Functional dynamics of a single tryptophan residue in a BLUF protein revealed by fluorescence spectroscopy

Blue Light Using Flavin (BLUF) domains are increasingly being adopted for use in optogenetic constructs. Despite this, much remains to be resolved on the mechanism of their activation. The advent of unnatural amino acid mutagenesis opens up a new toolbox for the study of protein structural dynamics. The tryptophan analogue, 7-aza-Trp (7AW) was incorporated in the BLUF domain of the Activation of Photopigment and pucA (AppA) photoreceptor in order to investigate the functional dynamics of the crucial W104 residue during photoactivation of the protein. The 7-aza modification to Trp makes selective excitation possible using 310 nm excitation and 380 nm emission, separating the signals of interest from other Trp and Tyr residues. We used Förster energy transfer (FRET) between 7AW and the flavin to estimate the distance between Trp and flavin in both the light- and dark-adapted states in solution. Nanosecond fluorescence anisotropy decay and picosecond fluorescence lifetime measurements for the flavin revealed a rather dynamic picture for the tryptophan residue. In the dark-adapted state, the major population of W104 is pointing away from the flavin and can move freely, in contrast to previous results reported in the literature. Upon blue-light excitation, the dominant tryptophan population is reorganized, moves closer to the flavin occupying a rigidly bound state participating in the hydrogen-bond network around the flavin molecule

Fourier transform infrared investigation of non-heme Fe(III) and Fe(II) decomposition of artemisinin and of a simplified trioxane alcohol

Fourier transform infrared spectra are reported for the Fe(III)- and Fe(II)-mediated activation of the antimalarial agents artemisinin I and its simplified synthetic analogue, trioxane alcohol 2. By monitoring the frequencies of the newly established marker lines in the FTIR spectra, the products of the Fe(II) and Fe(III) reactions have been characterized. In both reactions, artemisinin is activated giving a product mixture of a ring-contracted tetrahydrofuran acetatal 3, C4-hydroxy deoxyartemisinin 4, and deoxyartemisinin 5. These data illustrate that the oxidation state of the iron places no restrictions on the endoperoxide reduction mechanism. The FTIR difference (light - dark) spectra indicate that the endoperoxide moiety of artemisinin is photolabile and that the resulted products have the same vibrational characteristics as those observed in the reactions with Fe(II) and Fe(III). The use of 18O-18O enriched endoperoxide in 2 has allowed us to identify two oxygen sensitive modes in the reactions with Fe(II). The reduction of the peroxide bond by Fe(II) in trioxane alcohol 2 follows both the C - C cleavage and 1,5-H shift pathways and produces a ring-contracted tetrahydrofuran acetal 6 which is converted to tetrahydrofuran aldehyde 7 and C4-hydroxy deoxytrioxane alcohol 8, respectively. The cleavage of the O - O bond in 1 and 2 by iron and the ability to correlate vibrational properties of the reaction products with structural properties of the isolated products suggest that infrared spectroscopy is an appropriate tool to study the mode of action of antimalarial endoperoxide

Ferryl–oxo heme intermediate in the antimalarial mode of action of artemisinin

Fourier transform infrared (FTIR) and resonance Raman (RR) spectroscopies have been employed to investigate the reductive cleavage of the O-O bond of the endoperoxide moiety of the antimalarial drug artemisinin and its analog trioxane alcohol by hemin dimer. We have recorded FTIR spectra in the ν(O-O) and ν(as)(Fe-O-Fe) regions of artemisinin and of the hemin dimer that show the cleavage of the endoperoxide and that of the hemin dimer, respectively. We observed similar results in the trioxane alcohol/hemin dimer reaction. The RR spectrum of the artemisinin/hemin dimer reaction displays a vibrational mode at 850 cm-1 that shifts to 818 cm-1 when the experiment is repeated with 18O-O18 endoperoxide enriched trioxane alcohol. The frequency of this vibration and the magnitude of the 18O-O18 isotopic shift led us to assign the 850 cm-1 mode to the Fe(IV) = O stretching vibration of a ferryl-xoxo heme intermediate that occurs in the artemisinin/hemin dimer and trioxane alcohol/hemin reactions. These results provide the first direct characterization of the antimalarial mode of action of artemisinin and its trioxane analog, and suggest that artemisinin appears to react with heme molecules that have been incorporated into hemozoin and subsequently the heme performs cytochrome P450-type chemistr

Ferryl–oxo heme intermediate in the antimalarial mode of action of artemisinin

Fourier transform infrared (FTIR) and resonance Raman (RR) spectroscopies have been employed to investigate the reductive cleavage of the O-O bond of the endoperoxide moiety of the antimalarial drug artemisinin and its analog trioxane alcohol by hemin dimer. We have recorded FTIR spectra in the ν(O-O) and ν(as)(Fe-O-Fe) regions of artemisinin and of the hemin dimer that show the cleavage of the endoperoxide and that of the hemin dimer, respectively. We observed similar results in the trioxane alcohol/hemin dimer reaction. The RR spectrum of the artemisinin/hemin dimer reaction displays a vibrational mode at 850 cm-1 that shifts to 818 cm-1 when the experiment is repeated with 18O-O18 endoperoxide enriched trioxane alcohol. The frequency of this vibration and the magnitude of the 18O-O18 isotopic shift led us to assign the 850 cm-1 mode to the Fe(IV) = O stretching vibration of a ferryl-xoxo heme intermediate that occurs in the artemisinin/hemin dimer and trioxane alcohol/hemin reactions. These results provide the first direct characterization of the antimalarial mode of action of artemisinin and its trioxane analog, and suggest that artemisinin appears to react with heme molecules that have been incorporated into hemozoin and subsequently the heme performs cytochrome P450-type chemistr

