UV resonance Raman detection of a ligand vibration on ferric nitrosyl heme proteins

The Biologically Relevant Coordination Chemistry of Iron and Nitric Oxide: Electronic Structure and Reactivity

Nitric oxide (NO) is an important signaling molecule that is involved in a wide range of physiological and pathological events in biology. Metal coordination chemistry, especially with iron, is at the heart of many biological transformations involving NO. A series of heme proteins, nitric oxide synthases (NOS), soluble guanylate cyclase (sGC), and nitrophorins, are responsible for the biosynthesis, sensing, and transport of NO. Alternatively, NO can be generated from nitrite by heme- and copper-containing nitrite reductases (NIRs). The NO-bearing small molecules such as nitrosothiols and dinitrosyl iron complexes (DNICs) can serve as an alternative vehicle for NO storage and transport. Once NO is formed, the rich reaction chemistry of NO leads to a wide variety of biological activities including reduction of NO by heme or non-heme iron-containing NO reductases and protein post-translational modifications by DNICs. Much of our understanding of the reactivity of metal sites in biology with NO and the mechanisms of these transformations has come from the elucidation of the geometric and electronic structures and chemical reactivity of synthetic model systems, in synergy with biochemical and biophysical studies on the relevant proteins themselves. This review focuses on recent advancements from studies on proteins and model complexes that not only have improved our understanding of the biological roles of NO but also have provided foundations for biomedical research and for bio-inspired catalyst design in energy science.

Structure and reactivity of chlorite dismutase nitrosyls

Ferric nitrosyl ({FeNO}6) and ferrous nitrosyl ({FeNO}7) complexes of the chlorite dismutases (Cld) from Klebsiella pneumoniae and Dechloromonas aromatica have been characterized using UV-visible absorbance and Soret-excited resonance Raman spectroscopy. Both of these Clds form kinetically stable {FeNO}6 complexes and they occupy a unique region of ν(Fe-NO)/ν(N-O) correlation space for proximal histidine liganded heme proteins, characteristic of weak Fe-NO and N-O bonds. This location is attributed to admixed FeIII-NO character of the {FeNO}6 ground state. Cld {FeNO}6 complexes undergo slow reductive nitrosylation to yield {FeNO}7 complexes. The effects of proximal and distal environment on reductive nitroylsation rates for these dimeric and pentameric Clds are reported. The ν(Fe-NO) and ν(N-O) frequencies for Cld {FeNO}7 complexes reveal both six-coordinate (6c) and five-coordinate (5c) nitrosyl hemes. These 6c and 5c forms are in a pH dependent equilibrium. The 6c and 5c {FeNO}7 Cld frequencies provided positions of both Clds on their respective ν(Fe-NO) vs ν(N-O) correlation lines. The 6c {FeNO}7 complexes fall below (along the ν(Fe-NO) axis) the correlation line that reports hydrogen-bond donation to NNO, which is consistent with a relatively weak Fe-NO bond. Kinetic and spectroscopic evidence is consistent with the 5c {FeNO}7 Clds having NO coordinated on the proximal side of the heme, analogous to 5c {FeNO}7 hemes in proteins known to have NO sensing functions.

Ferric Heme-Nitrosyl Complexes: Kinetically Robust or Unstable Intermediates?

