Photo-isomerization of the isolated photoactive yellow protein chromophore: what comes before the primary step?

Photoactive proteins typically rely on structural changes in a small chromophore to initiate a biological response. While these changes often involve isomerization as the "primary step", preceding this is an ultrafast relaxation of the molecular framework caused by the sudden change in electronic structure upon photoexcitation. Here, we capture this motion for an isolated model chromophore of the photoactive yellow protein using time-resolved photoelectron imaging. It occurs in <150 fs and is apparent from a spectral shift of ∼70 meV and a change in photoelectron anisotropy. Electronic structure calculations enable the quantitative assignment of the geometric and electronic structure changes to a planar intermediate from which the primary step can then proceed.

Design and Synthesis of Novel Peptides to Protect Ferulic Acid against Ultraviolet Radiation Based on Domain Site IIA of Bovine Serum Albumin.

Ferulic acid (FA) is known for its excellent antioxidant properties, which can provide many health benefits. One of its drawbacks is its instability under UVA light, which limits its potency. In this study, the new peptides LW2 (QNKRFYFRKNQ) and CW2 (a cyclic form of LW2) were designed based on bovine serum albumin site IIA conformation. A UVA irradiation experiment was performed to investigate the protective ability of these peptides towards FA against UVA damage. The percentages of FA remaining under UV irradiation due to the protection of CW2 and LW2 were 83% and 76%, respectively. The results showed the importance of the cationic residues and hydrophobic residues included in the peptide sequences. Moreover, the cyclic rigid structure showed greater protective ability as compared to its linear counterpart.

Innovative Bio-Based Organic UV-A and Blue Light Filters from Meldrum's Acid.

Faced with the ban of some organic UV filters such as octinoxate or avobenzone, especially in Hawaii, it became essential to offer new alternatives that are both renewable and safe for humans and the environment. In this context, a class of bio-based molecules displaying interesting UV filter properties and great (photo)stability has been developed from Meldrum's acid and bio-based and synthetic p-hydroxycinnamic acids, furans and pyrroles. Moreover, p-hydroxycinnamic acid-based Meldrum's derivatives possess valuable secondary activities sought by the cosmetic industry such as antioxidant and anti-tyrosinase properties. The evaluation of the properties of mixture of judiciously chosen Meldrum's acid derivatives highlighted the possibility to modulate secondary activity while maintaining excellent UV protection. Meldrum's acid derivatives are not only competitive when benchmarked against organic filters currently on the market (i.e., avobenzone), but they also do not exhibit any endocrine disruption activity.

Soft Microwave Pretreatment to Extract P-Hydroxycinnamic Acids from Grass Stalks.

The aim of this article is to provide an analysis of microwave effects on ferulic and coumaric acids (FA and CA, respectively) extraction from grass biomass (corn stalks and miscanthus). Microwave pretreatment using various solvents was first compared to conventional heating on corn stalks. Then, microwave operational conditions were extended in terms of incident power and treatment duration. Optimal conditions were chosen to increase p-hydroxycinnamic acids release. Finally, these optimal conditions determined on corn stalks were tested on miscanthus stalks to underlie the substrate incidence on p-hydroxycinnamic acids release yields. The optimal conditions-a treatment duration of 405 s under 1000 W-allowed extracting 1.38% FA and 1.97% CA in corn stalks and 0.58% FA and 3.89% CA in miscanthus stalks. The different bioaccessibility of these two molecules can explain the higher or lower yields between corn and miscanthus stalks.

Bactericidal action of ferulic acid with ultraviolet-A light irradiation.

