Reaction intermediate rotation during the decarboxylation of coproheme to heme b in C. diphtheriae.

Monoderm bacteria utilize coproheme decarboxylases (ChdCs) to generate heme b by a stepwise decarboxylation of two propionate groups of iron coproporphyrin III (coproheme), forming two vinyl groups. This work focuses on actinobacterial ChdC from Corynebacterium diphtheriae (CdChdC) to elucidate the hydrogen peroxide-mediated decarboxylation of coproheme via monovinyl monopropionyl deuteroheme (MMD) to heme b, with the principal aim being to understand the reorientation mechanism of MMD during turnover. Wild-type CdChdC and variants, namely H118A, H118F, and A207E, were studied by resonance Raman and ultraviolet-visible spectroscopy, mass spectrometry, and molecular dynamics simulations. As actinobacterial ChdCs use a histidine (H118) as a distal base, we studied the H118A and H118F variants to elucidate the effect of 1) the elimination of the proton acceptor and 2) steric constraints within the active site. The A207E variant mimics the proximal H-bonding network found in chlorite dismutases. This mutation potentially increases the rigidity of the proximal site and might impair the rotation of the reaction intermediate MMD. We found that both wild-type CdChdC and the variant H118A convert coproheme mainly to heme b upon titration with H2O2. Interestingly, the variant A207E mostly accumulates MMD along with small amounts of heme b, whereas H118F is unable to produce heme b and accumulates only MMD. Together with molecular dynamics simulations, the spectroscopic data provide insight into the reaction mechanism and the mode of reorientation of MMD, i.e., a rotation in the active site versus a release and rebinding.

Exciplex Formation in Lipid-bound Escherichia coli Flavohemoglobin.

Flavohemoglobins have the particular capability of binding unsaturated and cyclopropanated fatty acids as free acids or phospholipids. Fatty acid binding to the ferric heme results in a weak but direct bonding interaction. Ferrous and ferric protein, in presence or absence of a bound lipid molecule, have been characterized by transient absorption spectroscopy. Measurements have been also carried out both on the ferrous deoxygenated and on the CO bound protein to investigate possible long-range interaction between the lipid acyl chain moiety and the ferrous heme. After excitation of the deoxygenated derivatives the relaxation process reveals a slow dynamics (350 ps) in lipid-bound protein but is not observed in the lipid-free protein. The latter feature and the presence of an extra contribution in the absorption spectrum, indicates that the interaction of iron heme with the acyl chain moiety occurs only in the excited electronic state and not in the ground electronic state. Data analysis highlights the formation of a charge-transfer complex in which the iron ion of the lipid-bound protein in the expanded electronic excited state, possibly represented by a high spin Fe III intermediate, is able to bind to the sixth coordination ligand placed at a distance of at 3.5 Šfrom the iron. A very small nanosecond geminate rebinding is observed for CO adduct in lipid-free but not in the lipid-bound protein. The presence of the lipid thus appears to inhibit the mobility of CO in the heme pocket.

Surface Enhanced Raman Spectroscopy for In-Field Detection of Pesticides: A Test on Dimethoate Residues in Water and on Olive Leaves.

Dimethoate (DMT) is an organophosphate insecticide commonly used to protect fruit trees and in particular olive trees. Since it is highly water-soluble, its use on olive trees is considered quite safe, because it flows away in the residual water during the oil extraction process. However, its use is strictly regulated, specially on organic cultures. The organic production chain certification is not trivial, since DMT rapidly degrades to omethoate (OMT) and both disappear in about two months. Therefore, simple, sensitive, cost-effective and accurate methods for the determination of dimethoate, possibly suitable for in-field application, can be of great interest. In this work, a quick screening method, possibly useful for organic cultures certification will be presented. DMT and OMT in water and on olive leaves have been detected by surface enhanced Raman spectroscopy (SERS) using portable instrumentations. On leaves, the SERS signals were measured with a reasonably good S/N ratio, allowing us to detect DMT at a concentration up to two orders of magnitude lower than the one usually recommended for in-field treatments. Moreover, detailed information on the DMT distribution on the leaves has been obtained by Raman line- (or area-) scanning experiments.

High-Resolution Spectroscopic Studies of Complexes Formed by Medium-Size Organic Molecules.

