New Insight into the Peroxidase−Hydroxamic Acid Interaction Revealed by the Combination of Spectroscopic and Crystallographic Studies

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.

Paper-Based Potentiometric Device for Rapid and Selective Determination of Salicylhydroxamate as a Urinary Struvite Stone Inhibitor

Novel paper-based potentiometric platforms for rapid, cost-effective, and simple determination of the salicylhydroxamic acid (SHAM) drug are presented. Both the SHAM sensor and the reference Ag/AgCl electrode were integrated together on the miniaturized paper platforms. The ion-sensing membrane for the presented sensor is based on the use of SnIV-tetraphenylporphyrin (SnIVTPP) as a charged carrier within a plasticized poly(vinyl chloride) (PVC) matrix. Multiwalled carbon nanotubes (MWCNTs) were used as an ion-to-electron transducer. The resulting sensor revealed a rapid and stable response with a Nernstian slope of -59.3 ± 0.7 mV/decade over the linear range of 1.0 × 10-6 to 1.0 × 10-3 M and a detection limit of 0.7 μM. All measurements were carried out in 30 mM phosphate-buffered solution (PBS) at pH 7.2. Intra- and interday precision were measured and found to be 1.7%. The relative standard deviation (RSD%) ( = 5) was calculated as 2.43% after utilizing five different electrodes (n = 5). The selectivity behavior of the prepared electrodes in the absence and presence of ionic additives was evaluated. The selectivity pattern showed a non-Hofmeister selectivity pattern in the existence of anionic additives with enhanced potentiometric selectivity for SHAM over different lipophilic anions (e.g., ClO4 -, SCN-, and I-). The presented device was successfully applied for SHAM determination in pharmaceutical preparations. This paper-based analytical device can be potentially manufactured at large scales and provides a portable, rapid, disposable, and cost-effective analytical tool for measuring the SHAM drug.

Solution and crystal phase resonance Raman spectroscopy: Valuable tools to unveil the structure and function of heme proteins

In the present review, examples are provided illustrating the application of resonance Raman microscopy to heme protein single crystals to highlight the artifacts induced by the crystallization process or the conformational alteration induced by cooling. Moreover, the structural information determined from the RR spectra of heme proteins in solution and crystals is compared to that obtained from their X-ray structures to show how the combined spectroscopic/crystallographic approach is a powerful weapon in the structural biologist’s armamentarium.

trans-Bis(dimethyl sulfoxide-κO)bis(3-nitrobenzohydroxamato-κ2 O,O′)zinc(II)

Single crystals of the title complex, [Zn(C7H5N2O4)2(C2H6OS)2] or [Zn(NBZH)2(DMSO)2], were isolated from a dimethyl sulfoxide (DMSO) solution containing [Zn(NBZH)2]·2H2O (NBZH = 3-nitrobenzohydroxamate anion). The asymmetric unit comprises of one O,O′-chelating NBZH anion, one O-bound DMSO ligand and one zinc(II) cation localized on an inversion centre. The three-dimensional crystal packing includes N—H...O and C—H...O hydrogen bonding, as well as O...H and H...H contacts identified by Hirshfeld isosurface analysis.

Molecular Mechanism of Enzymatic Chlorite Detoxification: Insights from Structural and Kinetic Studies

The heme enzyme chlorite dismutase (Cld) catalyzes the degradation of chlorite to chloride and dioxygen. Although structure and steady-state kinetics of Clds have been elucidated, many questions remain (e.g., the mechanism of chlorite cleavage and the pH dependence of the reaction). Here, we present high-resolution X-ray crystal structures of a dimeric Cld at pH 6.5 and 8.5, its fluoride and isothiocyanate complexes and the neutron structure at pH 9.0 together with the pH dependence of the Fe(III)/Fe(II) couple, and the UV–vis and resonance Raman spectral features. We demonstrate that the distal Arg127 cannot act as proton acceptor and is fully ionized even at pH 9.0 ruling out its proposed role in dictating the pH dependence of chlorite degradation. Stopped-flow studies show that (i) Compound I and hypochlorite do not recombine and (ii) Compound II is the immediately formed redox intermediate that dominates during turnover. Homolytic cleavage of chlorite is proposed.

