Collisional cooling enhances the ability to observe non-covalent interactions within the inducible nitric oxide synthase oxygenase domain: Dimerization,complexation, and dissociation

The investigation of protein quaternary structure, protein-cofactor, and protein-ligand interactions by mass spectrometry is often limited by the fragility of such interactions under experimental conditions. To develop more gentle conditions of perhaps general use, we used as a model for study the oxygenase domain of murine inducible nitric oxide synthase (iNOS), which is homodimeric, binds heme and tetrahydrobiopterin H(4)B cofactors, and the substrate L-arginine. The energetics of the collisions in q2 and in the lens region of the mass spectrometer were manipulated for varying the degree of solvation around the non-covalently bound ions. Furthermore, the number of low-energy collisions in the collision cell of the instrument was varied, focusing and dampening the ion beam. Under gentle source collision conditions, and using multiple low-energy collisions in the collision cell of the mass spectrometer, dimers of the iNOS oxygenase domain containing heme, H(4)B, and arginine were observed intact after electrospraying at pH values near neutrality; a mutant of this protein (Trp188 --> Phe) was monomeric and did not bind cofactors. The pH dependence of the iNOS oxygenase domain under acidic conditions was also studied; while heme remained bound to the protein between pH 2.5 and 4.0, the dimeric structure was disrupted. Our findings confirm that non-covalently bound macromolecular complexes are retained and observable using electrospray mass spectrometry under the appropriate experimental conditions.     

Dioxygen reactivity of meso -hydroxylated hemes: Intermediates in heme degradation process catalyzed by heme oxygenase

Heme oxygenase (HO) is the only enzyme in mammals known to catalyse the physiological degradation of unwanted heme into biliverdin, Fe ion and CO. The process involves introduction of the hydroxyl group at one of itsmeso-positions as the first fundamental step of the heme cleavage process. It was also found thatmeso-amino heme undergoes similar ring-cleavage process while reacting with dioxygen in presence of pyridine as an axial ligand. The present paper briefly reviews the reactions of modelmeso-hydroxylated heme and its analogues with dioxygen, and their relevance in the heme degradation process.     

Kinetic stability of the peroxidase activity of unfolded cytochrome c: heme degradation and catalyst inactivation by hydrogen peroxide

Unfolding converts Paracoccus versutus cytochrome c-550 into a potent peroxidase (Diederix, R. E. M.; Ubbink, M.; Canters, G. W. ChemBioChem 2002, 3, 110-112). The catalytic activity is accompanied by peroxide-driven inactivation that is prevented, in part, by reducing substrate. Here, the kinetics of inactivation are described, and evidence is presented for the occurrence of a labile intermediate on the catalytic peroxidase pathway of unfolded cytochrome c-550. This intermediate represents a branching point, whereby the protein proceeds along either the productive pathway or self-inactivates. Reducing substrate suppresses inactivation by decreasing the steady-state concentration of the labile intermediate. Inactivation is accompanied by heme degradation. Its chemical reactivity, UV-vis, and EPR properties identify the first intermediate as hydroxyheme-cytochrome c-550, i.e. with heme hydroxylated at one of the heme meso positions. The occurrence of this species argues for the peroxo-iron species in the peroxidase mechanism as the labile intermediate leading to inactivated cytochrome c-550.     

Exploring the redox reactions between heme and tetrahydrobiopterin in the nitric oxide synthases

The NO synthases (NOSs) catalyze a two-step oxidation of L-arginine (Arg) to generate nitric oxide (NO) plus L-citrulline. Because NOSs are the only hemeproteins known to contain tetrahydrobiopterin (H4B) as a bound cofactor, the function and role of H4B in their heme-based oxygen activation and catalysis is of current interest. Distinct oxidative and reductive transitions of bound H4B cofactor occur during catalysis and are associated with distinct redox transitions of the NOS heme and flavin prosthetic groups. In this perspective, we discuss the redox transitions of H4B and heme with regard to their kinetics, regulation, role in the catalytic mechanism, and how and why they may be linked.     

