Primary reactions of bacteriophytochrome observed with ultrafast mid-infrared spectroscopy

Phytochromes are red-light photoreceptor proteins that regulate a variety of responses and cellular processes in plants, bacteria, and fungi. The phytochrome light activation mechanism involves isomerization around the C(15)═C(16) double bond of an open-chain tetrapyrrole chromophore, resulting in a flip of its D-ring. In an important recent development, bacteriophytochrome (Bph) has been engineered for use as a fluorescent marker in mammalian tissues. Bphs covalently bind a biliverdin (BV) chromophore, naturally abundant in mammalian cells. Here, we report an ultrafast time-resolved mid-infrared spectroscopic study on the Pr state of two highly related Bphs from Rps. palustris , RpBphP2 (P2) and RpBphP3 (P3) with distinct photoconversion and fluorescence properties. We observed that the BV excited state of P2 decays in 58 ps, while the BV excited state of P3 decays in 362 ps. By combining ultrafast mid-IR spectroscopy with FTIR spectroscopy on P2 and P3 wild type and mutant proteins, we demonstrate that the hydrogen bond strength at the ring D carbonyl of the BV chromophore is significantly stronger in P3 as compared to P2. This result is consistent with the X-ray structures of Bph, which indicate one hydrogen bond from a conserved histidine to the BV ring D carbonyl for classical bacteriophytochromes such as P2, and one or two additional hydrogen bonds from a serine and a lysine side chain to the BV ring D carbonyl for P3. We conclude that the hydrogen-bond strength at BV ring D is a key determinant of excited-state lifetime and fluorescence quantum yield. Excited-state decay is followed by the formation of a primary intermediate that does not decay on the nanosecond time scale of the experiment, which shows a narrow absorption band at ～1540 cm(-1). Possible origins of this product band are discussed. This work may aid in rational structure- and mechanism-based conversion of BPh into an efficient near-IR fluorescent marker.     

Sub-picosecond mid-infrared spectroscopy of phytochrome Agp1 from Agrobacterium tumefaciens.

The photoinduced primary reaction of the biliverdin binding phytochrome Agp1 (Agp1-BV) from Agrobacterium tumefaciens was investigated by sub-picosecond time-resolved Vis pump-IR probe spectroscopy. Three time constants of tau(1)=0.7+/-0.05 ps, tau(2)=3.3+/-0.2 ps and tau(3)=33.3+/-1.5 ps could be isolated from the dynamics of structurally specific marker bands of the BV chromophore. These results together with those of accompanying sub-picosecond Vis pump-Vis probe spectroscopy allow the extension of the reaction scheme for the primary process by a vibrationally excited electronic ground state. The isomerization at the C15=C16 bond occurs within the lifetime of the excited electronic state. A quantum yield of 0.094 for the primary reaction is determined, suggesting that the quantum yield of formation of the P(fr) far-red-absorbing form is already established in the primary photoreaction of the P(r) (red-absorbing) form.     

15N MAS NMR studies of cph1 phytochrome: Chromophore dynamics and intramolecular signal transduction

Solid-state nuclear magnetic resonance (NMR) is applied for the first time to the photoreceptor phytochrome. The two stable states, Pr and Pfr, of the 59-kDa N-terminal module of the cyanobacterial phytochrome Cph1 from Synechocystis sp. PCC 6803 containing a uniformly 15N-labeled phycocyanobilin cofactor are explored by 15N cross-polarization (CP) magic-angle spinning (MAS) NMR. As recently shown by 15N solution-state NMR using chemical shifts [Strauss, H. M.; Hughes, J.; Schmieder, P. Biochemistry 2005, 44, 8244], all four nitrogens are protonated in both states. CP/MAS NMR provides two additional independent lines of evidence for the protonation of the nitrogens. Apparent loss of mobility during photoactivation, indicated by the decrease of line width, demonstrates strong tension of the entire chromophore in the Pfr state, which is in clear contrast to a more relaxed Pr state. The outer rings (A and D) of the chromophore are significantly affected by the phototransformation, as indicated by both change of chemical shift and line width. On the other hand, on the inner rings (B and C) only minor changes of chemical shifts are detected, providing evidence for a conserved environment during phototransformation. In a mechanical model, the phototransformation is understood in terms of rotations between the A-B and C-D methine bridges, allowing for intramolecular signal transduction to the protein surface by a unit composed of the central rings B and C and its tightly linked protein surroundings during the highly energetic Pfr state.     