Active Sites of O2-Evolving Chlorite Dismutases Probed by Halides and Hydroxides and New Iron-Ligand Vibrational Correlations

O₂-evolving chlorite dismutases (Clds) fall into two subfamilies, which efficiently convert ClO₂^- to O₂ and Cl^-. The Cld from Dechloromonas aromatica (DaCld) represents the chlorite-decomposing homopentameric enzymes found in perchlorate- and chlorate-respiring bacteria. The Cld from the Gram-negative human pathogen Klebsiella pneumoniae (KpCld) is representative of the second subfamily, comprising homodimeric enzymes having truncated N-termini. Here steric and nonbonding properties of the DaCld and KpCld active sites have been probed via kinetic, thermodynamic, and spectroscopic behaviors of their fluorides, chlorides, and hydroxides. Cooperative binding of Cl^- to KpCld drives formation of a hexacoordinate, high-spin aqua heme, whereas DaCld remains pentacoordinate and high-spin under analogous conditions. Fluoride coordinates to the heme iron in KpCld and DaCld, exhibiting ν(Fe^III-F) bands at 385 and 390 cm^-1, respectively. Correlation of these frequencies with their CT1 energies reveals strong H-bond donation to the F^- ligand, indicating that atoms directly coordinated to heme iron are accessible to distal H-bond donation. New vibrational frequency correlations between either ν(Fe^III-F) or ν(Fe^III-OH) and ν(Fe^II-His) of Clds and other heme proteins are reported. These correlations orthogonalize proximal and distal effects on the bonding between iron and exogenous π-donor ligands. The axial Fe-X vibrations and the relationships between them illuminate both similarities and differences in the H-bonding and electrostatic properties of the distal and proximal heme environments in pentameric and dimeric Clds. Moreover, they provide general insight into the structural basis of reactivity toward substrates in heme-dependent enzymes and their mechanistic intermediates, especially those containing the ferryl moiety.

Ionic-liquid-based hollow-fiber liquid-phase microextraction method combined with hybrid artificial neural network-genetic algorithm for speciation and optimized determination of ferro and ferric in environmental water samples

A novel and environmentally friendly ionic-liquid-based hollow-fiber liquid-phase microextraction method combined with a hybrid artificial neural network (ANN)-genetic algorithm (GA) strategy was developed for ferro and ferric ions speciation as model analytes. Different parameters such as type and volume of extraction solvent, amounts of chelating agent, volume and pH of sample, ionic strength, stirring rate, and extraction time were investigated. Much more effective parameters were firstly examined based on one-variable-at-a-time design, and obtained results were used to construct an independent model for each parameter. The models were then applied to achieve the best and minimum numbers of candidate points as inputs for the ANN process. The maximum extraction efficiencies were achieved after 9 min using 22.0 μL of 1-hexyl-3-methylimidazolium hexafluorophosphate ([C6MIM][PF6]) as the acceptor phase and 10 mL of sample at pH = 7.0 containing 64.0 μg L(-1) of benzohydroxamic acid (BHA) as the complexing agent, after the GA process. Once optimized, analytical performance of the method was studied in terms of linearity (1.3-316 μg L(-1), R (2) = 0.999), accuracy (recovery = 90.1-92.3%), and precision (relative standard deviation (RSD) <3.1). Finally, the method was successfully applied to speciate the iron species in the environmental and wastewater samples.

Structural flexibility of the heme cavity in the cold-adapted truncated hemoglobin from the Antarctic marine bacterium Pseudoalteromonas haloplanktis TAC125

Truncated hemoglobins build one of the three branches of the globin protein superfamily. They display a characteristic two-on-two α-helical sandwich fold and are clustered into three groups (I, II and III) based on distinct structural features. Truncated hemoglobins are present in eubacteria, cyanobacteria, protozoa and plants. Here we present a structural, spectroscopic and molecular dynamics characterization of a group-II truncated hemoglobin, encoded by the PSHAa0030 gene from Pseudoalteromonas haloplanktis TAC125 (Ph-2/2HbO), a cold-adapted Antarctic marine bacterium hosting one flavohemoglobin and three distinct truncated hemoglobins. The Ph-2/2HbO aquo-met crystal structure (at 2.21 Å resolution) shows typical features of group-II truncated hemoglobins, namely the two-on-two α-helical sandwich fold, a helix Φ preceding the proximal helix F, and a heme distal-site hydrogen-bonded network that includes water molecules and several distal-site residues, including His(58)CD1. Analysis of Ph-2/2HbO by electron paramagnetic resonance, resonance Raman and electronic absorption spectra, under varied solution conditions, shows that Ph-2/2HbO can access diverse heme ligation states. Among these, detection of a low-spin heme hexa-coordinated species suggests that residue Tyr(42)B10 can undergo large conformational changes in order to act as the sixth heme-Fe ligand. Altogether, the results show that Ph-2/2HbO maintains the general structural features of group-II truncated hemoglobins but displays enhanced conformational flexibility in the proximity of the heme cavity, a property probably related to the functional challenges, such as low temperature, high O2 concentration and low kinetic energy of molecules, experienced by organisms living in the Antarctic environment.

