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Vibrio cholerae cryptochrome-1 (VcCRY-1) is a member of the cryptochrome DASH family. The flavoprotein appears to use blue light both for repair of cyclobutane pyrimidine dimers (CPDs) on DNA and signal transduction. Earlier, we found that it was almost impossible to oxidize the FADH· state upon binding to a CPD, and, in the absence of substrate, the rate of FADH· oxidation was much larger at high pH (Gindt et al. in Biochemistry 54:2802-2805, 2015). Here, we present the pH-dependence of the oxidation of FADH· by ferricyanide, which revealed a switch between slow and fast oxidation with a pKa ≈ 7.0. Stopped-flow mixing was used to measure the oxidation of FADH- to FADH· at pH 6.7 and 7.5. Substrate binding was required to slow down this oxidation such that it could be measured with stopped flow, but there was only a small effect of pH. In addition, resonance Raman measurements of FADH· in VcCRY-1 at pH 6.5 and 7.5 were performed to probe for structural changes near the FAD cofactor related to the observed changes in rate of FADH· oxidation. Only substrate binding seemed to induce a change near the FAD cofactor that may relate to the change in oxidation kinetics. The pH-effect on the FADH· oxidation rate, which is rate-limited by the proton acceptor, does not seem to be due to a protein structural change near the FAD cofactor. Instead, a conserved glutamate in CRY-DASH may control the deprotonation of FADH· and give rise to the pH-effect.

Resonance Raman spectroscopy is a powerful tool to investigate flavins and flavoproteins, and a good understanding of the flavin vibrational normal modes is essential for the interpretation of the Raman spectra. Isotopic labeling is the most effective tool for the assignment of vibrational normal modes, but such studies have been limited to labeling of rings II and III of the flavin isoalloxazine ring. In this paper, we report the resonance and pre-resonance Raman spectra of flavin mononucleotide (FMN) and its N5-methyl neutral radical semiquinone (5-CH 3FMN(*)), of which the 8-methyl group of ring I has been deuterated. The experiments indicate that the Raman bands in the low-frequency region are the most sensitive to 8-methyl deuteration. Density functional theory (DFT) calculations have been performed on lumiflavin to predict the isotope shifts, which are used to assign the calculated normal modes to the Raman bands of FMN. A first assignment of the low-frequency Raman bands on the basis of isotope shifts is proposed. Partial deuteration of the 8-methyl group reveals that the changes in the Raman spectra do not always occur gradually. These observations are reproduced by the DFT calculations, which provide detailed insight into the underlying modifications of the normal modes that are responsible for the changes in the Raman spectra. Two types of isotopic shift patterns are observed: either the frequency of the normal mode but not its composition changes or the composition of the normal mode changes, which then appears at a new frequency. The DFT calculations also reveal that the effect of H/D-exchange in the 8-methyl group on the composition of the vibrational normal modes is affected by the position of the exchanged hydrogen, i.e., whether it is in or out of the isoalloxazine plane.

We report key evidence on the framework destruction in ultramarine pigments upon color fading. Experiments on faded pigments in a fresco painting environment reveal that the paramagnetic chromophores are set free via sodalite framework destruction and are subsequently degraded. Fading in acidic media produces similar results, although a larger number of beta-cages appear to be destroyed, and H2S is released. The findings are further supported by studies on natural and synthetic ultramarine pigments of various shades via solid-state resonance-Raman spectroscopy, colorimentry, and solid-state 29Si and 27Al NMR spectroscopy. NMR parameters are shown to correlate well with the intensities of Raman signals corresponding to the S3(-*) chromophores. A further correlation is established between the colorimetric parameters, L* (lightness) and C* (chroma), and the paramagnetic shift and paramagnetic linebroadening in NMR spectra for both 27Al and 29Si.