Effects of surface passivation on the exciton dynamics of CdSe nanocrystals as observed by ultrafast fluorescence upconversion spectroscopy

The exciton dynamics of CdSe nanocrystals are intimately linked to the surface morphology. Photo-oxidation of the selenium surfaces of the nanocrystal leads to an increase in radiative decay efficiency from both the band edge and deep trap emission states. The addition of the primary amine hexadecylamine curtails nonradiative excitonic decay attributed to the dangling surface selenium orbitals by passivation of those trap sites by the methylene protons on the amine, leading to enhanced band edge emission and the absence of deep trap emission. Furthermore, CdSeZnSe core/shell nanocrystals are not immune from contributions from surface states because of the alignment of the band structures of the core and shell materials.     

Analytical investigation of salivary calculi, by mid-infrared spectroscopy

Sialolithiasis is common in salivary glands, especially in the submandibular and parotid ducts. X-Ray diffractometry was the principal technique used for their analysis, sometimes associated with scanning electron microscopy. Hydroxyapatite was the most frequently described constituent, in association with whitlockite and other calcium phosphates as brushite or octocalcium phosphate. Proteic matter was detected, as mucoproteins, albumin, nucleoproteins or as degenerative bacterial matter. This study presents the identification of constituents by mid-infrared spectrometry of 74 sialoliths. Their successive layers are analyzed from their crust to the nucleus, using absorbance measurements. Spectra are compared with reference mixtures of two or more constituents. Approximately 99% of sialoliths are constituted of calcium phosphates, under carbonated forms. More than three-quarters contain proteins, in which mucins represent the majority and albumin is found in 10% of all the specimens. Only 7% calculi are an association of two constituents, 66% are made of three and 27% have four or more components. For the 74 studied sialoliths, no specimen contains hydroxyapatite; but they are composed of carbonate apatites with irregular microcrystallized forms, even if proteins are present. Some of them have a pure protein nucleus, surrounded by carbonate apatite layers; the other stones are made of internal layers of apatites and covered with a dense and varnished crust of proteins.     

Heteronuclear NMR investigation on the structure and dynamics of the chromophore binding pocket of the cyanobacterial phytochrome Cph1

Structural changes of the chromophore in phytochrome proteins associated with its photocycle are still not fully understood. We use heteronuclear NMR to investigate the conformation and dynamics of the chromophore in the binding pocket of the cyanobacterial phytochrome Cph1. On the basis of distance information obtained from three-dimensional nuclear Overhauser enhancement (3D-NOESY) spectra using the photochemically intact photosensory module of Cph1 we demonstrate that the chromophore is in the ZZZssa form in the P(r) (red absorbing form) state and the ZZEssa form in the P(fr) (far-red absorbing form) state of the protein. While ZZZssa for the P(r) state is in agreement with a recently determined X-ray structure, no comparable information for the P(fr) state of photochemically intact phytochrome has been available up to now. In addition, the chromophore in the binding pocket of Cph1 exhibits a notable mobility, which is distinctly different in the two photostates.     