The bactericidal activity of ferulic acid (FA) against various microorganisms was remarkably enhanced by ultraviolet-A (UV-A) irradiation (wavelength, 365 nm). However, the bactericidal mechanism in the photo-combination system has not been evaluated. In the present study, this combined treatment was characterized by investigating associated changes in cellular functions of Escherichia coli, including assessments of respiratory activity, lipid peroxidation, membrane permeability, and damage to DNA and the cell surface. FA adsorbed onto and was incorporated into bacterial membranes, and the affinity resulted in decreased respiratory activity and enhanced lipid peroxidation in the cytoplasmic membrane with low-fluence (1.0 J/cm2) UV-A irradiation. Flow cytometry analysis revealed that additional exposure (8 J/cm2) combined with FA (1 mg/mL) induced increased cell permeability, yielding a 4.8-log decrease in the viable cell count. Morphologically, the treated cells exhibited a bacterial membrane dysfunction, producing many vesicles on the cell surface. However, despite this effect on the cell surface, plasmid DNA transformed into FA-treated E. coli maintained supercoiled integrity with negligible DNA oxidation. Our data strongly suggested that FA functions inside and outside the bacterial membrane; UV-A exposure in the presence of FA then causes increased oxidative modification and subsequent disruption of the bacterial membrane, without causing detectable genotoxicity.

Dynamic metabolic changes in seeds and seedlings of Brassica napus (oilseed rape) suppressing UGT84A9 reveal plasticity and molecular regulation of the phenylpropanoid pathway.

In Brassica napus, suppression of the key biosynthetic enzyme UDP-glucose:sinapic acid glucosyltransferase (UGT84A9) inhibits the biosynthesis of sinapine (sinapoylcholine), the major phenolic component of seeds. Based on the accumulation kinetics of a total of 158 compounds (110 secondary and 48 primary metabolites), we investigated how suppression of the major sink pathway of sinapic acid impacts the metabolome of developing seeds and seedlings. In UGT84A9-suppressing (UGT84A9i) lines massive alterations became evident in late stages of seed development affecting the accumulation levels of 58 secondary and 7 primary metabolites. UGT84A9i seeds were characterized by decreased amounts of various hydroxycinnamic acid (HCA) esters, and increased formation of sinapic and syringic acid glycosides. This indicates glycosylation and ß-oxidation as metabolic detoxification strategies to bypass intracellular accumulation of sinapic acid. In addition, a net loss of sinapic acid upon UGT84A9 suppression may point to a feedback regulation of HCA biosynthesis. Surprisingly, suppression of UGT84A9 under control of the seed-specific NAPINC promoter was maintained in cotyledons during the first two weeks of seedling development and associated with a reduced and delayed transformation of sinapine into sinapoylmalate. The lack of sinapoylmalate did not interfere with plant fitness under UV-B stress. Increased UV-B radiation triggered the accumulation of quercetin conjugates whereas the sinapoylmalate level was not affected.

Improved discrimination between monocotyledonous and dicotyledonous plants for weed control based on the blue-green region of ultraviolet-induced fluorescence spectra.

Precision weeding by spot spraying in real time requires sensors to discriminate between weeds and crop without contact. Among the optical based solutions, the ultraviolet (UV) induced fluorescence of the plants appears as a promising alternative. In a first paper, the feasibility of discriminating between corn hybrids, monocotyledonous, and dicotyledonous weeds was demonstrated on the basis of the complete spectra. Some considerations about the different sources of fluorescence oriented the focus to the blue-green fluorescence (BGF) part, ignoring the chlorophyll fluorescence that is inherently more variable in time. This paper investigates the potential of performing weed/crop discrimination on the basis of several large spectral bands in the BGF area. A partial least squares discriminant analysis (PLS-DA) was performed on a set of 1908 spectra of corn and weed plants over 3 years and various growing conditions. The discrimination between monocotyledonous and dicotyledonous plants based on the blue-green fluorescence yielded robust models (classification error between 1.3 and 4.6% for between-year validation). On the basis of the analysis of the PLS-DA model, two large bands were chosen in the blue-green fluorescence zone (400-425 nm and 425-490 nm). A linear discriminant analysis based on the signal from these two bands also provided very robust inter-year results (classification error from 1.5% to 5.2%). The same selection process was applied to discriminate between monocotyledonous weeds and maize but yielded no robust models (up to 50% inter-year error). Further work will be required to solve this problem and provide a complete UV fluorescence based sensor for weed-maize discrimination.

Stress tensor analysis of the protein quake of photoactive yellow protein.