Flavin radical semiquinones are intermediates in important physiological processes. Resonance Raman (RR) spectroscopy is an important tool to determine the interactions between these radical intermediates and their protein environment that regulate their reactivity and role in the reaction mechanisms. RR spectra of flavin radical semiquinones have been available for several flavoproteins, and those in the glucose oxidase (GO) seem significantly different from all the other available data. Since GO is often used not only as a standard for flavin-containing proteins but also in biotechnological applications, we decided to reexamine the RR spectra of the neutral and anionic radical semiquinone forms of the flavin adenine dinucleotide (FAD) cofactor in this enzyme. The new data show that the vibrational wavenumbers of the neutral and anionic radical semiquinone forms of FAD in GO are very similar to those in other flavoproteins. The discrepancies that were observed earlier seem related to contributions of the FAD in different redox and protonation states. We also obtained the first RR spectra of the oxidized FAD cofactor in GO. Analysis of the vibrations of the oxidized FAD and its anionic radical semiquinone in GO in H2O and D2O solutions indicates that the subtle differences between these spectra in GO and in other flavoproteins are related to the weak hydrogen-bonding environment of the FAD cofactor in GO. Copyright © 2006 John Wiley & Sons, Ltd.

Escherichia coli photolyase uses blue light to repair cyclobutane pyrimidine dimers which are formed upon irradiation of DNA with ultraviolet (UV) light. E. coli photolyase is a flavoenzyme which c...

We report the first low-frequency resonance Raman spectra of ferric endothelial nitric oxide synthase (eNOS) holoenzyme, including the frequency of the Fe-S vibration in the presence of the substrate L-arginine. This is the first direct measurement of the strength of the Fe-S bond in NOS. The Fe-S vibration is observed at 338 cm(-1) with excitation at 363.8 nm. The assignment of this band to the Fe-S stretching vibration was confirmed by the observation of isotopic shifts in eNOS reconstituted with 54Fe- and 57Fe-labeled hemin. Furthermore, the frequency of this vibration is close to those observed in cytochrome P450(cam) and chloroperoxidase (CPO). The frequency of this vibration is lower in eNOS than in P450(cam) and CPO, which can be explained by differences in hydrogen bonding to the proximal cysteine heme ligand. On addition of substrate to eNOS, we also observe several low-frequency vibrations, which are associated with the heme pyrrole groups. The enhancement of these vibrations suggests that substrate binding results in protein-mediated changes of the heme geometry, which may provide the protein with an additional tuning element for the redox potential of the heme iron. The implications of our findings for the function of eNOS will be discussed by comparison with P450(cam) and model compounds.

Proton-coupled electron-transfer (PCET) is a mechanism of great importance in protein electron transfer and enzyme catalysis, and the involvement of aromatic amino acids in this process is of much interest. The DNA repair enzyme photolyase provides a natural system that allows for the study of PCET using a neutral radical tryptophan (Trp(•)). In Escherichia coli photolyase, photoreduction of the flavin adenine dinucleotide (FAD) cofactor in its neutral radical semiquinone form (FADH(•)) results in the formation of FADH(-) and (306)Trp(•). Charge recombination between these two intermediates requires the uptake of a proton by (306)Trp(•). The rate constant of charge recombination has been measured as a function of temperature in the pH range from 5.5 to 10.0, and the data are analyzed with both classical Marcus and semi-classical Hopfield electron transfer theory. The reorganization energy associated with the charge recombination process shows a pH dependence ranging from 2.3 eV at pH ≤ 7 and 1.2 eV at pH(D) 10.0. These findings indicate that at least two mechanisms are involved in the charge recombination reaction. Global analysis of the data supports the hypothesis that PCET during charge recombination can follow two different mechanisms with an apparent switch around pH 6.5. At lower pH, concerted electron proton transfer (CEPT) is the favorable mechanism with a reorganization energy of 2.1-2.3 eV. At higher pH, a sequential mechanism becomes dominant with rate-limiting electron-transfer followed by proton uptake which has a reorganization energy of 1.0-1.3 eV. The observed 'inverse' deuterium isotope effect at pH < 8 can be explained by a solvent isotope effect that affects the free energy change of the reaction and masks the normal, mass-related kinetic isotope effect that is expected for a CEPT mechanism. To the best of our knowledge, this is the first time that a switch in PCET mechanism has been observed in a protein.