A wealth of structural and dynamical information has been obtained in the last 30 years from the study of high-resolution spectra of molecular clusters generated in a cold supersonic expansion by means of highly resolved spectroscopic methods. The data obtained, generally lead to determination of the structures of stable conformations. In addition, in the case of weakly bound molecular complexes, it is usual to observe the effects of internal motions due to the shallowness of the potential energy surfaces involved and the flexibility of the systems. In the case of electronic excitation experiments, also the effect of electronic distribution changes on both equilibrium structures and internal motions becomes accessible. The structural and dynamical information that can be obtained by applying suitable theoretical models to the analysis of these unusually complex spectra allows the determination and understanding of the driving forces involved in formation of the molecular complex. In this way, many types of non-covalent interactions have been characterized, from pure van der Waals interactions in complexes of rare gases to moderate-strength and weak hydrogen bonds and to the most recent halogen bonds and n-π interactions. The aim of this review is to underline how the different experimental and theoretical methods converge in giving a detailed picture of weak interactions in small molecular adducts involving medium-size molecules. The conclusions regarding geometries and energies can contribute to understanding of the different driving forces involved in the dynamics of the processes and can be exploited in all fields of chemistry and biochemistry, from design of new materials with novel properties to rational design of drugs.

Non-covalent interactions in anisole-(CO2)n (n = 1, 2) complexes.

Non-covalent interactions are ubiquitous and represent a very important binding motif. The direct experimental measurement of binding energies in complexes has been elusive for a long time despite its importance, for instance, for understanding and predicting the structure of bio-macromolecules. Here, we report a combined experimental and computational analysis on the 1 : 1 and 1 : 2 clusters formed by anisole (methoxybenzene) and carbon dioxide molecules. We have obtained a detailed description of the interaction between CO2 and anisole. This system represents quite a challenging test for the presently available experimental and theoretical methods for the characterization of weakly bound molecular complexes. The results, evaluated in the framework of previous studies on anisole clusters, show a very good agreement between experimental and theoretical data. A comparison of the experimental and computational data enabled the binding energy values of the 1 : 1 and 1 : 2 clusters to be determined in the ground electronic state of the neutral and cation complex and in the first excited singlet state of the neutral complex. In addition, it was possible to adduce the presence of different 1 : 1+ conformers, prepared by direct ionization of the 1 : 1 complex or by dissociative ionization of the 1 : 2 complex.

Resonance Raman Spectra of o-Safranin Dye, Free and Adsorbed on Silver Nanoparticles: Experiment and Density Functional Theory Calculation.

The properties of o-Safranin (SO) dye in the first electronic excited state were studied with combined experimental and theoretical methods. The electronic absorption spectra of SO molecules are measured in water solution and in the presence of silver nanoparticles. The normal Raman (NRS) and resonance Raman (RR) spectra of solid SO and the surface enhanced Raman (SERS) and surface enhanced resonance Raman (SE[R]RS) spectra of SO adsorbed on silver nanoparticles are measured at different excitation energies. The enhancement factors for selected vibrational bands of the RR, SERS, and SE[R]RS spectra of SO have been obtained with respect to the NRS spectra of the solid after a careful evaluation of the experimental conditions. The data furnished useful information on the excited electronic states and the interactions of SO with silver nanoparticles. The experimental results are discussed on the basis of DFT and TD-DFT calculations (B3LYP/6-311+G(d,p)) on the isolated SO molecule.

Binding energies of the π-stacked anisole dimer: new molecular beam-laser spectroscopy experiments and CCSD(T) calculations.

Among noncovalent interactions, π-π stacking is a very important binding motif governed mainly by London dispersion. Despite its importance, for instance, for the structure of bio-macromolecules, the direct experimental measurement of binding energies in π-π stacked complexes has been elusive for a long time. Only recently, an experimental value for the binding energy of the anisole dimer was presented, determined by velocity mapping ion imaging in a two-photon resonant ionisation molecular beam experiment. However, in that paper, a discrepancy was already noted between the obtained experimental value and a theoretical estimate. Here, we present an accurate recalculation of the binding energy based on the combination of the CCSD(T)/CBS interaction energy and a DFT-D3 vibrational analysis. This proves unambiguously that the previously reported experimental value is too high and a new series of measurements with a different, more sensitive apparatus was performed. The new experimental value of 1800±100 cm(-1) (5.15±0.29 kcal mol(-1)) is close to the present theoretical prediction of 5.04±0.40 kcal mol(-1). Additional calculations of the properties of the cationic and excited states involved in the photodissociation of the dimer were used to identify and rationalise the difficulties encountered in the experimental work.