Measurement of sugar content by multidimensional analysis and mid-infrared spectroscopy

The advent of more and more powerful micro-computers has allowed the introduction of multidimensional analysis in research laboratories. Complex mathematical treatments are now possible within a few seconds. Prediction equations that linked sucrose, fructose, glucose, total sugars and reducing sugars concentrations to the spectral data, were established by regression on the principal components. Very high correlation coefficient values between the first ten axes and the chemical values were obtained. The bias and standard deviation (S.D.) values obtained between reference and predicted values were good. From such aqueous biological samples containing a ternary mixture of sucrose, fructose and glucose it was possible to (i) identify the characteristic IR bands of these different sugars (and their combination: reducing sugars, total sugars)-using spectral pattern; and (ii) to specifically measure their concentrations with good accuracy.     

Structures and dynamics of self-assembled surface monolayers observed by ultrafast electron crystallography

In this communication, we report our first study of self-assembled adsorbates on metal surfaces. Specifically, we studied single-crystal clean surfaces of Au(111) with and without a monolayer of reaction involving the assembly of 2-mercaptoacetic acid from 2,2'-dithiodiacetic acid. We also studied monolayers of iron hemes. With ultrafast electron crystallography, we are able to observe and isolate structural dynamics of the substrate (gold) and adsorbate(s) following an ultrafast temperature jump.     

The pure rotational spectrum of cyclobutane-d1 observed by microwave Fourier transform spectroscopy

Pure rotational transitions of both equatorial and axial conformers of cyclobutane-d₁ in their vibronic ground state have been observed between 12 and 40 GHz with a pulsed microwave Fourier transform (MWFT) spectrometer. Twenty-four transitions of the equatorial as well as 29 transitions of the axial conformer with J⩽40 have been measured. Their assignment has been confirmed by microwave-microwave double-resonance experiments. Rotational constants and the quartic centrifugal distortion constants have been determined for both conformers from the measured frequencies. The r₀ structure has been deduced from these rotational constants.     

Solvent-dependent photoacidity state of pyranine monitored by transient mid-infrared spectroscopy.

We investigate with femtosecond mid-infrared spectroscopy the vibrational-mode characteristics of the electronic states involved in the excited-state dynamics of pyranine (HPTS) that ultimately lead to efficient proton (deuteron) transfer in H2O (D2O). We also study the methoxy derivative of pyranine (MPTS), which is similar in electronic structure but does not have the photoacidity property. We compare the observed vibrational band patterns of MPTS and HPTS after electronic excitation in the solvents: deuterated dimethylsulfoxide, deuterated methanol and H2O/D2O, from which we conclude that for MPTS and HPTS photoacids the first excited singlet state appears to have charge-transfer (CT) properties in water within our time resolution (150 fs), whereas in aprotic dimethylsulfoxide the photoacid appears to be in a non-polar electronic excited state, and in methanol (less polar and less acidic than water) the behaviour is intermediate between these two extremes. For the fingerprint vibrations we do not observe dynamics on a time scale of a few picoseconds, and with our results obtained on the O-H stretching vibration we argue that the dynamic behaviour observed in previous UV/Vis pump-probe studies is likely to be related to solvation dynamics.     

The dynamics of water-protein interaction studied by ultrafast optical Kerr-effect spectroscopy

Changes in the ultrafast dynamics and terahertz Raman spectrum accompanying a helix-to-coil transition of a homo-polypeptide have been observed for the first time. Formation of the alpha-helix is associated with a shift to lower frequency of a broad Raman band attributable to solvent-peptide intermolecular hydrogen bonding. This band facilitates direct spectroscopic observation of so-called hydration water near a peptide and yields the first quantitative estimate of the time scale of the ultrafast dynamics in the solvation shell, which range from 0.18 to 0.33 ps (185-100 cm(-1)) depending on the secondary structure of the peptide. Such fast motions of solvent molecules have been referred to as the "lubricant of life" and are thought to play key roles in determining structure and activity of proteins.     