We have determined a convenient method for the bulk synthesis of high-purity ferric heme-nitrosyl complexes ({FeNO}⁶ in the Enemark-Feltham notation); this method is based on the chemical or electrochemical oxidation of corresponding {FeNO}⁷ precursors. We used this method to obtain the five- and six-coordinate complexes [Fe(TPP)(NO)]⁺ (TPP^2- = tetraphenylporphyrin dianion) and [Fe(TPP)(NO)(MI)]⁺ (MI = 1-methylimidazole) and demonstrate that these complexes are stable in solution in the absence of excess NO gas. This is in stark contrast to the often-cited instability of such {FeNO}⁶ model complexes in the literature, which is likely due to the common presence of halide impurities (although other impurities could certainly also play a role). This is avoided in our approach for the synthesis of {FeNO}⁶ complexes via oxidation of pure {FeNO}⁷ precursors. On the basis of these results, {FeNO}⁶ complexes in proteins do not show an increased stability toward NO loss compared to model complexes. We also prepared the halide-coordinated complexes [Fe(TPP)(NO)(X)] (X = Cl^-, Br^-), which correspond to the elusive, key reactive intermediate in the so-called autoreduction reaction, which is frequently used to prepare {FeNO}⁷ complexes from ferric precursors. All of the complexes were characterized using X-ray crystallography, UV-vis, IR, and nuclear resonance vibrational spectroscopy (NRVS). On the basis of the vibrational data, further insight into the electronic structure of these {FeNO}⁶ complexes, in particular with respect to the role of the axial ligand trans to NO, is obtained.

Structural changes and picosecond to second dynamics of cytochrome c in interaction with nitric oxide in ferrous and ferric redox states

After dissociation NO rebinds to Cyt c in 10 ps whereas Met80 rebinds in 5 μs after NO release from Cyt c. A complete view of heme – NO dynamics within 12 orders of magnitude of time in Cyt c is presented.

Nitric oxide activation by caa3 oxidoreductase from Thermus thermophilus

We present UV-Raman evidence for the formation of the hyponitrite (HO–NN–O⁻) species in the binuclear heme a₃ Fe–Cu_B center (νN–N = 1330 cm⁻¹) of caa₃ heme-copper oxidoreductase from Thermus thermophilus.

CO, NO and O2 as Vibrational Probes of Heme Protein Interactions

The gaseous XO molecules (X = C, N or O) bind to the heme prosthetic group of heme proteins, and thereby activate or inhibit key biological processes. These events depend on interactions of the surrounding protein with the FeXO adduct, interactions that can be monitored via the frequencies of the Fe-X and X-O bond stretching modes, νFeX and νXO. The frequencies can be determined by vibrational spectroscopy, especially resonance Raman spectroscopy. Backbonding, the donation of Fe dπ electrons to the XO π* orbitals, is a major bonding feature in all the FeXO adducts. Variations in backbonding produce negative νFeX/νXO correlations, which can be used to gauge electrostatic and H-bonding effects in the protein binding pocket. Backbonding correlations have been established for all the FeXO adducts, using porphyrins with electron donating and withdrawing substituents. However the adducts differ in their response to variations in the nature of the axial ligand, and to specific distal interactions. These variations provide differing vantages for evaluating the nature of protein-heme interactions. We review experimental studies that explore these variations, and DFT computational studies that illuminate the underlying physical mechanisms.

New light on NO bonding in Fe(III) heme proteins from resonance Raman spectroscopy and DFT modeling

Visible and ultraviolet resonance Raman (RR) spectra are reported for Fe(III)(NO) adducts of myoglobin variants with altered polarity in the distal heme pockets. The stretching frequencies of the Fe(III)-NO and N-O bonds, nu(FeN) and nu(NO), are negatively correlated, consistent with backbonding. However, the correlation shifts to lower nu(NO) for variants lacking a distal histidine. DFT modeling reproduces the shifted correlations and shows the shift to be associated with the loss of a lone-pair donor interaction from the distal histidine that selectively strengthens the N-O bond. However, when the model contains strongly electron-withdrawing substituents at the heme beta-positions, nu(FeN) and nu(NO) become positively correlated. This effect results from Fe(III)-N-O bending, which is induced by lone-pair donation to the N(NO) atom. Other mechanisms for bending are discussed, which likewise lead to a positive nu(FeN)/nu(NO) correlation, including thiolate ligation in heme proteins and electron-donating meso-substituents in heme models. The nu(FeN)/nu(NO) data for the Fe(III) complexes are reporters of heme pocket polarity and the accessibility of lone pair, Lewis base donors. Implications for biologically important processes, including NO binding, reductive nitrosylation, and NO reduction, are discussed.

