Femtosecond kinetics of photoconversion of the higher plant photoreceptor phytochrome carrying native and modified chromophores

The photoprocesses of native (phyA of oat), and of C-terminally truncated recombinant phytochromes, assembled instead of the native phytochromobilin with phycocyanobilin (PCB-65 kDa-phy) and iso-phycocyanobilin (iso-PCB-65 kDa-phy) chromophores, have been studied by femtosecond transient absorption spectroscopy in both their red absorbing phytochrome (P_r) and far-red absorbing phytochrome (P_fr) forms. Native P_r phytochrome shows an excitation wavelength dependence of the kinetics with three main picosecond components. The formation kinetics of the first ground-state intermediate I₇₀₀, absorbing at ∼690 nm, is mainly described by 28 ps or 40 ps components in native and PCB phytochrome, respectively, whereas additional ∼15 and 50 ps components describe conformational dynamics and equilibria among different local minima on the excited-state hypersurface. No significant amount of I₇₀₀ formation can be observed on our timescale for iso-PCB phytochrome. We suggest that iso-PCB-65 kDa-phy either interacts with the protein differently leading to a more twisted and/or less protonated configuration, or undergoes P_r to P_fr isomerization primarily via a different configurational pathway, largely circumventing I₇₀₀ as an intermediate. The isomerization process is accompanied by strong coherent oscillations due to wavepacket motion on the excited-state surface for both phytochrome forms. The femto- to (sub-)nanosecond kinetics of the P_fr forms is again quite similar for the native and the PCB phytochromes. After an ultrafast excited-state relaxation within ∼150 fs, the chromophores return to the first ground-state intermediate in 400-800 fs followed by two additional ground-state intermediates which are formed with 2-3 ps and ∼400 ps lifetimes. We call the first ground-state intermediate in native phytochrome I_fr·750, due to its pronounced absorption at that wavelength. The other intermediates are termed I_fr·675 and pseudo-P_r. The absorption spectrum of the latter already closely resembles the absorption of the P_r chromophore. PCB-65 kDa-phy shows a very similar kinetics, although many of the detailed spectral features in the transients seen in native phy are blurred, presumably due to wider inhomogeneous distribution of the chromophore conformation. Iso-PCB-65 kDa-phy shows similar features to the PCB-65 kDa-phy, with some additional blue-shift of the transient spectra of ∼10 nm. The sub-200 fs component is, however, absent, and the picosecond lifetimes are somewhat longer than in 124 kDa phytochrome or in PCB-65 kDa-phy. We interpret the data within the framework of two- and three-dimensional potential energy surface diagrams for the photoisomerization processes and the ground-state intermediates involved in the two photoconversions.     

Formation and decay of P680 (PD1–PD2)PheoD1 radical ion pair in photosystem II core complexes

Under physiological conditions (278 K) femtosecond pump-probe laser spectroscopy with 20-fs time resolution was applied to study primary charge separation in spinach photosystem II (PSII) core complexes excited at 710 nm. It was shown that initial formation of anion radical band of pheophytin molecule (Pheo⁻) at 460 nm is observed with rise time of ~ 11 ps. The kinetics of the observed rise was ascribed to charge separation between Chl (chlorophyll a) dimer, primary electron donor in PSII (P680*) and Pheo located in D1 protein subunit (Pheo_D1) absorbing at 420 nm, 545 nm and 680 nm with formation of the ion-radical pair P680⁺Pheo_DI⁻. The subsequent electron transfer from Pheo_D1⁻ to primary plastoquinone electron acceptor (Q_A) was accompanied by relaxation of the 460-nm band and occurred within ~ 250 ps in good agreement with previous measurements in Photosystem II-enriched particles and bacterial reaction centers. The subtraction of the P680⁺ spectrum measured at 455 ps delay from the spectra at 23 ps or 44 ps delay reveals the spectrum of Pheo_DI⁻, which is very similar to that measured earlier by accumulation method. The spectrum of Pheo_DI⁻ formation includes a bleaching (or red shift) of the 670 nm band indicating that Chl-670 is close to Pheo_D1. According to previous measurements in the femtosecond–picosecond time range this Chl-670 was ascribed to Chl_D1 [Shelaev, Gostev, Vishnev, Shkuropatov, Ptushenko, Mamedov, Sarkisov, Nadtochenko, Semenov and Shuvalov, J. Photochemistry and Photobiology, B: Biology 104 (2011) 45–50]. Stimulated emission at 685 nm was found to have two decaying components with time constants of ~ 1 ps and ~ 14 ps. These components appear to reflect formation of P680⁺Chl_D1⁻ and P680⁺Pheo_D1⁻, respectively, as found earlier. This article is part of a Special Issue entitled: Photosynthesis Research for Sustainability: Keys to Produce Clean Energy.     