Pulsed ENDOR determination of relative orientation of g-frame and molecular frame of imidazole-coordinated heme center of iNOS

Mammalian nitric oxide synthase (NOS) is a flavo-hemoprotein that catalyzes the oxidation of L-arginine to nitric oxide. Information about the relative alignment of the heme and FMN domains of NOS is important for understanding the electron transfer between the heme and FMN centers, but no crystal structure data for NOS holoenzyme are available. In our previous work [Astashkin, A. V.; Elmore, B. O.; Fan, W.; Guillemette, J. G.; Feng, C. J. Am. Chem. Soc. 2010, 132, 12059-12067], the distance between the imidazole-coordinated low-spin Fe(III) heme and FMN semiquinone in a human inducible NOS (iNOS) oxygenase/FMN construct has been determined by pulsed electron paramagnetic resonance (EPR). The orientation of the Fe-FMN radius vector, R(Fe-FMN), with respect to the heme g-frame was also determined. In the present study, pulsed electron-nuclear double resonance (ENDOR) investigation of the deuterons at carbons C2 and C5 in the deuterated coordinated imidazole was used to determine the relative orientation of the heme g-frame and molecular frame, from which R(Fe-FMN) can be referenced to the heme molecular frame. Numerical simulations of the ENDOR spectra showed that the g-factor axis corresponding to the low-field EPR turning point is perpendicular to the heme plane, whereas the axis corresponding to the high-field turning point is in the heme plane and makes an angle of about 80° with the coordinated imidazole plane. The FMN-heme domain docking model obtained in the previous work was found to be in qualitative agreement with the combined experimental results of the two pulsed EPR works.     

L-arginine binding to human inducible nitric oxide synthase: an antisymmetric funnel route toward isoform-specific inhibitors?

Nitric oxide (NO) is an important signaling molecule produced by a family of enzymes called nitric oxide synthases (NOS). Because NO is involved in various pathological conditions, the development of potent and isoform-selective NOS inhibitors is an important challenge. In the present study, the dimer of oxygenase domain of human iNOS (iNOSoxy) complexed to its natural substrate L-arginine (L-Arg) and both heme and tetrahydro-L-biopterin (BH4) cofactors was studied through multiple molecular dynamics simulations. Starting from the X-ray structure available for that complex (PDB: 1NSI ), a 16 ns equilibration trajectory was first obtained. Twelve dynamics of slow extraction of L-Arg out from the iNOSoxy active site were then performed. The steered molecular dynamics (SMD) approach was used starting from three different points of the reference trajectory for a total simulation time of 35 ns. A probable unbinding/binding pathway of L-Arg was characterized. It was suggested that a driving force directed the substrate toward the heme pocket. Key intermediate steps/residues along the access route to the active site were identified along this "funnel shape" pathway and compared to existing data. A quasi-normal mode analysis performed on the SMD data suggested that large collective motions of the protein may be involved in L-Arg binding and that opening the route to the active site in one monomer promoted an inverse, closing motion in the second monomer. Finally, our findings might help to rationalize the design of human iNOS isoform competitive inhibitors.     

Soluble factor from tumor cells induces heme oxygenase-1 by a nitric oxide-independent mechanism in murine peritoneal macrophages

Tumor target-derived soluble secretary factor has been known to influence macrophage activation to induce nitric oxide (NO) production. Since heme oxygenase-1 (HO-1) is induced by a variety of conditions associated with oxidative stress, we questioned whether soluble factor from tumor cells induces HO-1 through NO-dependent mechanism in macrophages. We designated this factor as a tumor-derived macrophage-activating factor (TMAF), because of its ability to activate macrophages to induce iNOS. Although TMAF alone showed modest activity, TMAF in combination with IFN-gamma significantly induced iNOS expression and NO synthesis. Simultaneously, TMAF induced HO-1 and this induction was slightly augmented by IFN-gamma. Surprisingly, however, induction of HO-1 by TMAF was not inhibited by the treatment with the highly selective iNOS inhibitor, 1400 W, indicating that TMAF induces the HO-1 enzyme by a NO-independent mechanism. While rIFN-gamma alone induced iNOS, it had no effect on HO-1 induction by itself. Collectively, the current study reveals that soluble factor from tumor target cells induces HO-1 enzyme in macrophages. However, overall biological significance of this phenomenon remains to be determined.     