A functional nitric oxide reductase model

A functional heme/nonheme nitric oxide reductase (NOR) model is presented. The fully reduced diiron compound reacts with two equivalents of NO leading to the formation of one equivalent of N(2)O and the bis-ferric product. NO binds to both heme Fe and nonheme Fe complexes forming individual ferrous nitrosyl species. The mixed-valence species with an oxidized heme and a reduced nonheme Fe(B) does not show NO reduction activity. These results are consistent with a so-called "trans" mechanism for the reduction of NO by bacterial NOR.

Spectroscopic characterization of heme iron-nitrosyl species and their role in NO reductase mechanisms in diiron proteins

Nitric oxide (NO) plays an important role in cell signalling and in the mammalian immune response to infection. On its own, NO is a relatively inert radical, and when it is used as a signalling molecule, its concentration remains within the picomolar range. However, at infection sites, the NO concentration can reach the micromolar range, and reactions with other radical species and transition metals lead to a broad toxicity. Under aerobic conditions, microorganisms cope with this nitrosative stress by oxidizing NO to nitrate (NO3−). Microbial hemoglobins play an essential role in this NO-detoxifying process. Under anaerobic conditions, detoxification occurs via a 2-electron reduction of two NO molecules to N2O. In many bacteria and archaea, this NO-reductase reaction is catalyzed by diiron proteins. Despite the importance of this reaction in providing microorganisms with a resistance to the mammalian immune response, its mechanism remains ill-defined. Because NO is an obligatory intermediate of the denitrification pathway, respiratory NO reductases also provide resistance to toxic concentrations of NO. This family of enzymes is the focus of this review. Respiratory NO reductases are integral membrane protein complexes that contain a norB subunit evolutionarily related to subunit I of cytochrome c oxidase (Cc O). NorB anchors one high-spin heme b3 and one non-heme iron known as FeB, i.e ., analogous to CuB in Cc O. A second group of diiron proteins with NO-reductase activity is comprised of the large family of soluble flavoprotein A found in strict and facultative anaerobic bacteria and archaea. These soluble detoxifying NO reductases contain a non-heme diiron cluster with a Fe–Fe distance of 3.4 Å and are only briefly mentioned here as a promising field of research. This article describes possible mechanisms of NO reduction to N2O in denitrifying NO-reductase (NOR) proteins and critically reviews recent experimental results. Relevant theoretical model calculations and spectroscopic studies of the NO-reductase reaction in heme/copper terminal oxidases are also overviewed.

Detection and determination of the {Fe(NO)(2)} core vibrational features in dinitrosyl-iron complexes from experiment, normal coordinate analysis, and density functional theory: an avenue for probing the nitric oxide oxidation state