The effect on structural and solvent water molecules of substrate binding to ferric horseradish peroxidase

Ultrafast, multi-dimensional infrared spectroscopy, in the form of 2D-IR and pump–probe measurements, has been employed to investigate the effect of substrate binding on the structural dynamics of the horseradish peroxidase (HRP) enzyme. Using nitric oxide bound to the ferric haem of HRP as a sensitive probe of local dynamics, we report measurements of the frequency fluctuations (spectral diffusion) and vibrational lifetime of the NO stretching mode with benzohydroxamic acid (BHA) located in the substrate-binding position at the periphery of the haem pocket, in both D₂O and H₂O solvents. The results reveal that, with BHA bound to the enzyme, the local structural dynamics are insensitive to H/D exchange. These results are in stark contrast to those found in studies of the substrate-free enzyme, which demonstrated that the local chemical and dynamic environment of the haem ligand is influenced by water molecules. In light of the large changes in solvent accessibility caused by substrate binding, we discuss the potential for varying roles for the solvent in the haem pocket of HRP at different stages along the reaction coordinate of the enzymatic mechanism.

Distinct structural and redox properties of the heme active site in bacterial dye decolorizing peroxidase-type peroxidases from two subfamilies: resonance Raman and electrochemical study

Spectroscopic data of dye decolorizing peroxidases (DyPs) from Bacillus subtilis (BsDyP), an A subfamily member, and Pseudomonas putida (PpDyP), a B subfamily enzyme, reveal distinct heme coordination patterns of the respective active sites. In solution, both enzymes show a heterogeneous spin population, with the six-coordinated low-spin state being the most populated in the former and the five-coordinated quantum mechanically mixed-spin state in the latter. We ascribe the poor catalytic activity of BsDyP to the presence of a catalytically incompetent six-coordinated low-spin population. The spin populations of the two DyPs are sensitively dependent on the pH, temperature, and physical, i.e., solution versus crystal versus immobilized, state of the enzymes. We observe a redox potential for the Fe(2+)/Fe(3+) couple in BsDyP (-40 mV) at pH 7.6 substantially more positive than those reported for the majority of other peroxidases, including PpDyP (-260 mV). Furthermore, we evaluate the potential of the studied enzymes for biotechnological applications on the basis of electrochemical and spectroelectrochemical data.

Fifteen years of Raman spectroscopy of engineered heme containing peroxidases: what have we learned?

Spectroscopic techniques have been fundamental to the comprehension of peroxidase function under physiological conditions. This Account examines the contribution to our understanding of heme peroxidases provided by electronic and resonance Raman spectroscopies in conjunction with site-directed mutagenesis. The results obtained over 15 years with several heme peroxidases and selected mutants have provided important insights into the influence exerted by the protein in the vicinity of the active site via key amino acids on the functionality and stability of the enzymes. Moreover, resonance Raman spectroscopy has revealed that a common feature of heme peroxidases is the presence of an extensive network of H-bonds coupling the distal and proximal sides, which has a profound influence on the heme ligation, affecting both the fifth and the sixth coordination sites.

Parallel synthesis and in vitro activity of novel anthranilic hydroxamate-based inhibitors of the prostaglandin H2 synthase peroxidase activity

Currently available non-steroidal anti-inflammatory drugs (NSAIDs) such as aspirin are directed at the cyclooxygenase (COX) site, but not the peroxidase (POX) activity of prostaglandin H2 synthase (PGHS). They are thus unable to inhibit the free-radical induced tissue injury associated with PGHS peroxidase activity, which can occur independently of the COX site. A lead compound, anthranilic hydroxamic acid (AHA) was found to have significant PGHS-POX inhibitory activity (IC50= 72 microM). To define the critical parameters for PGHS-POX inhibition, we investigated 29 AHA derivatives, synthesised from their acid precursors, using solid phase synthesis. In vitro analysis demonstrated a ten-fold improvement in inhibition with 3,5-diiodoanthranilic hydroxamic acid (IC50= 7 microM).