Tailored micro-extraction method for Raman/SERS detection of indigoids in ancient textiles.

Indigoid dyes are well known as vat dyes. In their oxidized dichetonic form they are stable and insoluble in water, whereas in their reduced form, commonly known as leuco, they are soluble in water and able to be attached to fabric for dyeing purposes. These blue dyes are usually easily detectable in art objects by means of Raman spectroscopy by adopting for analyses a laser line at a high wavelength, such as a 785 nm diode laser. Unfortunately, in ancient artworks, that are often highly degraded, it is not always possible to collect high quality Raman spectra, which makes the analysis and identification of these compounds particularly challenging. In this work, we present a tailor-made methodology for the extraction and the recognition of indigoid dyes in works of art, which exploits the solubility of these compounds in their reduced form. Excellent Raman and surface enhanced Raman spectroscopy (SERS) spectra of indigo were acquired after micro-extraction on ancient and reference textiles, confirming the reliability of the presented procedure. Moreover, the methodology has been applied also for the extraction of the indigoid dye Tyrian purple on a reference textile, showing excellent results. This analytical method has been found to be extremely safe both for the reference textiles and the investigated ancient textiles, thus being a promising procedure for the selective analysis and detection of indigoid compounds in objects of artistic relevance.

Structure and energetics of the anisole-Ar(n) (n = 1, 2, 3) complexes: high-resolution resonant two-photon and threshold ionization experiments, and quantum chemical calculations.

We present a concerted experimental and theoretical study of the anisole···Arn complexes with n = 1-3. Experimentally, anisole was seeded into a pulsed supersonic argon jet producing a molecular beam. Resonant two-photon, two-colour ionisation (R2PI) spectra of anisole···Arn complexes with n = 1-3 were obtained. Also, the photodissociation of the (1 : 1) cluster was probed synchronously by - Zero Electron Kinetic Energy Photoelectron Spectroscopy (ZEKE) - and - Mass Resolved Threshold Ionization (MATI) - measuring electrons and ions obtained from pulsed field ionization of high-n Rydberg states upon two-colour laser excitation. The experimental results are compared to quantum chemical calculations at the DFT-D3 (B-LYP/def2-QZVP level with Grimme's D3 dispersion correction) level. Structure and energetics due to microsolvation effects by the direct interaction of the argon atoms with the π-system were evaluated. The experimental binding energy of the 1 : 1 cluster is finally compared to computational results; in the S0 ground state the theoretical value based on the "gold standard" CCSD(T)/CBS calculations lies within the error bars of the observed value. In the excited state the agreement between theory and experiment is not so spectacular but relative values of observed dissociation energies (D0) in the ground and excited states and of calculated ones agree well.

Entrance channels to coproheme in coproporphyrin ferrochelatase probed by exogenous imidazole binding.

Iron insertion into porphyrins is an essential step in heme biosynthesis. In the coproporphyrin-dependent pathway, specific to monoderm bacteria, this reaction is catalyzed by the monomeric enzyme coproporphyrin ferrochelatase. In addition to the mechanistic details of the metalation of the porphyrin, the identification of the substrate access channel for ferrous iron to the active site is important to fully understand this enzymatic system. In fact, whether the iron reaches the active site from the distal or the proximal porphyrin side is still under debate. In this study we have thoroughly addressed this question in Listeria monocytogenes coproporphyrin ferrochelatase by X-ray crystallography, steady-state and pre-steady-state imidazole ligand binding studies, together with a detailed spectroscopic characterization using resonance Raman and UV-vis absorption spectroscopies in solution. Analysis of the X-ray structures of coproporphyrin ferrochelatase-coproporphyrin III crystals soaked with ferrous iron shows that iron is present on both sides of the porphyrin. The kinetic and spectroscopic study of imidazole binding to coproporphyrin ferrochelatase­iron coproporphyrin III clearly indicates the presence of two possible binding sites in this monomeric enzyme that influence each other, which is confirmed by the observed cooperativity at steady-state and a biphasic behavior in the pre-steady-state experiments. The current results are discussed in the context of the entire heme biosynthetic pathway and pave the way for future studies focusing on protein-protein interactions.