Direct measurement by laser flash photolysis of intramolecular electron transfer in a two-domain construct of murine inducible nitric oxide synthase

Intersubunit intramolecular electron transfer (IET) from FMN to heme is essential in the delivery of electrons required for O2 activation in the heme domain and the subsequent nitric oxide (NO) synthesis by NO synthase (NOS). Previous crystal structures and functional studies primarily concerned an enzyme conformation that serves as the input state for reduction of FMN by electrons from NADPH and FAD in the reductase domain. To favor formation of the output state for the subsequent IET from FMN to heme in the oxygenase domain, a novel truncated two-domain oxyFMN construct murine inducible nitric oxide synthase (iNOS), in which only the FMN and heme domains were present, was designed and expressed. The kinetics of the IET between the FMN and heme domains in this construct was directly determined using laser flash photolysis of CO dissociation in comparative studies on partially reduced oxyFMN and single domain heme oxygenase constructs.     

Substrate- and isoform-specific dioxygen complexes of nitric oxide synthase

Nitric oxide synthase (NOS) catalyzes the formation of NO via a consecutive two-step reaction. In the first step, L-arginine (Arg) is converted to N-hydroxy-L-arginine (NOHA). In the second step, NOHA is further converted to citrulline and nitric oxide (NO). To assess the mechanistic differences between the two steps of the reaction, we have used resonance Raman spectroscopy combined with a homemade continuous-flow rapid solution mixer to study the structural properties of the metastable dioxygen-bound complexes of the oxygenase domain of inducible NOS (iNOSoxy). We identified the O-O stretching frequency of the substrate-free enzyme at 1133 cm-1. This frequency is insensitive to the presence of tetrahydrobiopterin, but it shifts to 1126 cm-1 upon binding of Arg, which we attribute to H-bonding interactions to the terminal oxygen atom of the heme iron-bound dioxygen. In contrast, the addition of NOHA to the enzyme did not bring about a shift in the frequency of the O-O stretching mode, because, unlike Arg, there is no H-bond associated with the terminal oxygen atom of the dioxygen. The substrate-specific H-bonding interactions play a critical role in determining the fate of the key peroxy intermediate. In the first step of the reaction, the H-bonds facilitate the rupture of the O-O bond, leading to the formation of the active ferryl species, which is essential for the oxidation of the Arg. On the other hand, in the second step of the reaction, the absence of the H-bonds prevents the premature O-O bond cleavage, such that the peroxy intermediate can perform a nucleophilic addition reaction to the substrate, NOHA.     

Kinetic isotope effects on the rate-limiting step of heme oxygenase catalysis indicate concerted proton transfer/heme hydroxylation

Heme oxygenase (HO) catalyzes the O2 and NADPH/cytochrome P450 reductase-dependent conversion of heme to biliverdin, free iron ion, and CO through a process in which the heme participates as both dioxygen-activating prosthetic group and substrate. We earlier confirmed that the first step of HO catalysis is a monooxygenation in which the addition of one electron and two protons to the HO oxy-ferroheme produces ferric-alpha-meso-hydroxyheme (h). Cryoreduction/EPR and ENDOR measurements further showed that hydroperoxo-ferri-HO converts directly to h in a single kinetic step without formation of a Compound I. We here report details of that rate-limiting step. One-electron 77 K cryoreduction of human oxy-HO and annealing at 200 K generates a structurally relaxed hydroperoxo-ferri-HO species, denoted R. We here report the cryoreduction/annealing experiments that directly measure solvent and secondary kinetic isotope effects (KIEs) of the rate-limiting R --> h conversion, using enzyme prepared with meso-deuterated heme and in H2O/D2O buffers to measure the solvent KIE (solv-KIE), and the secondary KIE (sec-KIE) associated with the conversion. This approach is unique in that KIEs measured by monitoring the rate-limiting step are not susceptible to masking by KIEs of other processes, and these results represent the first direct measurement of the KIEs of product formation by a kinetically competent reaction intermediate in any dioxygen-activating heme enzyme.The observation of both solv-KIE(298) = 1.8 and sec-KIE(298) = 0.8 (inverse) indicates that the rate-limiting step for formation of h by HO is a concerted process: proton transfer to the hydroperoxo-ferri-heme through the distal-pocket H-bond network, likely from a carboxyl group acting as a general acid catalyst, occurring in synchrony with bond formation between the terminal hydroperoxo-oxygen atom and the alpha-meso carbon to form a tetrahedral hydroxylated-heme intermediate. Subsequent rearrangement and loss of H2O then generates h.     