Substrate Electric Dipole Moment Exerts a Ph-Dependent Effect On Electron Transfer in Escherichia Coli Photolyase

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

Resonance Raman Spectroscopy of Compound II and Its Decay in Mycobacterium Tuberculosis Catalase-Peroxidase KatG and its Isoniazid Resistant Mutant S315T

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

Modification of the Active Site of Mycobacterium Tuberculosis KatG after Disruption of the Met-Tyr-Trp Cross-Linked Adduct

Mycobacterium tuberculosis catalase-peroxidase (Mtb KatG) is a bifunctional enzyme that possesses both catalase and peroxidase activities and is responsible for the activation of the antituberculosis drug isoniazid. Mtb KatG contains an unusual adduct in its distal heme-pocket that consists of the covalently linked Trp107, Tyr229, and Met255. The KatG(Y229F) mutant lacks this adduct and has decreased steady-state catalase activity and enhanced peroxidase activity. In order to test a potential structural role of the adduct that supports catalase activity, we have used resonance Raman spectroscopy to probe the local heme environment of KatG(Y229F). In comparison to wild-type KatG, resting KatG(Y229F) contains a significant amount of 6-coordinate, low-spin heme and a more planar heme. Resonance Raman spectroscopy of the ferrous-CO complex of KatG(Y229F) suggest a non-linear Fe-CO binding geometry that is less tilted than in wild-type KatG. These data provide evidence that the Met-Tyr-Trp adduct imparts structural stability to the active site of KatG that seems to be important for sustaining catalase activity

Monitoring Changes in the Redox State of Myoglobin in Cardiomyocytes by Raman Spectroscopy Enables the Protective Effect of NO Donors to Be Evaluated

Raman microspectroscopy has been used to monitor changes in the redox and ligand-coordination states of the heme complex in myoglobin during the pre-conditioning of ex vivo cardiomyocytes with pharmacological drugs that release nitric oxide (NO). These chemical agents are known to confer protection on heart tissue against ischemia-reperfusion injury. Subsequent changes in the redox and ligand-coordination states during experimental simulations of ischemia and reperfusion have also been monitored. We found that these measurements, in real time, could be used to evaluate the pre-conditioning treatment of cardiomyocytes, and predict the likelihood of cell survival following a potentially-lethal period of ischemia. Evaluation of the pre-conditioning treatment was done at the single-cell level. The binding of NO to myoglobin, giving a 6-coordinate ferrous-heme complex, was inferred from the measured Raman bands of a cardiomyocyte by comparison to pure solution of the protein in the presence of NO. A key change in the Raman spectrum was observed after perfusion of the NO-donor was completed, where if the pre-conditioning treatment was successful then the bands corresponding to the nitrosyl complex were replaced by bands corresponding to metmyoglobin, Mb[SUPERSCRIPT: III]. An observation of Mb[SUPERSCRIPT: III] bands in the Raman spectrum was made for all the cardiomyocytes that recovered contractile function, whilst the absence of Mb[SUPERSCRIPT: III] bands always indicated that the cardiomyocyte would be unable to recover contractile function, following the simulated conditions of ischemia and reperfusion in these experiments

Mycobacterium Tuberculosis KatG(S315T) Catalase-Peroxidase Retains All Active Site Properties for Proper Catalytic Function

Mycobacterium tuberculosis (Mtb) KatG is a catalase-peroxidase that is thought to activate the antituberculosis drug isoniazid (INH). The local environment of Mtb KatG and its most prevalent INH-resistant mutant, KatG(S315T), is investigated with the exogenous ligands CO and NO in the absence and presence of INH by using resonance Raman, FTIR, and transient absorption spectroscopy. The Fe-His stretching vibration is detected at 244 cm-1 in the ferrous forms of both the wild-type enzyme and KatG(S315T). The ferrous-CO complex of both enzymes exhibits v(CO), v(Fe-CO), and δ(Fe-C-O) vibrations at 1925, 525, and 586 cm-1, respectively, indicating a positive electrostatic environment for the CO complex, which is probably weakly hydrogen-bonded to a distal residue. The CO geometry is nonlinear as indicated by the unusually high intensity of the Fe-C-O bending vibration. The v(Fe III-NO) and δ(FeIII-N-O) vibrations are detected at 596 and 571 cm-1, respectively, in the ferric forms of wild-type and mutant enzyme and are indicative of a nonlinear binding geometry in support of the CO data. Although the presence of INH does not affect the vibrational frequencies of the CO- and NO-bound forms of either enzyme, it seems to perturb slightly their Raman intensities. Our results suggest a minimal, if any, perturbation of the distal heme pocket in the S315T mutant. Instead, the S315T mutation seems to induce small changes in the KatG conformation/dynamics of the ligand access channel as indicated by CO rebinding kinetics in flash photolysis experiments. The implications of these findings for the catalytic mechanism and mechanism of INH resistance in KatG(S315T) are discussed

Solid-State NMR and Resonance Raman Studies of Ultramarine Pigments

We report on a study of ultramarine pigments via Colorimetry, resonance Raman, and 27Al, 29Si solid-state NMR spectroscopy. NMR parameters are shown to correlate well with the intensities of Raman signals corresponding to the chromophores S 3 -. and S 2 -.. Further, a correlation is established between the colorimetric parameters L* (lightness) and C* (chromaticity) and the paramagnetic shift in NMR spectra for both 27Al and 29Si. The parameter h (hue) appeared not to vary over the range of paramagnetic host concentrations studied. Preliminary results on faded pigments in both acidic and basic media show that the concentration of diamagnetic guest molecules in the sodalite lattice rises, and some of the paramagnetic species are replaced