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 C₁₅–H HOOP modes that appear because of symmetry-reducing distortions about the C₁₄–C₁₅ and C₁₅=C₁₆ 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 S₁ surface has a D-ring rotational barrier caused by steric interactions with the protein.     

Balance between ultrafast parallel reactions in the green fluorescent protein has a structural origin

The fluorescence photocycle of the green fluorescent protein is functionally dependent on the specific structural protein environment. A direct relationship between equilibrium protein side-chain conformation of glutamate 222 and reactivity is established, particularly the rate of ultrafast proton transfer reactions in the fluorescence photocycle. We show that parallel transformations in the photocycle have a structural origin, and we report on the vibrational properties of responsive amino acids on an ultrafast timescale. Blue excitation of GFP drives two parallel, excited-state deuteron transfer reactions with 10 ps and 75 ps time constants to the buried carboxylic acid side chain of glutamate 222 via a hydrogen-bonding network. Assignment of 1456 cm⁻¹ and 1441 cm⁻¹ modes to ν_sym and assignment of 1564 cm⁻¹ and 1570 cm⁻¹ features to ν_asym of E222 in the 10 ps and 75 ps components, respectively, was possible from the analysis of the transient absorption data of an E222D mutant and was consistent with photoselection measurements. In contrast to the wild-type, measurements of E222D can be described with only one difference spectrum, with the ν_sym mode at 1435 cm⁻¹ and the ν_asym mode at 1567 cm⁻¹, also correlating a large Δν_asym-sym with slow excited-state proton transfer kinetics. Density Functional Theory calculations and published model compound and theoretical studies relate differences in Δν_asym-sym to the strength and number of hydrogen-bonding interactions that are detected via equilibrium geometry and COO⁻ stretching frequency differences of the carboxylate. The correlation of photocycle kinetics with side-chain conformation of the acceptor suggests that proton transfer from S205 to E222 controls the rate of the overall excited-state proton transfer process, which is consistent with recent theoretical predictions. Photoselection measurements show agreement for localized CO vibrations of chromophore, Q69, and E222 with Density Functional Theory and ab initio calculations placed in the x-ray geometry and provide their vibrational response in the intermediates in the photocycle.     

Femtosecond pump-supercontinuum probe and transient lens spectroscopy of adonixanthin

The ultrafast internal conversion (IC) dynamics of adonixanthin in organic solvents were studied by pump-supercontinuum probe (PSCP) and transient lens (TL) spectroscopy after photoexcitation to the S₂ state. Transient PSCP spectra in the range 344-768 nm provided the spectral evolution of the S₀ → S₂ ground state bleach and S₁ → S_n excited state absorption. Time constants were τ₂ = 115 and 111 fs for the S₂ → S₁ IC and τ₁ = 6.4 and 5.8 ps for the S₁ → S₀ IC in acetone and methanol, respectively. There was only an insignificant polarity dependence of τ₁, underlining the negligible importance of intramolecular charge transfer (ICT) in the lowest-lying excited state of C₄₀ carotenoids with carbonyl substitution on the β-ionone ring. A blueshift and a spectral narrowing of the S₁ → S_n ESA band, likely due to solvation dynamics, and formation of the adonixanthin radial cation at high pump energies via resonant two-photon ionization were found.     

Protein disulfide isomerase and glutathione are alternative substrates in the one Cys catalytic cycle of glutathione peroxidase 7

Background

Mammalian GPx7 is a monomeric glutathione peroxidase of the endoplasmic reticulum (ER), containing a Cys redox center (CysGPx). Although containing a peroxidatic Cys (C_P) it lacks the resolving Cys (C_R), that confers fast reactivity with thioredoxin (Trx) or related proteins to most other CysGPxs.

Methods

Reducing substrate specificity and mechanism were addressed by steady-state kinetic analysis of wild type or mutated mouse GPx7. The enzymes were heterologously expressed as a synuclein fusion to overcome limited expression. Phospholipid hydroperoxide was the oxidizing substrate. Enzyme–substrate and protein–protein interaction were analyzed by molecular docking and surface plasmon resonance analysis.

