Heme Spin Distribution in the Substrate-Free and Inhibited Novel CYP116B5hd: A Multifrequency Hyperfine Sublevel Correlation (HYSCORE) Study.

The cytochrome P450 family consists of ubiquitous monooxygenases with the potential to perform a wide variety of catalytic applications. Among the members of this family, CYP116B5hd shows a very prominent resistance to peracid damage, a property that makes it a promising tool for fine chemical synthesis using the peroxide shunt. In this meticulous study, we use hyperfine spectroscopy with a multifrequency approach (X- and Q-band) to characterize in detail the electronic structure of the heme iron of CYP116B5hd in the resting state, which provides structural details about its active site. The hyperfine dipole-dipole interaction between the electron and proton nuclear spins allows for the locating of two different protons from the coordinated water and a beta proton from the cysteine axial ligand of heme iron with respect to the magnetic axes centered on the iron. Additionally, since new anti-cancer therapies target the inhibition of P450s, here we use the CYP116B5hd system-imidazole as a model for studying cytochrome P450 inhibition by an azo compound. The effects of the inhibition of protein by imidazole in the active-site geometry and electron spin distribution are presented. The binding of imidazole to CYP116B5hd results in an imidazole-nitrogen axial coordination and a low-spin heme FeIII. HYSCORE experiments were used to detect the hyperfine interactions. The combined interpretation of the gyromagnetic tensor and the hyperfine and quadrupole tensors of magnetic nuclei coupled to the iron electron spin allowed us to obtain a precise picture of the active-site geometry, including the orientation of the semi-occupied orbitals and magnetic axes, which coincide with the porphyrin N-Fe-N axes. The electronic structure of the iron does not seem to be affected by imidazole binding. Two different possible coordination geometries of the axial imidazole were observed. The angles between gx (coinciding with one of the N-Fe-N axes) and the projection of the imidazole plane on the heme were determined to be -60° and -25° for each of the two possibilities via measurement of the hyperfine structure of the axially coordinated 14N.

Enhanced Dihydrogen Activation by Mononuclear Iridium(II) Compounds: A Mechanistic Study.

The organometallic chemistry of 4d and 5d transition metals has been vastly dominated by closed-shell states. The reactivity of their metalloradical species is though remarkable, albeit yet poorly understood and with limited mechanistic investigations available. In this work we report the synthesis and characterization of two mononuclear IrII species, including the first dinitrogen adduct. These compounds activate dihydrogen at a dissimilar rate, in the latter case several orders of magnitude faster than its IrI precursor. A combined experimental/computational investigation to ascertain the mechanism of this transformation in IrII compounds is reported.

CYP116B5hd, a self-sufficient P450 cytochrome: A dataset of its electronic and geometrical properties.

This paper documents the dataset obtained from the Electron Paramagnetic Resonance (EPR) study of the electronic properties of a self-sufficient cytochrome P450, CYP116B5hd, which possesses an interesting catalytic activity for synthetic purposes. In fact, when isolated, its heme domain can act as a peroxygenase on different substrates of biotechnological interest. Raw data shown in Famulari et al. (2022) and supplementary data in raw and processed forms (figures) are documented and available in this paper. Additionally, simulations of the experimental data together with simulation scripts based for EasySpin, a widespread MATLAB toolbox for EPR spectral simulations, are provided. The procedure for g-value analysis based on a crystal-field theory is also detailed here, offering an interesting tool for comparison of FeIII-heme P450 systems. Due to the catalytic interest of the protein, which has been recently discovered, and the correlation that has been reported between g-values and peroxidase function, both, CW-EPR and HYSCORE spectra and data set of the model CYPBM3hd are also provided. Finally, the materials and methods for enzyme production and purification, sample preparation and experimental and spectroscopic procedures a together with instrumental details are described in detail. The data files and simulation scripts can be found in: https://doi.org/10.5281/zenodo.6418626.

EPR characterization of the heme domain of a self-sufficient cytochrome P450 (CYP116B5).