Immediately after photon absorption, the photoenergy is converted to local stress energy via the ultrafast photoisomerization reaction of the p-coumaric acid (pCA) chromophore in a small water-soluble blue light receptor, photoactive yellow protein (PYP), derived from the halophilic bacterium, Halorhodospira halophila. A series of conformational changes are then induced, which are intimately related with the relaxation process on the energy landscape of PYP. In order to understand the signaling function of PYP in atomic detail, the characterization of the physical mechanism of the protein quake of PYP is important, as is the atomic description of the series of conformational changes associated with the photocycle. Here, we report a theoretical/computational study for the analysis of the intramolecular stress tensor for the dark state and three intermediate states, pR, pB1 and pB2, of PYP. As a result, we found that the magnitude of the stress released during the change from the pR to the pB1 state is significantly large at the hydroxyl oxygen atom of Tyr42, suggesting that this atom is the focus of the protein quake of PYP. This is consistent with previous experimental observations.

Coumaric amide rotaxanes: effects of hydrogen bonding and mechanical interlocking on the photochemistry and photophysics.

Secondary amide derivatives of coumaric and ferulic acid are shown to undergo photoisomerization, forming a photostationary mixture of E- and Z-isomers. When the same chromophores are incorporated in rotaxanes, the extent of conversion to the Z-isomers is much smaller. Low temperature fluorescence experiments show that the energy barrier for non-radiative decay of the excited state is higher in the rotaxanes than in the corresponding threads, but the barriers are low in all cases.

Combined experimental-theoretical study of the lower excited singlet states of paravinyl phenol, an analog of the paracoumaric acid chromophore.

The low-lying excited singlet states of paravinyl phenol (pVP) are investigated experimentally and theoretically paying attention to their similarity to excited states of paracoumaric acid, the chromophore of the photoactive yellow protein (PYP). Resonance enhanced multiphoton ionization and laser induced fluorescence spectroscopic techniques are employed to obtain supersonically cooled, vibrationally resolved excitation and emission spectra related to the lowest (1)A'(V') excited state of pVP. Comprehensive analyses of the spectral structures are carried out by means of the equation-of-motion coupled cluster singles and doubles and time dependent density functional theory methods in combination with the linear vibronic coupling model and Franck-Condon calculations. The assignments of the spectral patterns are given, mostly in terms of excitations of totally symmetric modes. Weak activity of the non-totally-symmetric modes indicates low probability of photochemical processes in the Franck-Condon region of the (1)A'(V') state. The second (1)A'(V) and third (1)A" (Ryd) excited states of pVP are characterized with regard to their electronic structure, properties, and effects of geometry relaxations. The lengthening of the double bond relevant to the trans-cis isomerization of the PYP chromophore is found for the (1)A'(V) state. A possibility of photochemical processes and strong vibronic interactions in this state can be expected. The theoretical results for the (1)A"(Ryd) state predict that dissociation with respect to the O-H bond is possible.

Molecular dynamics simulation of laser desorption of a fragment of protein kinase A from two MALDI matrices.

We have carried out molecular dynamics simulations to study the desorption of a dephosphorylated fragment of protein kinase A from two matrices, sinapic acid (SA) and 2,5-dihydroxybenzoic acid (DHB), after laser excitation. We have examined the results as a function of the laser fluence and of the burial depth of the guest peptide in the matrices. In most cases, we found that the energy transferred from the matrix to the guest peptide was not sufficiently large to fragment the peptide. Exceptions occurred when the peptide was more buried. This finding suggested that protein analytes might be less likely to break into smaller fragments if they were placed closer to the surface of the matrix. We have also examined how likely the guest peptide could form small clusters with the matrix molecules and found that the results depended on the degree of burial of the peptide, on the laser fluence, and on which matrix was used. Generally, stable clusters were more likely to be formed for guest peptides that were more buried, at a lower laser fluence, and in the SA rather than the DHB matrix. In addition, we found that the DHB matrix was broken down more easily by the laser than the SA matrix.

Photo-Fenton-assisted ozonation of p-Coumaric acid in aqueous solution.