Results

Oxidation of the C_P is fast (k_+ 1 > 10³ M^− 1 s^− 1), however the rate of reduction by GSH is slow (k′_+ 2 = 12.6 M^− 1 s^− 1) even though molecular docking indicates a strong GSH–GPx7 interaction. Instead, the oxidized C_P can be reduced at a fast rate by human protein disulfide isomerase (HsPDI) (k_+ 1 > 10³ M^− 1 s^− 1), but not by Trx. By surface plasmon resonance analysis, a K_D = 5.2 μM was calculated for PDI–GPx7 complex. Participation of an alternative non-canonical C_R in the peroxidatic reaction was ruled out. Specific activity measurements in the presence of physiological reducing substrate concentration, suggest substrate competition in vivo.

Conclusions

GPx7 is an unusual CysGPx catalyzing the peroxidatic cycle by a one Cys mechanism in which GSH and PDI are alternative substrates.

General significance

In the ER, the emerging physiological role of GPx7 is oxidation of PDI, modulated by the amount of GSH.     

Identification of the first steps in charge separation in bacterial photosynthetic reaction centers of Rhodobacter sphaeroides by ultrafast mid-infrared spectroscopy: electron transfer and protein dynamics

Time-resolved visible pump/mid-infrared (mid-IR) probe spectroscopy in the region between 1600 and 1800 cm⁻¹ was used to investigate electron transfer, radical pair relaxation, and protein relaxation at room temperature in the Rhodobacter sphaeroides reaction center (RC). Wild-type RCs both with and without the quinone electron acceptor Q_A, were excited at 600 nm (nonselective excitation), 800 nm (direct excitation of the monomeric bacteriochlorophyll (BChl) cofactors), and 860 nm (direct excitation of the dimer of primary donor (P) BChls (P_L/P_M)). The region between 1600 and 1800 cm⁻¹ encompasses absorption changes associated with carbonyl (CO) stretch vibrational modes of the cofactors and protein. After photoexcitation of the RC the primary electron donor P excited singlet state (P*) decayed on a timescale of 3.7 ps to the state (where B_L is the accessory BChl electron acceptor). This is the first report of the mid-IR absorption spectrum of ; the difference spectrum indicates that the 9-keto CO stretch of B_L is located around 1670-1680 cm⁻¹. After subsequent electron transfer to the bacteriopheophytin H_L in ∼1 ps, the state was formed. A sequential analysis and simultaneous target analysis of the data showed a relaxation of the radical pair on the ∼20 ps timescale, accompanied by a change in the relative ratio of the and bands and by a minor change in the band amplitude at 1640 cm⁻¹ that may be tentatively ascribed to the response of an amide CO to the radical pair formation. We conclude that the drop in free energy associated with the relaxation of , is due to an increased localization of the electron hole on the P_L half of the dimer and a further consequence is a reduction in the electrical field causing the Stark shift of one or more amide CO oscillators.     

Photochemical and Nonphotochemical Reactions of Phytochrome in vivo

The nonphotochemical reactions of phytochrome in the coleoptiles of dark-grown corn seedlings were studied at 3 temperatures: 14°, 24°, and 34°. The data obtained show that the destruction of P_fr is the only measurable reaction occurring; reversion of P_fr to P_r was not found. The Q₁₀'s (2.7 and 3.5) and zero order kinetics found for the destruction reaction are consistent with the hypothesis that the reaction is enzyme-mediated.

In vivo action spectra for phytochrome transformation in the coleoptiles of darkgrown corn seedlings were obtained which agree qualitatively with those obtained by other workers for phytochrome-mediated physiological responses and in vitro action spectra. In vivo conversion of phytochrome by blue light, as determined from spectrophotometric measurements of phytochrome itself, is reported. Action peaks for P_r were found at 667 mμ and in the blue in the region of 400 mμ, with a broad shoulder from 590 mμ to 640 mμ. Action peaks for P_fr were found at 725 mμ and in the blue in the region of 400 mμ with a minor peak at 670 mμ, and a broad shoulder from 590 mμ to 640 mμ. The ratio of the quantum efficiencies of P_r at 667 mμ and P_fr at 725 mμ (Φ_r667/Φ_fr725) was estimated to be 1.0.