Revisiting catalytic His and Glu residues in coproporphyrin ferrochelatase - unexpected activities of active site variants.

The identification of the coproporphyrin-dependent heme biosynthetic pathway, which is used almost exclusively by monoderm bacteria in 2015 by Dailey et al. triggered studies aimed at investigating the enzymes involved in this pathway that were originally assigned to the protoporphyrin-dependent heme biosynthetic pathway. Here, we revisit the active site of coproporphyrin ferrochelatase by a biophysical and biochemical investigation using the physiological substrate coproporphyrin III, which in contrast to the previously used substrate protoporphyrin IX has four propionate substituents and no vinyl groups. In particular, we have compared the reactivity of wild-type coproporphyrin ferrochelatase from the firmicute Listeria monocytogenes with those of variants, namely, His182Ala (H182A) and Glu263Gln (E263Q), involving two key active site residues. Interestingly, both variants are active only toward the physiological substrate coproporphyrin III but inactive toward protoporphyrin IX. In addition, E263 exchange impairs the final oxidation step from ferrous coproheme to ferric coproheme. The characteristics of the active site in the context of the residues involved and the substrate binding properties are discussed here using structural and functional means, providing a further contribution to the deciphering of this enigmatic reaction mechanism.

Proximal ligand tunes active site structure and reactivity in bacterial L. monocytogenes coproheme ferrochelatase.

Ferrochelatases catalyze the insertion of ferrous iron into the porphyrin during the heme b biosynthesis pathway, which is fundamental for both prokaryotes and eukaryotes. Interestingly, in the active site of ferrochelatases, the proximal ligand coordinating the porphyrin iron of the product is not conserved, and its catalytic role is still unclear. Here we compare the L. monocytogenes bacterial coproporphyrin ferrochelatase native enzyme together with selected variants, where the proximal Tyr residue was replaced by a His (i.e. the most common ligand in heme proteins), a Met or a Phe (as in human and actinobacterial ferrochelatases, respectively), in their Fe(III), Fe(II) and Fe(II)-CO adduct forms. The study of the active site structure and the activity of the proteins in solution has been performed by UV-vis electronic absorption and resonance Raman spectroscopies, biochemical characterization, and classical MD simulations. All the mutations alter the H-bond interactions between the iron porphyrin propionate groups and the protein, and induce effects on the activity, depending on the polarity of the proximal ligand. The overall results confirm that the weak or non-existing coordination of the porphyrin iron by the proximal residue is essential for the binding of the substrate and the release of the final product.

Iron insertion into coproporphyrin III-ferrochelatase complex: Evidence for an intermediate distorted catalytic species.

Understanding the reaction mechanism of enzymes at the molecular level is generally a difficult task, since many parameters affect the turnover. Often, due to high reactivity and formation of transient species or intermediates, detailed information on enzymatic catalysis is obtained by means of model substrates. Whenever possible, it is essential to confirm a reaction mechanism based on substrate analogues or model systems by using the physiological substrates. Here we disclose the ferrous iron incorporation mechanism, in solution, and in crystallo, by the coproporphyrin III-coproporphyrin ferrochelatase complex from the firmicute, pathogen, and antibiotic resistant, Listeria monocytogenes. Coproporphyrin ferrochelatase plays an important physiological role as the metalation represents the penultimate reaction step in the prokaryotic coproporphyrin-dependent heme biosynthetic pathway, yielding coproheme (ferric coproporphyrin III). By following the metal titration with resonance Raman spectroscopy and x-ray crystallography, we prove that upon metalation the saddling distortion becomes predominant both in the crystal and in solution. This is a consequence of the readjustment of hydrogen bond interactions of the propionates with the protein scaffold during the enzymatic catalysis. Once the propionates have established the interactions typical of the coproheme complex, the distortion slowly decreases, to reach the almost planar final product.

The Role of the Hydrogen Bond Network in Maintaining Heme Pocket Stability and Protein Function Specificity of C. diphtheriae Coproheme Decarboxylase.