The secondary electron transfer from reduced bacteriopheophytin (BPhA) to the first acceptor quinone (QA) in variously modified reaction centers from Rhodobacter sphaeroides was studied by transient absorption spectroscopy and compared with native reaction centers. In intact reaction centers, neither substitution of the native QA, ubiquinone-10(UQ10), with menaquinone (MK), nor shortening of the isoprene tail of ubiquinone (UQ) down to 4 and that of MK down to 2 isoprene units changed the rate of electron transfer to QA. However, in Fe2+-depleted reaction centers the electron transfer rate decreased by a factor of 5 upon MK-reconstitution and by a factor of 20–50 upon non-native UQ-reconstitution. In the latter particles, the electron transfer rate decreased with decreasing tail length of UQ, suggesting that the displacement of UQ within the QA pocket as proposed in previous work (Liu B.-L., Van Kan P.J.M. and Hoff A.J. (1991) FEBS Lett. 289, 23–28), is tail-length-dependent.

Cyclobutane pyrimidine dimer (CPD) photolyases are structure specific DNA-repair enzymes that specialize in the repair of CPDs, the major photoproducts that are formed upon irradiation of DNA with ultraviolet light. The purified enzyme binds a flavin adenine dinucleotide (FAD), which is in the neutral radical semiquinone (FADH(*)) form. The CPDs are repaired by a light-driven, electron transfer from the anionic hydroquinone (FADH(-)) singlet excited state to the CPD, which is followed by reductive cleavage of the cyclobutane ring and subsequent monomerization of the pyrimidine bases. CPDs formed between two adjacent thymidine bases (T T) are repaired with greater efficiency than those formed between two adjacent cytidine bases (C C). In this paper, we investigate the changes in Escherichia coli photolyase that are induced upon binding to DNA containing C C lesions using resonance Raman, UV-vis absorption, and transient absorption spectroscopies, spectroelectrochemistry, and computational chemistry. The binding of photolyase to a C C lesion modifies the energy levels of FADH(*), the rate of charge recombination between FADH(-) and Trp(306)(*), and protein-FADH(*) interactions differently than binding to a T T lesion. However, the reduction potential of the FADH(-)/FADH(*) couple is modified in the same way with both substrates. Our calculations show that the permanent electric dipole moment of C C is stronger (12.1 D) and oriented differently than that of T T (8.7 D). The possible role of the electric dipole moment of the CPD in modifying the physicochemical properties of photolyase as well as in affecting CPD repair will be discussed.

Photolyases and cryptochromes are flavoproteins that belong to the class of blue-light photoreceptors. They usually bind two chromophores: flavin adenine dinucleotide (FAD), which forms the active site, and a light-harvesting pigment, which is a 5,10-methenyltetrahydrofolate polyglutamate (MTHF) in most cases. In Escherichia coli photolyase (EcPhr), the MTHF cofactor is present in substoichiometric amounts after purification, while in Vibrio cholerae cryptochrome-1 (VcCry1) the MTHF cofactor is bound more strongly and is present at stoichiometric levels after purification. In this paper, we have used resonance Raman spectroscopy to monitor the effect of loss of MTHF on the protein-FAD interactions in EcPhr and to probe the protein-MTHF interactions in both EcPhr and VcCry1. We find that removal of MTHF does not perturb protein-FAD interactions, suggesting that it may not affect the physicochemical properties of FAD in EcPhr. Our data demonstrate that the pteridine ring of MTHF in EcPhr has different interactions with the protein matrix than that of MTHF in VcCry1. Comparison to solution resonance Raman spectra of MTHF suggests that the carbonyl of its pteridine ring in EcPhr experiences stronger hydrogen bonding and a more polar environment than in VcCry1, but that hydrogen bonding to the pteridine ring amine hydrogens is stronger in VcCry-1. These differences in hydrogen bonding may account for the higher binding affinity of MTHF in VcCry1 compared to EcPhr.

The reaction of Mycobacterium tuberculosis KatG and the mutant KatG(S315T) with two different organic peroxides is studied using resonance Raman spectroscopy. For the first time, an intermediate is observed in a catalase-peroxidase with vibrations that are characteristic of Compound II. The observation of this intermediate is consistent with photoreduction of Compound I and is in agreement with the formation of Compound I during the catalytic cycle of KatG. The same intermediate is detected in KatG(S315T), a mutant associated with resistance to isoniazid (INH), but with a lower yield, indicating that the organic peroxides cannot react with the heme iron in KatG(S315T) as efficiently as in wild-type KatG. Our results are consistent with catalytic competence of the S315T mutant and support the model that the S315T mutation confers antibiotic resistance by modifying the interaction between the enzyme and the drug.