CYP116B5 is a self-sufficient cytochrome P450 (CYP450) with interesting catalytic properties for synthetic purposes. When isolated, its heme domain can act as a peroxygenase on different substrates of biotechnological interest. Here, by means of continuous wave and advanced EPR techniques, the coordination environment of iron in the isolated CYP116B5 heme domain (CYP116b5hd) is characterized. The ligand-free protein shows the characteristic EPR spectrum of a low-spin (S = 1/2) FeIII-heme with [gz = 2.440 ± 0.005, gy = 2.25 ± 0.01, gx = 1.92 ± 0.01]. These g-values reflect an electronic ground state very similar to classical P450 monooxygenases rather than P450 peroxygenases. Binding of imidazole results in g-values very close to the ones reported for CYP152 peroxygenases. The detection of hyperfine interactions through HYperfine Sub-level CORrElation (HYSCORE) Spectroscopy experiments, shows that this is due to a nitrogen-mediated axial coordination. This work adds a piece of experimental evidence to the research, aimed at elucidating the features that distinguish the classical P450 enzymes from peroxygenases. It shows that the electronic environment of heme iron of CYP116B5 in the resting state is similar to the classical P450 monooxygenases. Therefore, it is not the critical factor that confers to CYP116B5hd its peroxygenase-like activity, suggesting a crucial role of the protein matrix.

Impact of the dynamics of the catalytic arginine on nitrite and chlorite binding by dimeric chlorite dismutase.

Chlorite dismutases (Clds) are heme b containing oxidoreductases able to decompose chlorite to chloride and molecular oxygen. This work analyses the impact of the distal, flexible and catalytic arginine on the binding of anionic angulate ligands like nitrite and the substrate chlorite. Dimeric Cld from Cyanothece sp. PCC7425 was used as a model enzyme. We have investigated wild-type CCld having the distal catalytic R127 hydrogen-bonded to glutamine Q74 and variants with R127 (i) being arrested in a salt-bridge with a glutamate (Q74E), (ii) being fully flexible (Q74V) or (iii) substituted by either alanine (R127A) or lysine (R127K). We present the electronic and spectral signatures of the high-spin ferric proteins and the corresponding low-spin nitrite complexes elucidated by UV-visible, circular dichroism and electron paramagnetic resonance spectroscopies. Furthermore, we demonstrate the impact of the dynamics of R127 on the thermal stability of the respective nitrite adducts and present the X-ray crystal structures of the nitrite complexes of wild-type CCld and the variants Q74V, Q74E and R127A. In addition, the molecular dynamics (MD) and the binding modi of nitrite and chlorite to the ferric wild-type enzyme and the mutant proteins and the interaction of the oxoanions with R127 have been analysed by MD simulations. The findings are discussed with respect to the role(s) of R127 in ligand and chlorite binding and substrate degradation.

Exploiting genetic diversity and gene synthesis to identify superior nitrogenase NifH protein variants to engineer N2-fixation in plants.

Engineering nitrogen fixation in eukaryotes requires high expression of functional nitrogenase structural proteins, a goal that has not yet been achieved. Here we build a knowledge-based library containing 32 nitrogenase nifH sequences from prokaryotes of diverse ecological niches and metabolic features and combine with rapid screening in tobacco to identify superior NifH variants for plant mitochondria expression. Three NifH variants outperform in tobacco mitochondria and are further tested in yeast. Hydrogenobacter thermophilus (Aquificae) NifH is isolated in large quantities from yeast mitochondria and fulfills NifH protein requirements for efficient N2 fixation, including electron transfer for substrate reduction, P-cluster maturation, and FeMo-co biosynthesis. H. thermophilus NifH expressed in tobacco leaves shows lower nitrogenase activity than that from yeast. However, transfer of [Fe4S4] clusters from NifU to NifH in vitro increases 10-fold the activity of the tobacco-isolated NifH, revealing that plant mitochondria [Fe-S] cluster availability constitutes a bottleneck to engineer plant nitrogenases.

Reactions of Late First-Row Transition Metal (Fe-Zn) Dichlorides with a PGeP Pincer Germylene.