As it is now well-established that nitric oxide plays an important role in many physiological processes, there is a renewed interest in dinitrosyl-iron complexes (DNICs). The question concerning the electronic structure of DNICs circles around the formal oxidation states of the iron and nitric oxide of the Fe(NO)2 core. Previous infrared measurements of nu(NO) alone point out inconsistencies in assigning electron configurations and charges on metals, inherent from the measurement of one parameter external to the metal. This work represents the first experimental and theoretical attempt to assign vibrational modes for the {Fe(NO)2}9 core of DNICs. The following complexes are investigated, [PPN][S5Fe(NO)2] (1), [PPN][Se5Fe(NO)2] (2), [PPN][(SPh)2Fe(NO)2] (3), and [PPN][(SePh)2Fe(NO)2] (4). The analysis of isotopically edited Raman data together with normal coordinate calculation permitted assignment of nu(NO) and nu(Fe-NO) stretching and delta(Fe-N-O) bending modes in these complexes. The assignments proposed are the first ever reported for the DNICs; a comparison of nu(NO) and nu(Fe-NO) stretching frequencies in DNICs is now feasible. The Fe(NO)2 core electronic configuration in these complexes is described as {Fe1+(*NO)2}. Results from 1 and 3 have been complemented by density functional theory (DFT) frequency calculations. In addition to providing a reasonably correct account of the observed frequencies, DFT calculations also give a good account of the frequency shifts upon 15NO substitution providing the first link between DFT and Raman spectroscopies for DNICs. Through the use of a combination of NO intraligand and metal-ligand vibrational data for the Fe(NO)2 core, normal coordinate analysis gives a NO stretching force constant, which compared to molecular NO gas, is significantly reduced for all four complexes. The hybrid U-B3LYP/6-311++G(3d,2p) density functional method has been employed to analyze the molecular orbital compositions of predominantly NO orbitals based on the crystal structure of complex 1. The molecular orbital not only revealed the bonding nature of the {Fe(NO)2}9 core but also provided a qualitative correct account of the observed low NO vibrational frequencies. The calculation shows that the NO is involved in a strong donor bonding interaction with the Fe1+. This donor bonding interaction involves the 5sigma molecular orbital of the NO, which is sigma-bonding with respect to the intramolecular NO bond, and removal of electron density from this orbital destabilizes the NO bond. Though it is too ambiguous to extrapolate a nu(Fe-NO)/nu(NO) correlation line for {Fe(NO)2}9 DNICs based only on the data reported here, the feasibility of using a vibrational systematics diagram to extract the electron configurations and charges on metals is demonstrated based on the vibrational data available in the literature for iron-nitrosyl complexes. The data provided here can be used as a model for the determination of effective charges on iron and the bonding of nitric oxides to metals in DNICs.

Interactions between substrates and the haem-bound nitric oxide of ferric and ferrous bacterial nitric oxide synthases

We report here the resonance Raman spectra of the FeIII-NO and FeII-NO complexes of the bacterial NOSs (nitric oxide synthases) from Staphylococcus aureus and Bacillus subtilis. The haem-NO complexes of these bacterial NOSs displayed Fe-N-O frequencies similar to those of the mammalian NOSs, in presence and absence of L-arginine, indicating that haem-bound NO and L-arginine had similar haem environments in bacterial and mammalian NOSs. The only notable difference between the two types of NOS was the lack of change in Fe-N-O frequencies of the FeIII-NO complexes upon (6R) 5,6,7,8-tetrahydro-L-biopterin binding to bacterial NOSs. We report, for the first time, the characterization of NO complexes with NOHA (N(omega)-hydroxy-L-arginine), the substrate used in the second half of the catalytic cycle of NOSs. In the FeIII-NO complexes, both L-arginine and NOHA induced the Fe-N-O bending mode at nearly the same frequency as a result of a steric interaction between the substrates and the haem-bound NO. However, in the FeII-NO complexes, the Fe-N-O bending mode was not observed and the nu(Fe-NO) mode displayed a 5 cm(-1) higher frequency in the complex with NOHA than in the complex with L-arginine as a result of direct interactions that probably involve hydrogen bonds. The different behaviour of the substrates in the FeII-NO complexes thus reveal that the interactions between haem-bound NO and the substrates are finely tuned by the geometry of the Fe-ligand structure and are relevant to the use of the FeII-NO complex as a model of the oxygenated complex of NOSs.

Protonation and Hydrogen-Bonding State of the Distal Histidine in the CO Complex of Horseradish Peroxidase As Studied by Ultraviolet Resonance Raman Spectroscopy