Monoderm bacteria accumulate heme b via the coproporphyrin-dependent biosynthesis pathway. In the final step, in the presence of two molecules of H2O2, the propionate groups of coproheme at positions 2 and 4 are decarboxylated to form vinyl groups by coproheme decarboxylase (ChdC), in a stepwise process. Decarboxylation of propionate 2 produces an intermediate that rotates by 90° inside the protein pocket, bringing propionate 4 near the catalytic tyrosine, to allow the second decarboxylation step. The active site of ChdCs is stabilized by an extensive H-bond network involving water molecules, specific amino acid residues, and the propionate groups of the porphyrin. To evaluate the role of these H-bonds in the pocket stability and enzyme functionality, we characterized, via resonance Raman and electronic absorption spectroscopies, single and double mutants of the actinobacterial pathogen Corynebacterium diphtheriae ChdC complexed with coproheme and heme b. The selective elimination of the H-bond interactions between propionates 2, 4, 6, and 7 and the polar residues of the pocket allowed us to establish the role of each H-bond in the catalytic reaction and to follow the changes in the interactions from the substrate to the product.

Graphene Oxide Nanosheets Reduce Astrocyte Reactivity to Inflammation and Ameliorate Experimental Autoimmune Encephalomyelitis.

In neuroinflammation, astrocytes play multifaceted roles that regulate the neuronal environment. Astrocytes sense and respond to pro-inflammatory cytokines (CKs) and, by a repertoire of intracellular Ca2+ signaling, contribute to disease progression. Therapeutic approaches wish to reduce the overactivation in Ca2+ signaling in inflammatory-reactive astrocytes to restore dysregulated cellular changes. Cell-targeting therapeutics might take advantage by the use of nanomaterial-multifunctional platforms such as graphene oxide (GO). GO biomedical applications in the nervous system involve therapeutic delivery and sensing, and GO flakes were shown to enable interfacing of neuronal and glial membrane dynamics. We exploit organotypic spinal cord cultures and optical imaging to explore Ca2+ changes in astrocytes, and we report, when spinal tissue is exposed to CKs, neuroinflammatory-associated modulation of resident glia. We show the efficacy of GO to revert these dynamic changes in astrocytic reactivity to CKs, and we translate this potential in an animal model of immune-mediated neuroinflammatory disease.

Active site architecture of coproporphyrin ferrochelatase with its physiological substrate coproporphyrin III: Propionate interactions and porphyrin core deformation.

Coproporphyrin ferrochelatases (CpfCs) are enzymes catalyzing the penultimate step in the coproporphyrin-dependent (CPD) heme biosynthesis pathway, which is mainly utilized by monoderm bacteria. Ferrochelatases insert ferrous iron into a porphyrin macrocycle and have been studied for many decades, nevertheless many mechanistic questions remain unanswered to date. Especially CpfCs, which are found in the CPD pathway, are currently in the spotlight of research. This pathway was identified in 2015 and revealed that the correct substrate for these ferrochelatases is coproporphyrin III (cpIII) instead of protoporphyrin IX, as believed prior the discovery of the CPD pathway. The chemistry of cpIII, which has four propionates, differs significantly from protoporphyrin IX, which features two propionate and two vinyl groups. These findings let us to thoroughly describe the physiological cpIII-ferrochelatase complex in solution and in the crystal phase. Here, we present the first crystallographic structure of the CpfC from the representative monoderm pathogen Listeria monocytogenes bound to its physiological substrate, cpIII, together with the in-solution data obtained by resonance Raman and UV-vis spectroscopy, for wild-type ferrochelatase and variants, analyzing propionate interactions. The results allow us to evaluate the porphyrin distortion and provide an in-depth characterization of the catalytically-relevant binding mode of cpIII prior to iron insertion. Our findings are discussed in the light of the observed structural restraints and necessities for this porphyrin-enzyme complex to catalyze the iron insertion process. Knowledge about this initial situation is essential for understanding the preconditions for iron insertion in CpfCs and builds the basis for future studies.

The role of the distal cavity in carbon monoxide stabilization in the coproheme decarboxylase enzyme from C. diphtheriae.