The reactivity of the PGeP germylene 2,2'-bis(di-isopropylphosphanylmethyl)-5,5'-dimethyldipyrromethane-1,1'-diylgermanium(II), Ge(pyrmPiPr2 )2 CMe2 , with late first-row transition metal (Fe-Zn) dichlorides has been investigated. All reactions led to PGeP pincer chloridogermyl complexes. The reactions with FeCl2 and CoCl2 afforded paramagnetic square planar complexes of formula [MCl{κ3 P,Ge,P-GeCl(pyrmPiPr2 )2 CMe2 }] (M=Fe, Co). While the iron complex maintained an intermediate spin state (S1 ; µeff =3.0 µB ) over the temperature range 50-380 K, the effective magnetic moment of the cobalt complex varied linearly with temperature from 1.9 µB at 10 K to 3.6 µB at 380 K, indicating a spin crossover behavior that involves S1/2 (predominant at T<180 K) and S3/2 (predominant at T>200 K) species. Both cobalt(II) species were detected by electron paramagnetic resonance at T<20 K. The reaction of Ge(pyrmPiPr2 )2 CMe2 with [NiCl2 (dme)] (dme=dimethoxyethane) gave a square planar nickel(II) complex, [NiCl{κ3 P,Ge,P-GeCl(pyrmPiPr2 )2 CMe2 }], whereas the reaction with CuCl2 involved a redox process that rendered a mixture of the germanium(IV) compound GeCl2 (pyrmPiPr2 )2 CMe2 and a binuclear copper(I) complex, [Cu2 {µ-κ3 P,Ge,P-GeCl(pyrmPiPr2 )2 CMe2 }2 ], whose metal atoms are in tetrahedral environments. The reaction of the germylene with ZnCl2 led to the tetrahedral derivative [ZnCl{κ3 P,Ge,P-GeCl(pyrmPiPr2 )2 CMe2 }].

EPR of site-directed spin-labeled proteins: A powerful tool to study structural flexibility.

Electron Paramagnetic Resonance is a spectroscopic technique which, in combination with site-directed spin-labeling, provides structural and dynamic information about proteins in conditions similar to those of their physiological environment. The information is sequence-resolved, as it is based on probing the local dynamics of a paramagnetic label incorporated as a side chain of a selected amino acid. EPR does not impose a limit on the size of the protein or protein complex, as long as it is amenable to site-directed mutagenesis, and is able to obtain reliable distance distributions between two or more labels (identical or different).. The mean value, width and shape of distance distributions, as well as their dependence upon the state of the protein or interactions with physiological partners, provide insight into order-disorder transitions and the roles of protein flexibility. The main potentialities and limitations of the technique are revised and illustrated with examples of proteins for which order-disorder play an important role.

Integrin α6ß4 Recognition of a Linear Motif of Bullous Pemphigoid Antigen BP230 Controls Its Recruitment to Hemidesmosomes.

Mechanical stability of epithelia requires firm attachment to the basement membrane via hemidesmosomes. Dysfunction of hemidesmosomal proteins causes severe skin-blistering diseases. Two plakins, plectin and BP230 (BPAG1e), link the integrin α6ß4 to intermediate filaments in epidermal hemidesmosomes. Here, we show that a linear sequence within the isoform-specific N-terminal region of BP230 binds to the third and fourth FnIII domains of ß4. The crystal structure of the complex and mutagenesis analysis revealed that BP230 binds between the two domains of ß4. BP230 induces closing of the two FnIII domains that are locked in place by an interdomain ionic clasp required for binding. Disruption of BP230-ß4 binding prevents recruitment of BP230 to hemidesmosomes in human keratinocytes, revealing a key role of this interaction for hemidesmosome assembly. Phosphomimetic substitutions in ß4 and BP230 destabilize the complex. Thus, our study provides insights into the architecture of hemidesmosomes and potential mechanisms of regulation.

The photosynthetic cytochrome c 550 from the diatom Phaeodactylum tricornutum.

The photosynthetic cytochrome c 550 from the marine diatom Phaeodactylum tricornutum has been purified and characterized. Cytochrome c 550 is mostly obtained from the soluble cell extract in relatively large amounts. In addition, the protein appeared to be truncated in the last hydrophobic residues of the C-terminus, both in the soluble cytochrome c 550 and in the protein extracted from the membrane fraction, as deduced by mass spectrometry analysis and the comparison with the gene sequence. Interestingly, it has been described that the C-terminus of cytochrome c 550 forms a hydrophobic finger involved in the interaction with photosystem II in cyanobacteria. Cytochrome c 550 was almost absent in solubilized photosystem II complex samples, in contrast with the PsbO and Psb31 extrinsic subunits, thus suggesting a lower affinity of cytochrome c 550 for the photosystem II complex. Under iron-limiting conditions the amount of cytochrome c 550 decreases up to about 45% as compared to iron-replete cells, pointing to an iron-regulated synthesis. Oxidized cytochrome c 550 has been characterized using continuous wave EPR and pulse techniques, including HYSCORE, and the obtained results have been interpreted in terms of the electrostatic charge distribution in the surroundings of the heme centre.