     

Excitation dynamics of two spectral forms of the core complexes from photosynthetic bacterium Thermochromatium tepidum

The intact core antenna-reaction center (LH1-RC) core complex of thermophilic photosynthetic bacterium Thermochromatium (Tch.) tepidum is peculiar in its long-wavelength LH1-Q_y absorption (915 nm). We have attempted comparative studies on the excitation dynamics of bacteriochlorophyll (BChl) and carotenoid (Car) between the intact core complex and the EDTA-treated one with the Q_y absorption at 889 nm. For both spectral forms, the overall Car-to-BChl excitation energy transfer efficiency is determined to be ∼20%, which is considerably lower than the reported values, e.g., ∼35%, for other photosynthetic purple bacteria containing the same kind of Car (spirilloxanthin). The RC trapping time constants are found to be 50∼60 ps (170∼200 ps) for RC in open (closed) state irrespective to the spectral forms and the wavelengths of Q_y excitation. Despite the low-energy LH1-Q_y absorption, the RC trapping time are comparable to those reported for other photosynthetic bacteria with normal LH1-Q_y absorption at 880 nm. Selective excitation to Car results in distinct differences in the Q_y-bleaching dynamics between the two different spectral forms. This, together with the Car band-shift signals in response to Q_y excitation, reveals the presence of two major groups of BChls in the LH1 of Tch. tepidum with a spectral heterogeneity of ∼240 cm⁻¹, as well as an alteration in BChl-Car geometry in the 889-nm preparation with respect to the native one.     

Highly efficient energy transfer from a carbonyl carotenoid to chlorophyll a in the main light harvesting complex of Chromera velia

We report on energy transfer pathways in the main light-harvesting complex of photosynthetic relative of apicomplexan parasites, Chromera velia. This complex, denoted CLH, belongs to the family of FCP proteins and contains chlorophyll (Chl) a, violaxanthin, and the so far unidentified carbonyl carotenoid related to isofucoxanthin. The overall carotenoid-to-Chl-a energy transfer exhibits efficiency over 90% which is the largest among the FCP-like proteins studied so far. Three spectroscopically different isofucoxanthin-like molecules were identified in CLH, each having slightly different energy transfer efficiency that increases from isofucoxanthin-like molecules absorbing in the blue part of the spectrum to those absorbing in the reddest part of spectrum. Part of the energy transfer from carotenoids proceeds via the ultrafast S₂ channel of both the violaxanthin and isofucoxanthin-like carotenoid, but major energy transfer pathway proceeds via the S₁/ICT state of the isofucoxanthin-like carotenoid. Two S₁/ICT-mediated channels characterized by time constants of ~ 0.5 and ~ 4 ps were found. For the isofucoxanthin-like carotenoid excited at 480 nm the slower channel dominates, while those excited at 540 nm employs predominantly the fast 0.5 ps channel. Comparing these data with the excited-state properties of the isofucoxanthin-like carotenoid in solution we conclude that, contrary to other members of the FCP family employing carbonyl carotenoids, CLH complex suppresses the charge transfer character of the S₁/ICT state of the isofucoxanthin-like carotenoid to achieve the high carotenoid-to-Chl-a energy transfer efficiency.     

Analysis of starch amylolysis using plots for first-order kinetics

Investigators often study product release from starches during prolonged incubations with α-amylase in vitro. The reaction time courses usually fit to a linear form of a first order rate equation, i.e., ln[(C_∞ − C_t)/C_∞] = −kt. This equation calls for an accurate estimate of C_∞, i.e., the concentration of product at the end of the reaction. Estimates of C_∞ from digestibility curves can be unreliable. The Guggenheim method does not require prior knowledge of C_∞ but seems not to have been applied to starch hydrolysis data. An alternative method is also available in which the logarithm of the slope (LOS) of a digestibility curve at various time points is plotted against time. This allows estimations of both k and C_∞ and can also reveal whether changes occur in digestion rate from rapid to slow as digestion proceeds. We describe the Guggenheim and LOS methods and provide examples of their application to starch digestibility data.     

Synthesis and characterization of silver(I) derivatives containing acylpyrazolonate and phosphino ligands: X-ray crystal structures of monomeric [Ag(Q)(PPh3)2] and of dimeric [{Ag(Q)(PiBu3)}2] (Q = 1-phenyl-3-methyl-4-tert-butylacetylpyrazolon-5-ato)

