Filip Desmet

Highly sensitive setup for tunable wavelength hyper-Rayleigh scattering with parallel detection and calibration data for various solvents.

A very sensitive experimental setup for accurate wavelength-dependent hyper-Rayleigh scattering (HRS) measurements of the molecular first hyperpolarizability beta in the broad fundamental wavelength range of 600 to 1800 nm is presented. The setup makes use of a stable continuously tunable picosecond optical parametric amplifier with kilohertz repetition rate. To correct for multi-photon fluorescence, a small spectral range around the second harmonic wavelength is detected in parallel using a spectrograph coupled to an intensified charge-coupled device. Reliable calibration against the pure solvent is possible over the full accessible spectral range. An extensive set of wavelength-dependent HRS calibration data for a wide range of solvents is presented, and very accurate measurements of the beta dispersion of the well-known nonlinear optical chromophore Disperse Red 1 are demonstrated.

Hise11 and Hisf8 Provide Bis-Histidyl Heme Hexa-Coordination in the Globin Domain of Geobacter Sulfurreducens Globin-Coupled Sensor.

Among heme-based sensors, recent phylogenomic and sequence analyses have identified 34 globin coupled sensors (GCS), to which an aerotactic or gene-regulating function has been tentatively ascribed. Here, the structural and biochemical characterization of the globin domain of the GCS from Geobacter sulfurreducens (GsGCS(162)) is reported. A combination of X-ray crystallography (crystal structure at 1.5 A resolution), UV-vis and resonance Raman spectroscopy reveals the ferric GsGCS(162) as an example of bis-histidyl hexa-coordinated GCS. In contrast to the known hexa-coordinated globins, the distal heme-coordination in ferric GsGCS(162) is provided by a His residue unexpectedly located at the E11 topological site. Furthermore, UV-vis and resonance Raman spectroscopy indicated that ferrous deoxygenated GsGCS(162) is a penta-/hexa-coordinated mixture, and the heme hexa-to-penta-coordination transition does not represent a rate-limiting step for carbonylation kinetics. Lastly, electron paramagnetic resonance indicates that ferrous nitrosylated GsGCS(162) is a penta-coordinated species, where the proximal HisF8-Fe bond is severed.

Marked difference in the electronic structure of cyanide-ligated ferric protoglobins and myoglobin due to heme ruffling.

Electron paramagnetic resonance experiments reveal a significant difference between the principal g values (and hence ligand-field parameters) of the ferric cyanide-ligated form of different variants of the protoglobin of Methanosarcina acetivorans (MaPgb) and of horse heart myoglobin (hhMb). The largest principal g value of the ferric cyanide-ligated MaPgb variants is found to be significantly lower than for any of the other globins reported so far. This is at least partially caused by the strong heme distortions as proven by the determination of the hyperfine interaction of the heme nitrogens and mesoprotons. Furthermore, the experiments confirm recent theoretical predictions [Forti, F.; Boechi, L., Bikiel, D., Martí, M.A.; Nardini, M.; Bolognesi, M.; Viappiani, C.; Estrin, D.; Luque, F. J. J. Phys. Chem. B 2011, 115, 13771-13780] that Phe(G8)145 plays a crucial role in the ligand modulation in MaPgb. Finally, the influence of the N-terminal 20 amino-acid chain on the heme pocket in these protoglobins is also proven.

Axial ligation of the high-potential heme center in an Arabidopsis cytochrome b561

Arabidopsis has four putative, di‐heme cytochrome b561 proteins, including one localized in the tonoplast (TCytb). From a comparative electron paramagnetic resonance (EPR), UV–Vis absorption and resonance Raman study, on wild type, H83A/H156A‐TCytb and H83L/H156L‐TCytb double mutants, it follows that the H83 and H156 residues are binding one of the two hemes. These measurements show that the high‐potential heme site is situated at the cytoplasmic side of the membrane and allow the unambiguous differentiation between two models on the heme localization in cytochrome b561 proteins.

The heme pocket of the globin domain of the globin-coupled sensor of **Geobacter sulfurreducens**: an EPR study

The globin-coupled sensor (GCS) of Geobacter sulfurreducens is unique amongst GCSs in that its signalling domain is a transmembrane domain with yet unknown function. In the present work we use X-band continuous-wave and pulsed electron paramagnetic resonance (EPR) to investigate the ferric form of the globin domain of the G. sulfurreducens GCS (GsGCS(162)) at pH 8.5. This form shows a unique bis-histidine coordination of the heme with the F8His and E11His. In contrast with previous crystal structure data, where three conformers of the heme structure were identified, ferric GsGCS(162) assumes only one conformation in frozen solution. The EPR data of ferric GsGCS162 are compared in detail with those of other bis-histidine coordinated globins, including other GCS systems.

The power of using continuous-wave and pulsed electron paramagnetic resonance methods for the structure analysis of ferric forms and nitric oxide-ligated ferrous forms of globins.

For several decades now, electron paramagnetic resonance (EPR) has been a valuable spectroscopic tool for the characterization of globin proteins. In the early years, the majority of EPR studies were performed using standard continuous-wave EPR techniques at conventional microwave frequencies. In the last years, the field of EPR has known tremendous technological developments, including the introduction of advanced pulsed EPR and high-frequency EPR techniques. After a short overview of the basics of EPR and recent advances in the field, we will illustrate how these different EPR methods can provide information about the dynamics and geometric and electronic structures of heme proteins. Although the main focus of this chapter lies on the EPR analysis of nitric oxide-ligated ferrous heme proteins and ferric heme systems, we also briefly outline the possibility of site-directed spin labeling of heme proteins. The last section highlights the future potential and challenges in using this magnetic resonance technique in globin research.