Early folding events during light harvesting complex II assembly in vitro monitored by pulsed electron paramagnetic resonance.

Efficient energy transfer in the major light harvesting complex II (LHCII) of green plants is facilitated by the precise alignment of pigments due to the protein matrix they are bound to. Much is known about the import of the LHCII apoprotein into the chloroplast via the TOC/TIC system and its targeting to the thylakoid membrane but information is sparse about when and where the pigments are bound and how this is coordinated with protein folding. In vitro, the LHCII apoprotein spontaneously folds and binds its pigments if the detergent-solubilized protein is combined with a mixture of chlorophylls a and b and carotenoids. In the present work, we employed this approach to study apoprotein folding and pigment binding in a time-resolved manner by using pulsed electron paramagnetic resonance (EPR). Intra-molecular distances were measured before folding, after 255 ms and 40 s folding time in the absence of cryoprotectant, and in the fully folded and assembled LHCII. In accordance with earlier results, the most of the folding of the three membrane-spanning alpha helices precedes their apposition into the final tertiary structure. However, their formation follows different kinetics, partially extending into the final phase of LHCII formation during which much of the condensation of the pigment-protein structure occurs, presumably governed by the binding of chlorophyll b. A rough timetable is proposed to sort partial events into the LHCII formation process.

Spin Densities in Flavin Analogs within a Flavoprotein.

Characterization by electron paramagnetic resonance techniques of several variants of Anabaena flavodoxin, where the naturally occurring FMN cofactor is substituted by different analogs, makes it possible to improve the details of the spin distribution map in the isoallosazine ring in its semiquinone state. The analyzed variants were selected to monitor the effects of intrinsic changes in the flavin ring electronic structure, as well as perturbations in the apoflavodoxin-flavin interaction, on the spin populations. When these effects were analyzed together with the functional properties of the different flavodoxin variants, a relationship between spin population and biochemical parameters, as the reduction potential, could be envisaged.

Purification and Structural Analysis of Plectin and BPAG1e.

Plectin and BPAG1e belong to the plakin family of high-molecular-weight proteins that interconnect the cytoskeletal systems and anchor them to junctional complexes. Plectin and BPAG1e are prototypical plakins with a similar tripartite modular structure. The N- and C-terminal regions are built of multiple discrete structural domains, while the central rod domain mediates dimerization by coiled-coil interactions. Owing to the mosaic organization of plakins, the structure of their constituent individual domains or small multi-domain segments can be analyzed isolated. Yet, understanding the integrated function of large regions, oligomers, and heterocomplexes of plakins is difficult due to the large and segmented structure. Here, we describe methods for the production of plectin and BPAG1e samples suitable for structural and biophysical analysis. In addition, we discuss the combination of hybrid methods that yield information at several resolution levels to study the complex, multi-domain, and flexible structure of plakins.

Haptoglobin Preserves Vascular Nitric Oxide Signaling during Hemolysis.