New silver(I) acylpyrazolonate derivatives [Ag(Q)], [Ag(Q)(PR₃)]₂ and [Ag(Q)(PR₃)₂] (HQ = 1-R¹-3-methyl-4-R²(CO)pyrazol-5-one, HQ^Bn = R¹ = C₆H₅, R² = CH₂C₆H₅; HQ^CHPh2 = R¹ = C₆H₅, R² = CH(C₆H₅)₂; HQ^nPe = R¹ = C₆H₅, R² = CH₂C(CH₃)₃; HQ^tBu = R¹ = C₆H₅, R² = C(CH₃)₃; HQ^fMe = R¹ = C₆H₄-p-CF₃, R² = CF₃; HQ^fEt = R¹ = C₆H₅, R² = CF₂CF₃; R = Ph or iBu) have been synthesized and characterized in the solid state and solution. The crystal structure of 1-(4-trifluoromethylphenyl)-3-methyl-5-pyrazolone, the precursor of proligand HQ^fMe and of derivatives [Ag(Q^nPe)(PPh₃)₂] and [Ag(Q^nPe)(PiBu₃)]₂ have been investigated. [Ag(Q^nPe)(PPh₃)₂] is a mononuclear compound with a silver atom in a tetrahedrally distorted AgO₂P₂ environment, whereas [Ag(Q^nPe)(PiBu₃)]₂ is a dinuclear compound with two O₂N-exotridentate bridging acylpyrazolonate ligands connecting both silver atoms, their coordination environment being completed by a phosphine ligand.     

Complex formation between protactinium(V) and sulfate ions at 10 and 60 °C

Protactinium complexation with sulfate ions was studied with the element at tracer scale (C_Pa ∼ 10⁻¹² M) by solvent extraction method. The involved aqueous system was Pa(V)/H₂O/HClO₄/Na₂SO₄/NaClO₄ at 10 and 60 °C. The extraction experiments were conducted using the chelating agent thenoyltrifluoroacetone (TTA) in toluene. For both values of temperature, a systematic study was performed in order to determine the formation constants (β₁, β₂ and β₃) of sulfate complexes of Pa(V) at different ionic strength. For each temperature, the extrapolation of these constants to zero ionic strength was performed using the Specific Interaction Theory, leading to values of 2.8 ± 0.5, 6.5 ± 0.5, 7.8 ± 0.5 at 10 °C and 4.3 ± 0.3, 8.4 ± 1.3, 9.6 ± 0.4 at 60 °C. Interaction coefficients involving the sulfate complexes of protactinium(V) were also derived.     

Effects of light regime and oxygen profile on transformation of oxolinic acid in pond sediment

This study investigated the effects of light (visible light - 5800 lux, 24 h) or dark regime and aerobic or anaerobic condition on the decay of added oxolinic acid (OA) at 5, 10 and 20 mg L⁻¹ in eel pond sediment. An asymptotic decaying exponential model C_t = C_min + C_o × exp (−k × t) was used to facilitate quantitative approach to OA transformation, where C_t is the concentration of OA after t days, C_min the estimated level-off concentration of OA residue, C_o the concentration of added OA and k the decaying coefficient. OA decayed faster under light (C_min = 4.6 mg L⁻¹) than under dark (C_min = 7.8 mg L⁻¹) and also decayed faster under aerobic (C_min = 4.0 mg L⁻¹) than under anaerobic condition (C_min = 8.5 mg L⁻¹). C_min increased with C_o. Sundrying and tilling eel pond bottom should be able to reduce OA residue significantly.     

Picosecond fluorescence of intact and dissolved PSI-LHCI crystals

Over the past several years, many crystal structures of photosynthetic pigment-protein complexes have been determined, and these have been used extensively to model spectroscopic results obtained on the same proteins in solution. However, the crystal structure is not necessarily identical to the structure of the protein in solution. Here, we studied picosecond fluorescence of photosystem I light-harvesting complex I (PSI-LHCI), a multisubunit pigment-protein complex that catalyzes the first steps of photosynthesis. The ultrafast fluorescence of PSI-LHCI crystals is identical to that of dissolved crystals, but differs considerably from most kinetics presented in the literature. In contrast to most studies, the data presented here can be modeled quantitatively with only two compartments: PSI core and LHCI. This yields the rate of charge separation from an equilibrated core (22.5 ± 2.5 ps) and rates of excitation energy transfer from LHCI to core (k_LC) and vice versa (k_CL). The ratio between these rates, R = k_CL/k_LC, appears to be wavelength-dependent and scales with the ratio of the absorption spectra of LHCI and core, indicating the validity of a detailed balance relation between both compartments. k_LC depends slightly but nonsystematically on detection wavelength, averaging (9.4 ± 4.9 ps)⁻¹. R ranges from 0.5 (<690 nm) to ∼1.3 above 720 nm.     