Ultraviolet resonance Raman (UVRR) spectroscopy has been used to characterize the structure and hydrogen bonding state of the distal histidine (His42) in horseradish peroxidase (HRP) complexed with carbon monoxide (HRP-CO). The HRP-CO - HRP UVRR difference spectrum in D(2)O solution at pD 7.0 shows two positive peaks at 1408 and 1388 cm(-)(1), which are ascribable to medium-to-weak and strong hydrogen bonding states, respectively, of the protonated imidazolium side chain of His42 in HRP-CO. Both His42 peaks decrease in intensity with increase of pD with a midpoint of transition at pD 8.8, indicating that the pK(a) of His42 in HRP-CO is 8.8. The CO ligand exhibits two C-O stretching Raman peaks at 1932 and 1902 cm(-)(1), the latter of which diminishes at alkaline pD and is assignable to a strong hydrogen-bonded state. It is most probable that the imidazolium side chain of His42 forms a strong hydrogen bond with CO, giving a His42 peak at 1388 cm(-)(1) and a CO peak at 1902 cm(-)(1), in one conformer. The other hydrogen bonding state of His42, giving the 1408 cm(-)(1) peak, is ascribed to another conformer forming a medium-to-weak hydrogen bond with a water molecule in the distal cavity. The present finding that His42 can act as a strong proton donor to CO and decrease the CO bond order is consistent with the role of His42 as a general acid to cleave the O-O bond of hydrogen peroxide, a specific oxidizing agent, in the catalytic cycle of HRP.

Sulfur K-edge XAS and DFT calculations on nitrile hydratase: geometric and electronic structure of the non-heme iron active site

The geometric and electronic structure of the active site of the non-heme iron enzyme nitrile hydratase (NHase) is studied using sulfur K-edge XAS and DFT calculations. Using thiolate (RS(-))-, sulfenate (RSO(-))-, and sulfinate (RSO(2)(-))-ligated model complexes to provide benchmark spectral parameters, the results show that the S K-edge XAS is sensitive to the oxidation state of S-containing ligands and that the spectrum of the RSO(-) species changes upon protonation as the S-O bond is elongated (by approximately 0.1 A). These signature features are used to identify the three cysteine residues coordinated to the low-spin Fe(III) in the active site of NHase as CysS(-), CysSOH, and CysSO(2)(-) both in the NO-bound inactive form and in the photolyzed active form. These results are correlated to geometry-optimized DFT calculations. The pre-edge region of the X-ray absorption spectrum is sensitive to the Z(eff) of the Fe and reveals that the Fe in [FeNO](6) NHase species has a Z(eff) very similar to that of its photolyzed Fe(III) counterpart. DFT calculations reveal that this results from the strong pi back-bonding into the pi antibonding orbital of NO, which shifts significant charge from the formally t(2)(6) low-spin metal to the coordinated NO.

Mycobacterium tuberculosis KatG(S315T) catalase-peroxidase retains all active site properties for proper catalytic function

Mycobacterium tuberculosis (Mtb) KatG is a catalase-peroxidase that is thought to activate the antituberculosis drug isoniazid (INH). The local environment of Mtb KatG and its most prevalent INH-resistant mutant, KatG(S315T), is investigated with the exogenous ligands CO and NO in the absence and presence of INH by using resonance Raman, FTIR, and transient absorption spectroscopy. The Fe-His stretching vibration is detected at 244 cm(-)(1) in the ferrous forms of both the wild-type enzyme and KatG(S315T). The ferrous-CO complex of both enzymes exhibits nu(CO), nu(Fe-CO), and delta(Fe-C-O) vibrations at 1925, 525, and 586 cm(-)(1), respectively, indicating a positive electrostatic environment for the CO complex, which is probably weakly hydrogen-bonded to a distal residue. The CO geometry is nonlinear as indicated by the unusually high intensity of the Fe-C-O bending vibration. The nu(Fe(III)-NO) and delta(Fe(III)-N-O) vibrations are detected at 596 and 571 cm(-)(1), respectively, in the ferric forms of wild-type and mutant enzyme and are indicative of a nonlinear binding geometry in support of the CO data. Although the presence of INH does not affect the vibrational frequencies of the CO- and NO-bound forms of either enzyme, it seems to perturb slightly their Raman intensities. Our results suggest a minimal, if any, perturbation of the distal heme pocket in the S315T mutant. Instead, the S315T mutation seems to induce small changes in the KatG conformation/dynamics of the ligand access channel as indicated by CO rebinding kinetics in flash photolysis experiments. The implications of these findings for the catalytic mechanism and mechanism of INH resistance in KatG(S315T) are discussed.