This work focuses on the carbon monoxide adducts of the wild-type and selected variants of the coproheme decarboxylase from actinobacterial Corynebacterium diphtheriae complexed with coproheme, monovinyl monopropionyl deuteroheme (MMD), and heme b. The UV - vis and resonance Raman spectroscopies together with the molecular dynamics simulations clearly show that the wild-type coproheme-CO adduct is characterized by two CO conformers, one hydrogen-bonded to the distal H118 residue and the other showing a weak polar interaction with the distal cavity. Instead, upon conversion to heme b, i.e. after decarboxylation of propionates 2 and 4 and rotation by 90o of the porphyrin ring inside the cavity, CO probes a less polar environment. In the absence of the H118 residue, both coproheme and heme b complexes form only the non-H-bonded CO species. The unrotated MMD-CO adduct as observed in the H118F variant, confirms that decarboxylation of propionate 2 only, does not affect the heme cavity. The rupture of both the H-bonds involving propionates 2 and 4 destabilizes the porphyrin inside the cavity with the subsequent formation of a CO adduct in an open conformation. In addition, in this work we present data on CO binding to reversed heme b, obtained by hemin reconstitution of the H118A variant, and to heme d, obtained by addition of an excess of hydrogen peroxide. The results will be discussed and compared with those reported for the representatives of the firmicute clade.

Microplastics in the Florence wastewater treatment plant studied by a continuous sampling method and Raman spectroscopy: A preliminary investigation.

The presence of an ever increasing amount of plastic in the Italian river system makes it necessary to understand the contribution of their different sources. We focus on the contribution from the wastewater treatment plants to the microplastics (MPs), size less than 5 mm, conveyed to the fluvial system, and on the development of methods for their detection in this matrix. This study, one of the first in Italy, is aimed to investigate the content of MPs present in the effluent of the main wastewater treatment plant in Florence (Italy). We sampled wastewater during dry season to mainly quantify the contribution from civil and municipal activities to the MPs release. The samples were continuously collected over a period of 24 h at the exit of the water line using a series of 8 sieves with different mesh sizes (almost 1000 L filtered volume). The sampled material was analyzed by optical microscopy and micro-Raman spectroscopy by use of low-cost, portable instruments. The spatial resolution of the spectrometer matches the minimum dimension of the mesh size in use (38 µm). The analysis detected an average concentration of 5 MPs per liter in the 38-1000 µm diameter range, corresponding to a daily release of about 35 kg/day into the River Arno, a result in line with other studies carried out on Europe's major rivers. We provide a classification of the polymer composition showing the predominant presence of Polypropylene (29%), Polyethylene (18%) and Polyester (14%). The MP shape classification reveals the relevance of fibers in effluents. The number of sieves used provided an accurate size distribution curve of the sampled MPs allowing to estimate, by extrapolation, a relevant quantity of MPs finer than 38 µm whose determination would otherwise require much more sophisticated methods.

An active site at work - the role of key residues in C. diphteriae coproheme decarboxylase.

Coproheme decarboxylases (ChdCs) are utilized by monoderm bacteria to produce heme b by a stepwise oxidative decarboxylation of the 2- and 4-propionate groups of iron coproporphyrin III (coproheme) to vinyl groups. This work compares the effect of hemin reconstitution versus the hydrogen peroxide-mediated conversion of coproheme to heme b in the actinobacterial ChdC from Corynebacterium diphtheriae (CdChdC) and selected variants. Both ferric and ferrous forms of wild-type (WT) CdChdC and its H118A, H118F, and A207E variants were characterized by resonance Raman and UV-vis spectroscopies. The heme b ligand assumes the same conformation in the WT active site for both the reconstituted and H2O2-mediated product, maintaining the same vinyl and propionate interactions with the protein. Nevertheless, it is important to note that the distal His118, which serves as a distal base, plays an important role in the stabilization of the cavity and for the heme b reconstitution. In fact, while the access of heme b is prevented by steric hindrance in the H118F variant, the substitution of His with the small apolar Ala residue favors the insertion of the heme b in the reversed conformation. The overall data strongly support that during decarboxylation, the intermediate product, a monovinyl-monopropionyl deuteroheme, rotates by 90o within the active site. Moreover, in the ferrous forms the frequency of the ν(Fe-Nδ(His)) stretching mode provides information on the strength of the proximal Fe-His bond and allows us to follow its variation during the two oxidative decarboxylation steps.