RATIONALE: Hemolysis occurs not only in conditions such as sickle cell disease and malaria but also during transfusion of stored blood, extracorporeal circulation, and sepsis. Cell-free Hb depletes nitric oxide (NO) in the vasculature, causing vasoconstriction and eventually cardiovascular complications. We hypothesize that Hb-binding proteins may preserve vascular NO signaling during hemolysis. OBJECTIVES: Characterization of an archetypical function by which Hb scavenger proteins could preserve NO signaling during hemolysis. METHODS: We investigated NO reaction kinetics, effects on arterial NO signaling, and tissue distribution of cell-free Hb and its scavenger protein complexes. MEASUREMENTS AND MAIN RESULTS: Extravascular translocation of cell-free Hb into interstitial spaces, including the vascular smooth muscle cell layer of rat and pig coronary arteries, promotes vascular NO resistance. This critical disease process is blocked by haptoglobin. Haptoglobin does not change NO dioxygenation rates of Hb; rather, the large size of the Hb:haptoglobin complex prevents Hb extravasation, which uncouples NO/Hb interaction and vasoconstriction. Size-selective compartmentalization of Hb functions as a substitute for red blood cells after hemolysis and preserves NO signaling in the vasculature. We found that evolutionarily and structurally unrelated Hb-binding proteins, such as PIT54 found in avian species, functionally converged with haptoglobin to protect NO signaling by sequestering cell-free Hb in large protein complexes. CONCLUSIONS: Sequential compartmentalization of Hb by erythrocytes and scavenger protein complexes is an archetypical mechanism, which may have supported coevolution of hemolysis and normal vascular function. Therapeutic supplementation of Hb scavengers may restore vascular NO signaling and attenuate disease complications in patients with hemolysis.

A Low-Valent Iron Imido Heterocubane Cluster: Reversible Electron Transfer and Catalysis of Selective C-C Couplings.

Enzymes and cofactors with iron-sulfur heterocubane core structures, [Fe4 S4 ], are often found in nature as electron transfer reagents in fundamental catalytic transformations. An artificial heterocubane with a [Fe4 N4 ] core is reported that can reversibly store up to four electrons at very negative potentials. The neutral [Fe4 N4 ] and the singly reduced low-valent [Fe4 N4 ](-) heterocubanes were isolated and fully characterized. The low-valent species bears one unpaired electron, which is localized predominantly at one iron center in the electronic ground state but fluctuates with increasing temperatures. The electrons stored or released by the [Fe4 N4 ]/[Fe4 N4 ](-) redox couple can be used in reductive or oxidative CC couplings and even allow catalytic one-pot reactions, which show a remarkably enhanced selectivity in the presence of the [Fe4 N4 ] heterocubanes.

Spin trapping combined with quantitative mass spectrometry defines free radical redistribution within the oxidized hemoglobin:haptoglobin complex.

Extracellular or free hemoglobin (Hb) accumulates during hemolysis, tissue damage, and inflammation. Heme-triggered oxidative reactions can lead to diverse structural modifications of lipids and proteins, which contribute to the propagation of tissue damage. One important target of Hb׳s peroxidase reactivity is its own globin structure. Amino acid oxidation and crosslinking events destabilize the protein and ultimately cause accumulation of proinflammatory and cytotoxic Hb degradation products. The Hb scavenger haptoglobin (Hp) attenuates oxidation-induced Hb degradation. In this study we show that in the presence of hydrogen peroxide (H2O2), Hb and the Hb:Hp complex share comparable peroxidative reactivity and free radical generation. While oxidation of both free Hb and Hb:Hp complex generates a common tyrosine-based free radical, the spin-trapping reaction with 5,5-dimethyl-1-pyrroline N-oxide (DMPO) yields dissimilar paramagnetic products in Hb and Hb:Hp, suggesting that radicals are differently redistributed within the complex before reacting with the spin trap. With LC-MS(2) mass spectrometry we assigned multiple known and novel DMPO adduct sites. Quantification of these adducts suggested that the Hb:Hp complex formation causes extensive delocalization of accessible free radicals with drastic reduction of the major tryptophan and cysteine modifications in the ß-globin chain of the Hb:Hp complex, including decreased ßCys93 DMPO adduction. In contrast, the quantitative changes in DMPO adduct formation on Hb:Hp complex formation were less pronounced in the Hb α-globin chain. In contrast to earlier speculations, we found no evidence that free Hb radicals are delocalized to the Hp chain of the complex. The observation that Hb:Hp complex formation alters free radical distribution in Hb may help to better understand the structural basis for Hp as an antioxidant protein.

Combination of X-ray crystallography, SAXS and DEER to obtain the structure of the FnIII-3,4 domains of integrin α6ß4.