Tracking of the nuclear wavepacket motion in cyanine photoisomerization by ultrafast pump-dump-probe spectroscopy

Understanding ultrafast reactions, which proceed on a time scale of nuclear motions, requires a quantitative characterization of the structural dynamics. To track such structural changes with time, we studied a nuclear wavepacket motion in photoisomerization of a prototype cyanine dye, 1,1'-diethyl-4,4'-cyanine, by ultrafast pump-dump-probe measurements in solution. The temporal evolution of wavepacket motion was examined by monitoring the efficiency of stimulated emission dumping, which was obtained from the recovery of a ground-state bleaching signal. The dump efficiency versus pump-dump delay exhibited a finite rise time, and it became longer (97 fs → 330 fs → 390 fs) as the dump pulse was tuned to longer wavelengths (690 nm → 950 nm → 1200 nm). This result demonstrates a continuous migration of the leading edge of the wavepacket on the excited-state potential from the Franck-Condon region toward the potential minimum. A slowly decaying feature of the dump efficiency indicated a considerable broadening of the wavepacket over a wide range of the potential, which results in the spread of a population distribution on the flat S(1) potential energy surface. The rapid migration as well as broadening of the wavepacket manifests a continuous nature of the structural dynamics and provides an intuitive visualization of this ultrafast reaction. We also discussed experimental strategies to evaluate reliable dump efficiencies separately from other ultrafast processes and showed a high capability and possibility of the pump-dump-probe method for spectroscopic investigation of unexplored potential regions such as conical intersections.     

Real-time monitoring of chemical transformations by ultrafast 2D NMR spectroscopy

An approach enabling the acquisition of 2D nuclear magnetic resonance (NMR) spectra within a single scan has been recently proposed. A promising application opened up by this "ultrafast" data acquisition format concerns the monitoring of chemical transformations as they happen, in real time. The present paper illustrates some of this potential with two examples: (i) following an H/D exchange process that occurs upon dissolving a protonated protein in D2O, and (ii) real-time in situ tracking of a transient Meisenheimer complex that forms upon rapidly mixing two organic reactants inside the NMR observation tube. The first of these measurements involved acquiring a train of 2D 1H-15N HSQC NMR spectra separated by ca. 4 s; following an initial dead time, this allowed us to monitor the kinetics of hydrogen exchange in ubiquitin at a site-resolved level. The second approach enabled us to observe, within ca. 2 s after the triggering of the reaction, a competition between thermodynamic and kinetic controls via changes in a series of 2D TOCSY patterns. The real-time dynamic experiments hereby introduced thus add to an increasing family of fast characterization techniques based on 2D NMR; their potential and limitations are briefly discussed.     

Continuous glucose monitoring by means of mid-infrared transmission laser spectroscopy in vitro

The continuous surveillance of glucose concentration reduces short-term risks and long-term complications for people with diabetes mellitus, a disorder of glucose metabolism. As a first step towards the continuous monitoring of glucose, reagent-free transmission spectroscopy in the mid-infrared region has been carried out in vitro using a quantum cascade laser and an optical silver halide fiber. A 30 μm gap in the fiber allowed for transmission spectroscopy of aqueous glucose solutions at a wavelength of 9.69 μm, which is specific to a molecular vibration of glucose. A noise-equivalent concentration as low as 4 mg/dL was achieved at an average power of 1.8 mW and an integration time of 50 s. This is among the most precise of glucose measurements using mid-infrared spectroscopy. Even with the very low average laser power of 0.07 mW the sensitivity of previous results (using a fiber optical evanescent field analysis) has been improved upon by almost one order of magnitude. Finally, the impact of potentially interfering substances such as other carbohydrates was analyzed.     

Folding structures of isolated peptides as revealed by gas-phase mid-infrared spectroscopy.