The structure of the excited state of low-spin ferric heme o has been studied using picosecond time-resolved resonance Raman spectroscopy. The excited state has a lifetime of 10–30 ps, and the heme skeletal vibrations are shifted to lower frequencies relative to those in the electronic ground state. Based on the relatively small frequency shifts, we conclude that the relatively long-lived heme o excited state is not a porphyrin ππ * state. We propose that the heme o excited state is a charge transfer state, in which the heme iron donates an electron to the porphyrin macrocycle.

Low-power picosecond resonance Raman spectroscopy was used to investigate the identity of the axial ligand of heme a3 and relaxation processes in the heme a3 pocket of cytochrome oxidase after CO photolysis. Our results show that the proximal histidine remains ligated to heme a3 after CO photolysis excluding the transient ligation of a photolabile, endogenous ligand. Furthermore, the relaxation of the heme a3 macrocycle modes occurs on the sub ps time scale, while relaxation of the heme pocket to its equilibrium conformation takes place on the μs time scale.

Several models have been proposed for the ligand dynamics in the heme a32+/Cu(B)1+ binuclear pocket in cytochrome oxidase following CO photodissociation. These range from straightforward heme pocket relaxation to a variety of ligand exchange processes that have been proposed to be of relevance to the proton pumping function of the enzyme. To provide discrimination between these models, we have used picosecond time-resolved, pump-probe resonance Raman spectroscopy to study the photolysis process in the enzyme isolated from beef heart and from Rhodobacter sphaeroides. The intermediate observed within 5 ps of photolysis with low-energy probe pulses (10-20 nJ/pulse) is the high-spin, five-coordinate heme a32+ to which a histidine is ligated, as indicated by the observation of the Fe-His vibration at 220 cm-1. Several control experiments demonstrate that the probe pulse energy is sufficiently low to avoid promoting any significant photochemistry during the spectral acquisition phase of the pump-probe experiment. From these observations, we conclude that histidine is ligated to high-spin heme a32+ on the picosecond time scale following photolysis. Since H376 is the proximal a32+ ligand in the CO complex, our results indicate that this proximal ligation survives photolysis and that the control of the access of exogenous ligands to the heme a3 site by means of a ligand exchange process can be ruled out. We observe similar picosecond transient resonance Raman spectra for the CO complex of Rb. sphaeroides cytochrome c oxidase. From these results and earlier time-resolved Raman and FTIR measurements, we propose a model for the relaxation dynamics of the heme as pocket that involves picosecond migration of CO to the Cu(B) center and relaxation of the a32+-proximal histidine bond on the microsecond time scale following CO photolysis

The resonance Raman spectrum of the tryptophan neutral radical in a protein, Escherichia coli photolyase, is reported for the first time. The data compare very well to a solution study and computational predictions, and tentative assignments are made for the observed vibrations. This important new result demonstrates the potential of time-resolved resonance Raman spectroscopy as a powerful tool to investigate these radicals in protein electron-transfer processes and in enzymatic reactions in real time.

Transient absorption spectroscopy is used to demonstrate that the electric dipole moment of the substrate cyclobutane thymine dimer affects the charge recombination reaction between fully reduced flavin adenine dinucleotide (FADH-) and the neutral radical tryptophan 306 (Trp306*) in Escherichia coli DNA photolyase. At pH 7.4, the charge recombination is slowed by a factor of 1.75 in the presence of substrate, but not at pH 5.4. Photolyase does bind substrate at pH 5.4, and it seems that this pH effect originates from the conversion of FADH- to FADH2 at lower pH. The free-energy changes calculated from the electric field parameters and from the change in electron transfer rate are in good agreement and support the idea that the substrate electric dipole is responsible for the observed change in electron transfer rate. It is expected that the substrate electric field will also modify the physiologically important from excited 1FADH- to the substrate in the DNA repair reaction.