The degradation of p-Coumaric acid present in olive oil mill wastewater was investigated as a pretreatment stage to obtain more easily biodegradable molecules, with lower toxicity that facilitates subsequent anaerobic digestion. Thus, photo-Fenton-assisted ozonation has been studied and compared with ozonation at alkaline pH and conventional single ultraviolet (UV) and acid ozonation treatments. In the combined process, the overall kinetic rate constant was split into various components: direct oxidation by UV light, direct oxidation by ozone and oxidation by hydroxyl radicals. Molecular and/or radical ozone reaction was studied by conducting the reaction in the presence and absence of tert-butylalcohol at pHs 2, 7 and 9. Ozone oxidation rate increases with pH or by the addition of Fenton reagent and/or UV radiation due to generation of hydroxyl radicals, *OH. Hydrogen peroxide and ferrous ion play a double role during oxidation since at low concentrations they act as initiators of hydroxyl radicals but at high concentrations they act as radical scavengers. Finally, the additional levels of degradation by formation of hydroxyl radicals have been quantified in comparison to the conventional single processes and an equation is proposed for the reaction rate as a function of studied operating variables.

Molecular dynamics simulations of photoactive yellow protein (PYP) in three states of its photocycle: a comparison with X-ray and NMR data and analysis of the effects of Glu46 deprotonation and mutation.

Photoactive yellow protein (PYP) is a prototype of the PAS domain superfamily of signaling proteins. The signaling process is coupled to a three-state photocycle. After the photoinduced trans-cis isomerization of the chromophore, 4-hydroxycinnamic acid (pCA), an early intermediate (pR) is formed, which proceeds to a second intermediate state (pB) on a sub-millisecond time scale. The signaling process is thought to be connected to the conformational changes upon the formation of pB and its recovery to the ground state (pG), but the exact signaling mechanism is not known. Experimental studies of PYP by solution NMR and X-ray crystallography suggest a very flexible protein backbone in the ground as well as in the signaling state. The relaxation from the pR to the pB state is accompanied by the protonation of the chromophore's phenoxyl group. This was found to be of crucial importance for the relaxation process. With the goal of gaining a better understanding of these experimental observations on an atomistic level, we performed five MD simulations on the three different states of PYP: a 1 ns simulation of PYP in its ground state [pG(MD)], a 1 ns simulation of the pR state [pR(MD)], a 2 ns simulation of the pR state with the chromophore protonated (pRprot), a 2 ns simulation of the pR state with Glu46 exchanged by Gln (pRGln) and a 2 ns simulation of PYP in its signaling state [pB(MD)]. Comparison of the pG simulation results with X-ray and NMR data, and with the results obtained for the pB simulation, confirmed the experimental observations of a rather flexible protein backbone and conformational changes during the recovery of the pG from the pB state. The conformational changes in the region around the chromophore pocket in the pR state were found to be crucially dependent on the strength of the Glu46-pCA hydrogen bond, which restricts the mobility of the chromophore in its unprotonated form considerably. Both the mutation of Glu46 with Gln and the protonation of the chromophore weaken this hydrogen bond, leading to an increased mobility of pCA and large structural changes in its surroundings. These changes, however, differ considerably during the pRGln and pRprot simulations, providing an atomistic explanation for the enhancement of the rate constant in the Gln46 mutant.

Interactions of lipoic acid radical cations with vitamins C and E analogue and hydroxycinnamic acid derivatives.

As a powerful natural antioxidant, lipoic acid exerts significant antioxidant activities in vivo and in vitro by deactivation of reactive oxygen and nitrogen species. In this study we present a novel synergistic interaction of lipoic acid with other endogenous or exogenous antioxidants. Antioxidants vitamins C and E analogue (Trolox C) and hydroxycinnamic acid derivatives were found to recycle lipoic acid by donating electrons to lipoic acid radical cations, thereby increasing the antioxidant capacity of lipoic acid in vivo and in vitro. The rate constant of the electron transfer is in the order 10(9)dm(3)mol(-1)s(-1), close to the diffusion-controlled limit, and transfer quantum yield is above 95%.

UV-B absorbance and UV-B absorbing compounds (para-coumaric acid) in pollen and sporopollenin: the perspective to track historic UV-B levels.