Fe−N−O Structure and Bonding in Six-Coordinate {FeNO}6 Porphyrinates Containing Imidazole: Implications for Reactivity of Coordinated NO

We report density functional theory calculations on six-coordinate ferric-NO ({FeNO}6) porphyrinates that contain either imidazole or imidazolate as the trans axial ligand. Our results show that the sensitivities of the Fe-NO and N-O stretching frequencies to cis and trans influences are directly correlated. In other words, as one decreases so does the other for both the imidazole and the imidazolate complexes. This correlation is opposite that of the isoelectronic ferrous-CO systems, whose Fe-CO and C-O frequencies are well-known to be inversely correlated. Based on the results of our calculations, the molecular origin of the direct correlation in {FeNO}6 porphyrinates can be explained by trends in the electron density distributions within the HOMO or HOMO-1, which exhibits Fe-NO and N-O pi-antibonding character. Variability in the Fe-N-O pi-antibonding character of the HOMO or the HOMO-1 modulates the angleFeNO as well as the Fe-NO and N-O bond strengths in concert. Orbital interactions in the six-coordinate FeIIINO porphyrin complexes are compared and contrasted with those of the isoelectronic FeIICO analogues, and an overall view of {FeNO}6 bonding in these complexes is set forth.

Resonance Raman Investigation of the Specific Sensing Mechanism of a Target Molecule by Gas Sensory Proteins

Specific sensing of gas molecules such as CO, NO, and O2 is a unique function of gas sensory hemoproteins, while hemoproteins carry out a wide variety of functions such as oxygen storage/transport, electron transfer, and catalysis as enzymes. It is important in gas sensory proteins that the heme domain not only recognizes its target molecule but also discriminates against other gases having similar molecular structures. Coordination of a target molecule to the heme is assumed to alter the protein conformation in the vicinity of heme, and the conformation change is propagated to the effector domain where substrate turnover, DNA binding, or interaction with a signal transduction protein is performed differently than the binding of other gases. To understand the appearance of such a specificity, we focus our attention on the ligand-protein interactions in the distal side of heme. In practice, the metal-ligand vibrations as well as internal modes of ligand and heme are measured with resonance Raman spectroscopy for wild-type and some mutant proteins with full-length or limited sensory regions. On the basis of such observations together with the knowledge currently available, we discuss the mechanism of specific sensing of a diatomic molecule in gas sensory proteins.

Nitric-oxide reductase. Structure and properties of the catalytic site from resonance Raman scattering

We have applied resonance Raman spectroscopy to investigate the properties of the dinuclear center of oxidized, reduced, and NO-bound nitric-oxide reductase from Paracoccus denitrificans. The spectra of the oxidized enzyme show two distinct nu(as)(Fe-O-Fe) modes at 815 and 833 cm(-1) of the heme/non-heme diiron center. The splitting of the Fe-O-Fe mode suggests that two different conformations (open and closed) are present in the catalytic site of the enzyme. We find evidence from deuterium exchange experiments that in the dominant conformation (833 cm(-1) mode, closed), the Fe-O-Fe unit is hydrogen-bonded to distal residue(s). The ferric nitrosyl complex of nitric-oxide reductase exhibits the nu(Fe(3+)-NO) and nu(N-O) at 594 and 1904 cm(-1), respectively. The nitrosyl species we detect is photolabile and can be photolyzed to generate a new form of oxidized enzyme in which the proximal histidine is ligated to heme b(3), in contrast to the resting form. Photodissociation of the NO ligand yields a five-coordinate high-spin heme b(3). Based on the findings reported here, the structure and properties of the dinuclear center of nitric- oxide reductase in the oxidized, reduced, and NO-bound form as well as its photoproduct can be described with certainty.