Integrin α6ß4 is a major component of hemidesmosomes that mediate the stable anchorage of epithelial cells to the underlying basement membrane. Integrin α6ß4 has also been implicated in cell proliferation and migration and in carcinoma progression. The third and fourth fibronectin type III domains (FnIII-3,4) of integrin ß4 mediate binding to the hemidesmosomal proteins BPAG1e and BPAG2, and participate in signalling. Here, it is demonstrated that X-ray crystallography, small-angle X-ray scattering and double electron-electron resonance (DEER) complement each other to solve the structure of the FnIII-3,4 region. The crystal structures of the individual FnIII-3 and FnIII-4 domains were solved and the relative arrangement of the FnIII domains was elucidated by combining DEER with site-directed spin labelling. Multiple structures of the interdomain linker were modelled by Monte Carlo methods complying with DEER constraints, and the final structures were selected against experimental scattering data. FnIII-3,4 has a compact and cambered flat structure with an evolutionary conserved surface that is likely to correspond to a protein-interaction site. Finally, this hybrid method is of general application for the study of other macromolecules and complexes.

Anisotropy of bullet-shaped magnetite nanoparticles in the magnetotactic bacteria Desulfovibrio magneticus sp. Strain RS-1.

Magnetotactic bacteria (MTB) build magnetic nanoparticles in chain configuration to generate a permanent dipole in their cells as a tool to sense the Earth's magnetic field for navigation toward favorable habitats. The majority of known MTB align their nanoparticles along the magnetic easy axes so that the directions of the uniaxial symmetry and of the magnetocrystalline anisotropy coincide. Desulfovibrio magneticus sp. strain RS-1 forms bullet-shaped magnetite nanoparticles aligned along their (100) magnetocrystalline hard axis, a configuration energetically unfavorable for formation of strong dipoles. We used ferromagnetic resonance spectroscopy to quantitatively determine the magnetocrystalline and uniaxial anisotropy fields of the magnetic assemblies as indicators for a cellular dipole with stable direction in strain RS-1. Experimental and simulated ferromagnetic resonance spectral data indicate that the negative effect of the configuration is balanced by the bullet-shaped morphology of the nanoparticles, which generates a pronounced uniaxial anisotropy field in each magnetosome. The quantitative comparison with anisotropy fields of Magnetospirillum gryphiswaldense, a model MTB with equidimensional magnetite particles aligned along their (111) magnetic easy axes in well-organized chain assemblies, shows that the effectiveness of the dipole is similar to that in RS-1. From a physical perspective, this could be a reason for the persistency of bullet-shaped magnetosomes during the evolutionary development of magnetotaxis in MTB.

Methyl rotors in flavoproteins.

In this contribution we present the study of the thermal dependence of the ENDOR spectra of flavodoxin at low temperatures which reveals the dynamics of the methyl groups bound to the flavin moiety in flavoproteins. The methyl groups behave as quantum rotors locked by a deep rotational well and undergoing a tunneling process. At room temperature, methyl rotors are locked and the hopping motion is slow. This picture of the dynamics of the methyl groups of the flavin ring is quite different from the one usually accepted and has relevant consequences on the understanding of the mechanisms of flavoproteins.

Structural Characterization of Polymer-Clay Nanocomposites Prepared by Co-Precipitation Using EPR Techniques.

Polymer-clay nanocomposites (PCNCs) containing either a rubber or an acrylate polymer were prepared by drying or co-precipitating polymer latex and nanolayered clay (synthetic and natural) suspensions. The interface between the polymer and the clay nanoparticles was studied by electron paramagnetic resonance (EPR) techniques by selectively addressing spin probes either to the surfactant layer (labeled stearic acid) or the clay surface (labeled catamine). Continuous-wave (CW) EPR studies of the surfactant dynamics allow to define a transition temperature T* which was tentatively assigned to the order-disorder transition of the surfactant layer. CW EPR studies of PCNC showed that completely exfoliated nanoparticles coexist with agglomerates. HYSCORE spectroscopy in PCNCs showed couplings within the probe -assigned with DFT computations- and couplings with nuclei of the environment, ¹H and 23Na for the surfactant layer probe, and 29Si, 7Li, 19F and 23Na for the clay surface probe. Analysis of these couplings indicates that the integrity of the surfactant layer is conserved and that there are sizeable ionic regions containing sodium ions directly beyond the surfactant layer. Simulations of the very weak couplings demonstrated that the HYSCORE spectra are sensitive to the composition of the clay and whether or not clay platelets stack.