The ferrous verdoheme-heme oxygenase complex is six-coordinate and low-spin

A biosynthetic and enzymatic method was developed for the preparation of 13C-labeled verdoheme, which permits the 13C NMR spectroscopic characterization of this elusive intermediate in the heme oxidation path catalyzed by the enzyme heme oxygenase. The 13C NMR data indicate that the ferrous verdoheme complex of Neisseria meningitides heme oxygenase is hexacoordinate and diamagnetic, with a proximal histidine and likely a distal hydroxide as axial ligands. The coordination number and spin state of the ferrous verdoheme-heme oxygenase complex is in stark contrast to the pentacoordinate and paramagnetic nature of the heme-heme oxygenase complex and heme centers in general.     

Probing heme coordination states of inducible nitric oxide synthase with a ReI(imidazole-alkyl-nitroarginine) sensitizer-wire

Mammalian inducible nitric oxide synthase (iNOS) catalyzes the production of l-citrulline and nitric oxide (NO) from L-arginine and O2. The Soret peak in the spectrum of the iNOS heme domain (iNOSoxy) shifts from 423 to 390 nm upon addition of a sensitizer-wire, [ReI-imidazole-(CH2)8-nitroarginine]+, or [ReC8argNO2]+, owing to partial displacement of the water ligand in the active site. From analysis of competitive binding experiments with imidazole, the dissociation constant (Kd) for [ReC8argNO2]+-iNOSoxy was determined to be 3.0+/-0.1 microM, confirming that the sensitizer-wire binds with higher affinity than both L-arginine (Kd=22+/-5 microM) and imidazole (Kd=14+/-3 microM). Laser excitation (355 nm) of [ReC8argNO2]+-iNOSoxy triggers electron transfer to the active site of the enzyme, producing a ferroheme in less than approximately 1 micros.     

Enantiocomplementary Epoxidation Reactions Catalyzed by an Engineered Cofactor‐Independent Non‐natural Peroxygenase

Peroxygenases are heme‐dependent enzymes that use peroxide‐borne oxygen to catalyze a wide range of oxyfunctionalization reactions. Herein, we report the engineering of an unusual cofactor‐independent peroxygenase based on a promiscuous tautomerase that accepts different hydroperoxides (t‐BuOOH and H₂O₂) to accomplish enantiocomplementary epoxidations of various α,β‐unsaturated aldehydes (citral and substituted cinnamaldehydes), providing access to both enantiomers of the corresponding α,β‐epoxy‐aldehydes. High conversions (up to 98 %), high enantioselectivity (up to 98 % ee), and good product yields (50–80 %) were achieved. The reactions likely proceed via a reactive enzyme‐bound iminium ion intermediate, allowing tweaking of the enzyme's activity and selectivity by protein engineering. Our results underscore the potential of catalytic promiscuity for the engineering of new cofactor‐independent oxidative enzymes.     

Alkyl peroxides reveal the ring opening mechanism of verdoheme catalyzed by heme oxygenase

Heme oxygenase (HO) catalyzes heme catabolism through three successive oxygenation steps where the substrate heme itself activates O2. Although a rate-determining step of the HO catalysis is considered as third oxygenation, the verdoheme degradation mechanism has been the least understood in the HO catalysis. In order to discriminate three possible pathways proposed for the verdoheme ring-opening, we have examined reactions of the verdoheme-HO-1 complex with alkyl peroxides, namely MeOOH. Under reducing conditions, the MeOOH reaction afforded two novel products whose absorption spectra are similar to but slightly different from that of biliverdin. HPLC, ESI-MS, and NMR analysis show that these products are 1- and 19-methoxy-deoxy-biliverdins. The addition of a methoxy group at one end of the linear tetrapyrrole unambiguously indicates transient formation of the Fe-OOMe intermediate and rearrangement of its terminal methoxy group to the alpha-pyrrole carbon. The corresponding OH transfer of the Fe-OOH species is highly probable in the H2O2-dependent verdoheme degradation and is likely to be the case in the O2-dependent reaction catalyzed by HO as well.     