UV-B absorbance and UV-B absorbing compounds (UACs) of the pollen of Vicia faba, Betula pendula, Helleborus foetidus and Pinus sylvestris were studied. Sequential extraction demonstrated considerable UV-B absorbance both in the soluble (acid methanol) and insoluble sporopollenin (acetolysis resistant residue) fractions of UACs, while the wall-bound fraction of UACs was small. The UV-B absorbance of the soluble and sporopollenin fraction of pollen of Vicia faba plants exposed to enhanced UV-B (10 kJ m(-2) day(-1) UV-B(BE)) was higher than that of plants that received 0 kJ m(-2) day(-1) UV-B(BB). Pyrolysis gas chromatography-mass spectrometry (py-GC-MS) analysis of pollen demonstrated that p-coumaric acid and ferulic acid formed part of the sporopollenin fraction of the pollen. The amount of these aromatic monomers in the sporopollenin of Vicia faba appeared to increase in response to enhanced UV-B (10 kJ m(-2) day(-1) UV-B(BE)). The detection limit of pyGC-MS was sufficiently low to quantify these phenolic acids in ten pollen grains of Betula and Pinus. The experimental data presented provide evidence for the possibility that polyphenolic compounds in pollen of plants are indicators of solar UV-B and may be applied as a new proxy for the reconstruction of historic variation in solar UV-B levels.

Electron transfer vs. proton transfer within radical-cation clusters of guanosine and deoxyguanosine with substituted naphthalenes and sinapinic acid.

Guanosine (G) and deoxyguanosine (dG) radical cations can be generated in the gas phase by single electron transfer (SET) within nucleoside-dimethoxynaphthalenes (1-2) electron-bound heterodimers produced by fast atom bombardment in a four sector mass spectrometer. The nucleobase guanine is much more easily oxidized when it is linked to a ribose moiety. The radical cation dimers formed by G and dG with sinapinic acid behave as proton-bound heterodimers. The experiments mimic to some extent the migration of radical sites within stacking bases which causes DNA damaging through depurination processes.

Effect of gamma-irradiation on phenolic compounds and phenylalanine ammonia-lyase activity during storage in relation to peel injury from peel of Citrus clementina hort. Ex. tanaka.

The influence of gamma-irradiation on the content of phenolic compounds was evaluated on Moroccan Citrus fruits (Citrus clementina Hort. ex. Tanaka) treated at a mean dose of 0.3 kGy and stored for 49 days at 3 degrees C. The results show that irradiation has enhanced the synthesis of total phenolic compounds and is correlated with phenylalanine ammonia-lyase activity (PAL) during storage. Accumulation of phenolic compounds in cells is demonstrated and may be explained by the enhancement of PAL activity. HPLC/UV (diode array detector) analysis demonstrated that hesperidin was the major flavanone and nobiletin and heptamethoxyflavone were the major polymethoxylated flavones. Hesperidin is also the major phenolic compound in clementines. Irradiation stimulates the biosynthesis of hesperidin after 14 days of storage, corresponding to the maximum of PAL activity. p-Coumaric acid was also identified, and its content was particularly high in irradiated fruits after 49 days of storage. Accumulation of flavonoids and p-coumaric acid could be related to a better resistance. The percentage of losses due to peel injury "pitting" during storage was between 1 and 5% after 49 days of storage. The connections between irradiation, enzyme activity, phenolic content, and peel injury are briefly discussed.

Evidence for trans-cis isomerization of the p-coumaric acid chromophore as the photochemical basis of the photocycle of photoactive yellow protein.

Analysis of the chromophore p-coumaric acid, extracted from the ground state and the long-lived blue-shifted photocycle intermediate of photoactive yellow protein, shows that the chromophore is reversibly converted from the trans to the cis configuration, while progressing through the photocycle. The detection of the trans and cis isomers was carried out by high performance capillary zone electrophoresis and further substantiated by 1H NMR spectroscopy. The data presented here establish the photo-isomerization of the vinyl double bond in the chromophore as the photochemical basis for the photocycle of photoactive yellow protein, a eubacterial photosensory protein. A similar isomerization process occurs in the structurally very different sensory rhodopsins, offering an explanation for the strong spectroscopic similarities between photoactive yellow protein and the sensory rhodopsins. This is the first demonstration of light-induced isomerization of a chromophore double bond as the photochemical basis for photosensing in the domain of Bacteria.