Ligation tunes protein reactivity in an ancient haemoglobin : kinetic evidence for an allosteric mechanism in **Methanosarcina acetivorans** protoglobin

Protoglobin from Methanosarcina acetivorans (MaPgb) is a dimeric globin with peculiar structural properties such as a completely buried haem and two orthogonal tunnels connecting the distal cavity to the solvent. CO binding to and dissociation from MaPgb occur through a biphasic kinetics. We show that the heterogenous kinetics arises from binding to (and dissociation from) two tertiary conformations in ligation-dependent equilibrium. Ligation favours the species with high binding rate (and low dissociation rate). The equilibrium is shifted towards the species with low binding (and high dissociation) rates for the unliganded molecules. A quantitative model is proposed to describe the observed carbonylation kinetics.

Is the heme pocket region modulated by disulfide-bridge formation in fish and amphibian neuroglobins as in humans?

Neuroglobin, a globin characterized by a bis-histidine ligation of the heme iron, has been identified in mammalian and non-mammalian vertebrates, including fish, amphibians and reptiles. In human neuroglobin, the presence of an internal disulfide bond in the CD loop (CD7-D5) is found to modulate the ligand binding through a change in the heme pocket structure. Although the neuroglobin sequences mostly display conserved Cys at positions CD7, D5 and G18/19, a number of exceptions are known. In this study, neuroglobins from amphibian (Xenopus tropicalis) and fish (Chaenocephalus aceratus, Dissostichus mawsoni and Danio rerio) are investigated using electron paramagnetic resonance and optical absorption spectroscopy. All these neuroglobins differ from human neuroglobin in their Cys-positions. It is demonstrated that if disulfide bonds are formed in fish and amphibian neuroglobins, the reduction of these bonds does not result in alteration of the heme pocket in these globins. Furthermore, it is shown that mutagenesis of the Cys residues of X. tropicalis neuroglobin influences the protein structure. The amphibian neuroglobin is also found to be more resistant to H2O2-induced denaturation than the other neuroglobins under study, although all show an overall large stability in high concentrations of this oxidant. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins.

Structural Bases for the Regulation of CO Binding in the Archaeal Protoglobin from Methanosarcina acetivorans

Studies of CO ligand binding revealed that two protein states with different ligand affinities exist in the protoglobin from Methanosarcina acetivorans (in MaPgb*, residue Cys(E20)101 was mutated to Ser). The switch between the two states occurs upon the ligation of MaPgb*. In this work, site-directed mutagenesis was used to explore the role of selected amino acids in ligand sensing and stabilization and in affecting the equilibrium between the “more reactive” and “less reactive” conformational states of MaPgb*. A combination of experimental data obtained from electronic and resonance Raman absorption spectra, CO ligand-binding kinetics, and X-ray crystallography was employed. Three amino acids were assigned a critical role: Trp(60)B9, Tyr(61)B10, and Phe(93)E11. Trp(60)B9 and Tyr(61)B10 are involved in ligand stabilization in the distal heme pocket; the strength of their interaction was reflected by the spectra of the CO-ligated MaPgb* and by the CO dissociation rate constants. In contrast, Phe(93)E11 is a key player in sensing the heme-bound ligand and promotes the rotation of the Trp(60)B9 side chain, thus favoring ligand stabilization. Although the structural bases of the fast CO binding rate constant of MaPgb* are still unclear, Trp(60)B9, Tyr(61)B10, and Phe(93)E11 play a role in regulating heme/ligand affinity.

A Globin Domain in a Neuronal Transmembrane Receptor of Caenorhabditis elegans and Ascaris suum: Molecular Modeling and Functional Properties

Background: GLB-33 is a putative neuropeptide receptor in C. elegans with a globin domain. Results: Recombinant globin domain displays a ferric hydroxide-ligated form. When reduced, it can bind CO or O2 and reduce nitrite to NO. Conclusion: The globin domain may serve as an oxygen sensor or nitrite reductase. Significance: Oxygen-sensing mechanisms are relevant for neuropeptide receptor binding. We report the structural and biochemical characterization of GLB-33, a putative neuropeptide receptor that is exclusively expressed in the nervous system of the nematode Caenorhabditis elegans. This unique chimeric protein is composed of a 7-transmembrane domain (7TM), GLB-33 7TM, typical of a G-protein-coupled receptor, and of a globin domain (GD), GLB-33 GD. Comprehensive sequence similarity searches in the genome of the parasitic nematode, Ascaris suum, revealed a chimeric protein that is similar to a Phe-Met-Arg-Phe-amide neuropeptide receptor. The three-dimensional structures of the separate domains of both species and of the full-length proteins were modeled. The 7TM domains of both proteins appeared very similar, but the globin domain of the A. suum receptor surprisingly seemed to lack several helices, suggesting a novel truncated globin fold. The globin domain of C. elegans GLB-33, however, was very similar to a genuine myoglobin-type molecule. Spectroscopic analysis of the recombinant GLB-33 GD showed that the heme is pentacoordinate when ferrous and in the hydroxide-ligated form when ferric, even at neutral pH. Flash-photolysis experiments showed overall fast biphasic CO rebinding kinetics. In its ferrous deoxy form, GLB-33 GD is capable of reversibly binding O2 with a very high affinity and of reducing nitrite to nitric oxide faster than other globins. Collectively, these properties suggest that the globin domain of GLB-33 may serve as a highly sensitive oxygen sensor and/or as a nitrite reductase. Both properties are potentially able to modulate the neuropeptide sensitivity of the neuronal transmembrane receptor.