Inactivation of microbial arginine deiminases by L-canavanine

Arginine deiminase (ADI) catalyzes the hydrolytic conversion of L-arginine to ammonia and L-citrulline as part of the energy-producing L-arginine degradation pathway. The chemical mechanism for ADI catalysis involves initial formation and subsequent hydrolysis of a Cys-alkylthiouronium ion intermediate. The structure of the Pseudomonas aeruginosa ADI-(L-arginine) complex guided the design of arginine analogs that might react with the ADIs to form inactive covalent adducts during catalytic turnover. One such candidate is L-canavanine, in which an N-methylene of L-arginine is replaced by an N-O. This substance was shown to be a slow substrate-producing O-ureido-L-homoserine. An in depth kinetic and mass spectrometric analysis of P. aeruginosa ADI inhibition by L-canavanine showed that two competing pathways are followed that branch at the Cys-alkylthiouronium ion intermediate. One pathway leads to direct formation of O-ureido-L-homoserine via a reactive thiouronium intermediate. The other pathway leads to an inactive form of the enzyme, which was shown by chemical model and mass spectrometric studies to be a Cys-alkylisothiourea adduct. This adduct undergoes slow hydrolysis to form O-ureido-L-homoserine and regenerated enzyme. In contrast, kinetic and mass spectrometric investigations demonstrate that the Cys-alkylthiouronium ion intermediate formed in the reaction of L-canavanine with Bacillus cereus ADI partitions between the product forming pathway (O-ureido-L-homoserine and free enzyme) and an inactivation pathway that leads to a stable Cys-alkylthiocarbamate adduct. The ADIs from Escherichia coli, Burkholderia mallei, and Giardia intestinalis were examined in order to demonstrate the generality of the L-canavanine slow substrate inhibition and to distinguish the kinetic behavior that defines the irreversible inhibition observed with the B. cereus ADI from the time controlled inhibition observed with the P. aeruginosa, E. coli, B. mallei, and G. intestinalis ADIs.     

Coupled oxidation vs heme oxygenation: insights from axial ligand mutants of mitochondrial cytochrome b5

Mutation of His-39, one of the axial ligands in rat outer mitochondrial membrane cytochrome b(5) (OM cyt b(5)), to Val produces a mutant (H39V) capable of carrying out the oxidation of heme to biliverdin when incubated with hydrazine and O(2). The reaction proceeds via the formation of an oxyferrous complex (Fe(II)(-)O(2)) that is reduced by hydrazine to a ferric hydroperoxide (Fe(III)(-)OOH) species. The latter adds a hydroxyl group to the porphyrin to form meso-hydroxyheme. The observation that catalase does not inhibit the oxidation of the heme in the H39V mutant is consistent with the formation of a coordinated hydroperoxide (Fe(III)(-)OOH), which in heme oxygenase is the precursor of meso-hydroxyheme. By comparison, mutation of His-63, the other axial ligand in OM cyt b(5), to Val results in a mutant (H63V) capable of oxidizing heme to verdoheme in the absence of catalase. However, the oxidation of heme by H63V is completely inhibited by catalase. Furthermore, whereas the incubation of Fe(III)(-)H63V with H(2)O(2) leads to the nonspecific degradation of heme, the incubation of Fe(II)(-)H63V with H(2)O(2) results in the formation of meso-hydroxyheme, which upon exposure to O(2) is rapidly converted to verdoheme. These findings revealed that although meso-hydroxyheme is formed during the degradation of heme by the enzyme heme oxygenase or by the process of coupled oxidation of model hemes and hemoproteins not involved in heme catabolism, the corresponding mechanisms by which meso-hydroxyheme is generated are different. In the coupled oxidation process O(2) is reduced to noncoordinated H(2)O(2), which reacts with Fe(II)-heme to form meso-hydroxyheme. In the heme oxygenation reaction a coordinated O(2) molecule (Fe(II)(-)O(2)) is reduced to a coordinated peroxide molecule (Fe(III)(-)OOH), which oxidizes heme to meso-hydroxyheme.     