Immunochemical and spectroscopic evidence for protein conformational changes in phytochrome transformations

Phytochrome was examined by immunochemical and spectroscopic techniques to detect differences between the protein moieties of red- and far red-absorbing phytochrome (P_r and P_fr). No differences in the reaction of P_r and P_fr with phytochrome antibody were discernible on Ouchterlony double diffusion plates. However, the microcomplement fixation assay showed a greater degree of antibody reaction with P_fr than with P_r, indicating some difference in the surface characteristics of the two forms. Circular dichroism spectroscopy between 300 and 200 nanometers revealed differences between P_r and P_fr which may reflect differences in the protein conformation. The circular dichroism spectrum of P_r showed a negative band at 285 nanometers which was not present in the spectrum of P_fr, and the large negative circular dichroism band at 222 nanometers with P_fr, associated with the α-helical content, was shifted 2 nanometers to shorter wave length with P_r although there was no change of magnitude of this band. The absorbancy of P_r and P_fr is very nearly the same in the 280 nanometer spectral region, but sensitive difference spectra between P_r and P_fr did reveal spectra which were similar to solvent perturbation spectra obtained by others with different proteins. In total, the experiments indicate that there are conformational differences between the protein moieties of P_r and P_fr but that these differences are rather slight from a standpoint of gross structure.     

Coordination environment friendly silicon in copper(I) chloride π-complexes with tetravinylsilane and dimethyltetravinyldisiloxane

Two crystal complexes of copper(I) chloride with tetravinylsilane (TVS) dimethyltetravinyldisiloxane (DMTVDS) were prepared and examined by IR spectroscopy and X-ray diffraction: sp. gr. P2/a, Z = 4, a = 13.428(1) Å, b = 7.9584(7) Å, c = 14.694(1) Å for [Cu₄Cl₄(TVS)]; sp. gr. P2₁/c, a = 10.505(1) Å, b = 13.487(1) Å, c = 13.870(1) Å for [Cu₄Cl₄(DMTVDS)]. The influence of the vinylsilicon ligands on the efficiency of the Cu?CC interaction is discussed. Thus, the consideration of d_Si ← π∗_CC ← d_Cu conjugate system may help to understand how the silicon π-acceptor properties influence on the degree of trigonal distortion of the Cu(I) coordination tetrahedron as well as on the inorganic part organization. The present studies are aimed at the use of the structure controlled nanoparticles supported on vinyl modified silicon (or silicone) substrate.     

Synthesis, structure and properties of a new layered gadolinium benzenedicarboxylate with piperazine

A hydrothermal reaction of a mixture of Gd(NO₃)₃, 1,2-benzenedicarboxylic acid (1,2-BDC), piperazine, NaOH and water at 180 °C for three days under autogeneous pressure gave rise to a new compound of the formula [C₄N₂H₁₂][Gd₂(H₂O)₂(C₆H₄(COO)₂)₂] (I). The connectivity between GdO₈ distorted dodecahedra and 1,2-BDC units gives rise to a two-dimensional structure with large apertures. The fully protonated piperazine molecule occupies the middle of these apertures. The compound has favorable CH?π interactions between the benzene rings of adjacent layers and shows photoluminescence at room temperature. Crystal data: monoclinic, space group = P2₁/c (No. 14), a = 13.1671(3) Å, b = 13.7336(3) Å, c = 11.3100(1) Å, β = 115.411(1)°, v = 1847.34(6) Å³, Z = 4, R₁ = 0.0238 for 2658 reflections [I > 2σ(I)].     

A Polarity Probe for Monitoring Light-induced Structural Changes at the Entrance of the Chromophore Pocket in a Bacterial Phytochrome