To understand the intrinsic properties of peptides, which are determined by factors such as intramolecular hydrogen bonding, van der Waals bonding and electrostatic interactions, the conformational landscape of isolated protein building blocks in the gas phase was investigated. Here, we present IR-UV double-resonance spectra of jet-cooled, uncapped peptides containing a tryptophan (Trp) UV chromophore in the 1000-2000 cm(-1) spectral range. In the series Trp, Trp-Gly and Trp-Gly-Gly (where Gly stands for glycine), the number of detected conformers was found to decrease from six (Snoek et al., PCCP, 2001, 3, 1819) to four and two, respectively, which indicates a trend to relaxation to a global minimum. Density functional theory calculations reveal that the O-H in-plane bending vibration, together with the N-H in-plane bend ing and the peptide C=O stretching vibrations, is a sensitive probe to hydrogen bonding and, thus, to the folding of the peptide backbone in these structures. This enables the identification of spectroscopic fingerprints for the various conformational structures. By comparing the experimentally observed IR spectra with the calculated spectra, a unique conformational assignment can be made in most cases. The IR-UV spectrum of a Trp-containing nonapeptide (Trp-Ala-Gly-Gly-Asp-Ala-Ser-Gly-Glu) was recorded as well and, although the IR spectrum is less well-resolved (and it probably results from different isomers), groups of amide I (peptide C=O stretching) and amide II (N-H in-plane bending) bands can still be recognised, in agreement with predictions at the AM1 level.     

Unravelling the ultrafast photodecomposition mechanism of dibenzoyl peroxide in solution by time-resolved IR spectroscopy

The ultrafast photo-fragmentation of dibenzoyl peroxide (DBPO) is studied using femtosecond UV excitation at 266 nm and mid-infrared broadband probe pulses to elucidate the dissociation mechanism. With the help of (13)C-labeled DBPO it was possible to unambiguously assign transient IR bands in the fingerprint region to the benzoyloxy radical. Our experiments show that the fragmentation is controlled by the S(1)-lifetime of DBPO and within 0.4 +/- 0.2 ps leads to a benzoyloxy/phenyl radical pair plus CO(2)via concerted bond breakage of the O-O and the phenyl-C(carbonyl) bond. 20% of the radical pairs geminately recombine to phenyl benzoate on a timescale of 70 ps.     

Pronounced non-Condon effects in the ultrafast infrared spectroscopy of water

In the context of vibrational spectroscopy in liquids, non-Condon effects refer to the dependence of the vibrational transition dipole moment of a particular molecule on the rotational and translational coordinates of all the molecules in the liquid. For strongly hydrogen-bonded systems, such as liquid water, non-Condon effects are large. That is, the bond dipole derivative of an OH stretch depends strongly on its hydrogen-bonding environment. Previous calculations of nonlinear vibrational spectroscopy in liquids have not included these non-Condon effects. We find that for water, inclusion of these effects is important for an accurate calculation of, for example, homodyned and heterodyned three-pulse echoes. Such echo experiments have been "inverted" to obtain the OH stretch frequency time-correlation function, but by necessity the Condon and other approximations are made in this inversion procedure. Our conclusion is that for water, primarily because of strong non-Condon effects, this inversion may not lead to the correct frequency time-correlation function. Nevertheless, one can still make comparison between theory and experiment by calculating the experimental echo observables themselves.     

Varietal discrimination of Australian wines by means of mid-infrared spectroscopy and multivariate analysis

This study outlines the use of mid-infrared (MIR) spectroscopy combined with principal component analysis (PCA) and linear discriminant analysis (LDA) for the varietal classification of commercial red and white table wines. Three red varieties (Cabernet Sauvignon, Shiraz and Merlot) and four white varieties (Chardonnay, Riesling, Sauvignon Blanc and Viognier) were sourced from different wine regions in Australia. Wine samples were scanned in transmission on a FOSS WineScan FT 120 from wave numbers 926 to 5012 cm⁻¹. All samples were sourced from the 2006 vintage and had not been blended with any other variety or wine from other regions. Spectral data were reduced to a small number of principal components (PCs) and LDA was then performed to successfully separate the wines into the different varieties. To test the robustness of the LDA models developed for the red wines, a set of red wines scanned in 2005 were used. Correct classification of over 95% was achieved for the validation set.