Similarity of and differences between the mechanisms of thermal inactivation of β-galactosidases of different origins

A comparative study of the thermal stabilities of five β-galactosidases of different origins in buffer solutions at pH of their highest activity was performed. The thermal inactivation of these enzymes was found to occur via different mechanisms. The thermal inactivation of four β-galactosidases followed the mechanism with intermediate stages not accompanied by catalytic activity loss. The dissociative mechanism of inactivation, including the reversible dissociation of the oligomeric enzyme and the irreversible dissociation of the monomeric enzyme, was observed for bacterial (Escherichia coli) and yeast (Kluyveromices fragilis) β-galactosidases. The kinetic parameters of dissociative thermal inactivation of these enzymes and the stability parameters of β-galactosidases studied were determined. The latter included the critical temperature of changes in the kinetic regime of inactivation, the smallest number of intermediate stages without catalytic activity loss, the temperature of the disappearance of the induction period of thermal inactivation, and induction period duration at the given temperature (40°C).     

Biliverdin reduction by cyanobacterial phycocyanobilin:ferredoxin oxidoreductase (PcyA) proceeds via linear tetrapyrrole radical intermediates

Cyanobacterial phycocyanobilin:ferredoxin oxidoreductase (PcyA) catalyzes the four electron reduction of biliverdin IXalpha (BV) to phycocyanobilin, a key step in the biosynthesis of the linear tetrapyrrole (bilin) prosthetic groups of cyanobacterial phytochromes and the light-harvesting phycobiliproteins. Using an anaerobic assay protocol, optically detected bilin-protein intermediates, produced during the PcyA catalytic cycle, were shown to correlate well with the appearance and decay of an isotropic g approximately 2 EPR signal measured at low temperature. Absorption spectral simulations of biliverdin XIIIalpha reduction support a mechanism involving direct electron transfers from ferredoxin to protonated bilin:PcyA complexes.     

Thermal inactivation of alkali phosphatases under various conditions

The thermal inactivation of alkali phosphatases from bacteria Escherichia coli (ECAP), bovine intestines (bovine IAP), and chicken intestines (chicken IAP) was studied in different buffer solutions and in the solid state. The conclusion was made that these enzymes had maximum stability in the solid state, and, in a carbonate buffer solution, their activity decreased most rapidly. It was found that the bacterial enzyme was more stable than animal phosphatases. It was noted that, for ECAP, four intermediate stages preceded the loss of enzyme activity, and, for bovine and chicken IAPs, three intermediate stages were observed. The activation energy of thermal inactivation of ECAP over the range 25–70°C was determined to be 80 kJ/mol; it corresponded to the dissociation of active dimers into inactive monomers. Higher activation energies (∼200 kJ/mol) observed at the initial stage of thermal inactivation of animal phosphatases resulted from the simultaneous loss of enzyme activity caused by dimer dissociation and denaturation. It was shown that the activation energy of denaturation of monomeric animal alkali phosphatases ranged from 330 to 380 kJ/mol depending on buffer media. It was concluded that the inactivation of solid samples of alkali phosphatases at 95°C was accompanied by an about twofold decrease in the content of β structures in protein molecules. Original Russian Text ? L.F. Atyaksheva, B.N. Tarasevich, E.S. Chukhrai, O.M. Poltorak, 2009, published in Zhurnal Fizicheskoi Khimii, 2009, Vol. 83, No. 2, pp. 391–396.     

v-Triazolines—VI: Rearrangement of triazolines from 2-substituted-1-aryl-and 1-heteroaryl-1-amino-ethylenes and tosylazide

Reaction of tosylazide with 2-substituted, 1-aryl- or 1-heteroaryl-1-amino-ethylenes affords, via unstable triazolines, a zwitterionic intermediate which can lead (i) through nitrogen loss and rearrangement to amidine (2) and (ii) through C₄-C₅ cleavage to the formation of a diazo compound and amidine (3).Some aspects of the two mechanistic pathways are discussed.