Light-induced structural changes at the entrance of the chromophore pocket of Agp1 phytochrome were investigated by using a thiol-reactive fluorescein derivative that is covalently attached to the genuine chromophore binding site (Cys-20) and serves as a polarity probe. In the apoprotein, the absorption spectrum of bound fluorescein is red-shifted with respect to that of the free label suggesting that the probe enters the hydrophobic chromophore pocket. Assembly of this construct with the chromophores phycocyanobilin or biliverdin is associated with a blue-shift of the fluorescein absorption band indicating the displacement of the probe out of the pocket. The probe does not affect the photochromic and kinetic properties of the noncovalent bilin adducts. Upon photoconversion to P_fr, the probe spectrum undergoes again a bathochromic shift and a strong rise in CD indicating a more hydrophobic and asymmetric environment. We propose that the environmental changes of the probe reflect conformational changes at the entrance of the chromophore pocket and are indicative for rearrangements of the chromophore ring A. Flash photolysis measurements showed that the absorption changes of the probe are kinetically coupled to the formation of Meta-R_C and P_fr. In the biliverdin adduct, an additional component occurs that probably reflects a transition between two Meta-R_C substates. Analogous results to that of the noncovalent phycocyanobilin adduct were obtained with the mutant V249C in which probe and chromophore are covalently attached. The conformational changes of the chromophore are correlated to proton transfer to the protein surface.Phytochromes are red-light photoreceptors occurring in plants, bacteria, and fungi where they control important developmental processes (1–6). The discovery of microbial phytochromes from genome sequencing (7–9) provided new prospects for biochemical, spectroscopic and structural analyses of this light sensor family. Agp1 (AtBphP1)³ from the soil bacterium Agrobacterium tumefaciens is a typical member of the widespread family of proteobacterial phytochromes (10, 11) and is the subject of the present study.The domain arrangement of canonical phytochromes consists of an N-terminal photosensory domain, including PAS, GAF, and PHY domains and a C-terminal regulatory kinase domain (see, e.g. Ref. 3). Bacterial phytochromes lack the N-terminal extension, and the PAS module insertion of plant phytochromes (3). In most of the bacterial phytochromes, the C-terminal regulatory domain is a histidine kinase (4). These kinases form homodimers as functional units (12) where the subunits transphosphorylate each other (13). The cofactors are linear tetrapyrroles that are covalently attached via a thioether linkage (14) to the side chains of specific conserved cysteine residues. The native chromophore of plant phytochromes is phytochromobilin (PΦB) (14), some cyanobacterial phytochromes incorporate phycocyanobilin (PCB) (15, 16), and all other bacterial phytochromes bind biliverdin (BV) (10, 11). Whereas the chromophore binding site of the more reduced bilins PΦB and PCB is located in the GAF domain, the binding site of BV is close to the N terminus upstream of the PAS domain (4, 11). The two distinct binding sites apparently require a specific substituent at the C3 carbon of pyrrole ring A, either an ethylidene (PΦB and PCB) or a vinyl (BV) group, for covalent attachment of the bilin chromophore (4). The holophytochrome assembly that includes covalent attachment of the chromophore is an autocatalytic process implying an intrinsic bilin C-S lyase activity of the apophytochrome (17). Kinetic studies of the autoassembly in vitro showed that ligation of the chromophore is the ultimate step following incorporation in the binding pocket and internal protonation (18).Phytochromes display photochromicity involving two either thermally stable or long-lived states, P_r and P_fr (red and far-red absorbing forms), that can be reversibly converted by light of appropriate wavelengths. The P_r to P_fr photoconversion is initiated by a rapid Z/E isomerization of the C-D methine bridge of the bilin chromophore (19–22) leading within picoseconds to the formation of the Lumi-R intermediate (23, 24). The following thermal relaxations via Meta-R_A and Meta-R_C intermediates to P_fr proceed on the time scale of microseconds and milliseconds (25–28).Assembly of Agp1 with locked BV derivatives showed that the geometry of the C-D methine bridge is 15Z_anti in P_r and 15E_anti in P_fr (29) suggesting that this methine bridge remains in the anti conformation during photoconversion. The crystal structures of the chromophore binding domains of the bacteriophytochromes from Deinococcus radiodurans and Rhodopseudomonas palustris revealed that the BV chromophore adopts a 5Z_syn,10Z_syn,15Z_anti configuration/conformation in the P_r state (30–32). The 5Z_syn geometry of the A-B methine bridge in the P_r state was confirmed by assembly of Agp1 with the corresponding locked BV chromophore (33). Recently, heteronuclear NMR investigations and crystallographic studies on the complete photosensory domain of the cyanobacterial phytochrome Cph1 from Synechocystis showed that the PCB chromophore is also in the 5Z_syn,10Z_syn,15Z_anti geometry in P_r (34, 35).Because the locked 5Z_syn adduct of Agp1 