effect on the response. In contrast, intermittent irradiation with red light immediately after each FR light pulse completely reversed the effect of FR light in each cycle. The results indicate that neither red-absorbing phytochrome synthesized in darkness nor photoconverted Pfr are physiologically active, and that a short-lived signal is induced during photoconversion from Pfr to red-absorbing phytochrome. The mode of photoperception by PhyA for HIR is essentially different from that by PhyA for very-low-fluence responses and phytochrome B for low-fluence responses.