did not show a P_fr-like photo-product, conformational changes of the A-B methine bridge in the thermal relaxation cascade have been predicted (33). Flash photolysis experiments with this adduct suggested that these changes occur in the Meta-R_A to Meta-R_C transition (36). The stereochemistry of the A-B methine bridge in the P_fr state and in the preceding intermediates could not be determined unambiguously yet. Recent studies with doubly locked chromophores suggest that the C5–C6 single bond undergoes a thermal rotation from syn to anti in the photoconversion of Agp1, whereas an additional Z/E isomerization around the C4C5 double bond (hula-twist mechanism) was postulated for Agp2 (37). However, the crystal structure of the photosensory domain of the bacteriophytochrome PaBphP in its P_fr-enriched dark-adapted state favors the 5Z_syn conformation of the BV chromophore (38). Structural changes of the A-B methine bridge were excluded for the PCB chromophore of Cph1 on the basis of heteronuclear NMR (34), whereas low temperature Fourier transform IR studies on plant phytochrome suggested an environmental change of the ring A carbonyl group and/or a twist of the A-B methine bridge (39).The mechanism by which the signal is transmitted from the bilin chromophore to the protein is still obscure. The recent three-dimensional structures of the complete photosensory domains of Cph1 (35) and PaBphP (38) reveal key interactions between GAF and PHY domains in the corresponding dark states reflecting P_r and P_fr, respectively. In view of the intrinsic differences between the two phytochromes, it is not trivial to differentiate which of the numerous structural differences arise from light-induced conformational changes and are thus potentially important for signal transmission. We note that many approaches to provide a clue on the mechanism of signal transmission from the bilin chromophore to its proximate environment imply that this process is exclusively coupled to the photo-isomerization localized at ring D and its environment and that the chromophore then remains a passive element in the thermal relaxation cascade. This point of view is supported by recent results from femtosecond stimulated Raman spectroscopy suggesting that the chromophore structures in Lumi-R and P_fr are very similar (24). On the other hand, size exclusion chromatography experiments demonstrated that the global conformational changes observed for the P_fr state of Agp1 WT are absent in constructs (locked 5Zs adduct and mutants D197A and H250A), where the formation of P_fr is inhibited but the primary photoreaction proceeds (33, 40). These results are difficult to explain in terms of an ultra-fast signal transmission from the chromophore to the surrounding residues in its pocket.Light-induced conformational changes at the surface of plant phytochrome were observed by using covalently attached labels that are sensitive to the polarity of the microenvironment (41, 42). Due to the accessibility of several binding sites (i.e. the sulfhydryl groups of cysteines) in these experiments, the labeling was unspecific preventing further assignment of the observed changes to particular regions of the protein. Time-resolved absorption measurements with a covalently attached fluorescein derivative showed that the changes occur in the Meta-R_C to P_fr transition (41). In the present work with Agp1 phytochrome, we take advantage of the highly reactive sulfhydryl group of Cys-20, the genuine binding site of the BV chromophore, to specifically attach a fluorescein derivative. We observed that this construct assembles with PCB and BV forming noncovalent photochromic adducts, spectrally and kinetically undisturbed by the fluorescein label. Upon photo-conversion, the absorption band of the label displays a bathochromic shift and increase in ellipticity suggesting that the label moves in a more hydrophobic and asymmetric environment in the P_fr state. The label thus serves as a polarity probe at the entrance of the binding pocket. We postulate that these polarity changes reflect conformational changes of the A-B methine of the bilin chromophore and/or the microenvironment of ring A at the entrance of the binding pocket. Time-resolved measurements reveal that the changes occur in the Meta-R_A to Meta-R_C and Meta-R_C to P_fr transitions. Analogous results were obtained with the V249C mutant of Agp1 in which both the fluorescein probe and the PCB chromophore are covalently attached.     

Crystal structure of a new cyclomaltoheptaose hydrate: β-cyclodextrin·7.5H2O

The crystallographic study of a partially hydrated form of cyclomaltoheptaose (β-cyclodextrin, βCD) is reported. C₄₂H₇₀O₃₅·7.5H₂O; space group P2₁ with unit cell constants a = 15.1667(5), b = 10.1850(3), c = 20.9694(7) Å, β = 110.993(2)°; final discrepancy index R = 0.0760 for the 6181 observed reflections and 784 refined parameters. One water molecule is included in the cavity and distributed over two partially occupied positions, the other 6.5 waters distributed over eight positions are located as space-filler between the macrocycles. The crystal structure belongs to the cage-type, like that observed in Form I (βCD·12H₂O; Lindner, K; Saenger, W. Carbohydr. Res. 1982, 99, 103-115) and Form II (βCD·11H₂O; Betzel, C., et al. J. Am. Chem. Soc., 1984, 106, 7545-7567).