The hydroxide complex of Pseudomonas aeruginosa heme oxygenase as a model of the low-spin iron(III) hydroperoxide intermediate in heme catabolism: 13C NMR spectroscopic studies suggest the active participation of the heme in macrocycle hydroxylation

13C NMR spectroscopic studies have been conducted with the hydroxide complex of Pseudomonas aeruginosa heme oxygenase (Fe(III)-OH), where OH(-) has been used as a model of the OOH(-) ligand to gain insights regarding the elusive ferric hydroperoxide (Fe(III)-OOH) intermediate in heme catabolism at ambient temperatures. Analysis of the heme core carbon resonances revealed that the coordination of hydroxide in the distal site of the enzyme results in the formation of at least three populations of Fe(III)-OH complexes with distinct electronic configurations and nonplanar ring distortions that are in slow exchange relative to the NMR time scale. The most abundant population exhibits a spin crossover between S = (1)/(2) and S = (3)/(2) spin states, and the two less abundant populations exhibit pure, S = (3)/(2) and S = (1)/(2), (d(xy)())(1) electronic configurations. We propose that the highly organized network of water molecules in the distal pocket of heme oxygenase, by virtue of donating a hydrogen bond to the coordinated hydroxide ligand, lowers its ligand field strength, thereby increasing the field strength of the porphyrin (equatorial) ligand, which results in nonplanar deformations of the macrocycle. This tendency to deform from planarity, which is imparted by the ligand field strength of the coordinated OH(-), is likely reinforced by the flexibility of the distal pocket in HO. These findings suggest that if the ligand field strength of the coordinated OOH(-) in heme oxygenase is modulated in a similar manner, the resultant large spin density at the meso carbons and nonplanar deformations of the pophyrin ring prime the macrocycle to actively participate in its own hydroxylation.     

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.     

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.     

Quantum mechanical/molecular mechanical study of mechanisms of heme degradation by the enzyme heme oxygenase: the strategic function of the water cluster

Heme degradation by heme oxygenase (HO) enzymes is important in maintaining iron homeostasis and prevention of oxidative stress, etc. In response to mechanistic uncertainties, we performed quantum mechanical/molecular mechanical investigations of the heme hydroxylation by HO, in the native route and with the oxygen surrogate donor H2O2. It is demonstrated that H2O2 cannot be deprotonated to yield Fe(III)OOH, and hence the surrogate reaction starts from the FeHOOH complex. The calculations show that, when starting from either Fe(III)OOH or Fe(III)HOOH, the fully concerted mechanism involving O-O bond breakage and O-C(meso) bond formation is highly disfavored. The low-energy mechanism involves a nonsynchronous, effectively concerted pathway, in which the active species undergoes first O-O bond homolysis followed by a barrier-free (small with Fe(III)HOOH) hydroxyl radical attack on the meso position of the porphyrin. During the reaction of Fe(III)HOOH, formation of the Por+*FeIV=O species, compound I, competes with heme hydroxylation, thereby reducing the efficiency of the surrogate route. All these conclusions are in accord with experimental findings (Chu, G. C.; Katakura, K.; Zhang, X.; Yoshida, T.; Ikeda-Saito, M. J. Biol. Chem. 1999, 274, 21319). The study highlights the role of the water cluster in the distal pocket in creating "function" for the enzyme; this cluster affects the O-O cleavage and the O-Cmeso formation, but more so it is responsible for the orientation of the hydroxyl radical and for the observed alpha-meso regioselectivity of hydroxylation (Ortiz de Montellano, P. R. Acc. Chem. Res. 1998, 31, 543). Differences/similarities with P450 and HRP are discussed.     

铁卟啉催化二乙基亚硝胺羟基化的反应机理

采用密度泛函理论(DFT)对P450酶活性中心铁卟啉Cpd I催化二乙基亚硝胺(NDEA)代谢活化的反应机理进行了研究.结果表明,Cpd I催化NDEA羟基化的过程包含氢抽提反应和回弹反应2个步骤.其中,氢抽提反应为控速步骤,氢自由基从NDEA转移到铁卟啉的Fe O上,是典型的氢原子传递(HAT)过程;紧接着铁卟啉上的羟基经历无能垒的反应过程回弹到NDEA自由基上,形成羟基化代谢产物.NDEA羟基化过程中高自旋态(HS)和低自旋态(LS)均参与反应,整个羟基化过程呈现明显的双态反应性(TSR).研究比较了NDEA分子侧链上Cα—H和Cβ—H羟基化反应的差异,得到Cα—H和Cβ—H羟基化所需跨越的能垒分别为57.7/57.7 k J/mol(LS/HS)和76.4/74.3 k J/mol(LS/HS),表明Cα—H比Cβ—H更易于在P450作用下发生羟基化;此外,Cβ—H羟基化所需克服的能垒并未过高,使得Cβ—H羟基化在生理条件下完全也有可能发生.本研究为深入揭示亚硝胺经代谢活化导致癌症的作用机制提供了可靠的理论依据.     

How heme metabolism occurs in heme oxygenase: computational study of oxygen-donation ability of the oxo and hydroperoxo species

We report a density functional theory study on the heme metabolism in heme oxygenase using iron-hydroperoxo and -oxo models. The activation energies for heme oxidation at the alpha-carbon by the iron-hydroperoxo and -oxo species are calculated to be 42.9 and 39.9 kcal/mol, respectively. These high activation barriers lead us to reconsider the catalytic mechanism of heme oxygenase     

Oxidation of heme to beta- and delta-biliverdin by Pseudomonas aeruginosa heme oxygenase as a consequence of an unusual seating of the heme

The origin of the unusual regioselectivity of heme oxygenation, i.e. the oxidation of heme to delta-biliverdin (70%) and beta-biliverdin (30%), that is exhibited by heme oxygenase from Pseudomonas aeruginosa (pa-HO) has been studied by (1)H NMR, (13)C NMR, and resonance Raman spectroscopies. Whereas resonance Raman indicates that the heme-iron ligation in pa-HO is homologous to that observed in previously studied alpha-hydroxylating heme oxygenases, the NMR spectroscopic studies suggest that the heme in this enzyme is seated in a manner that is distinct from that observed for all other alpha-hydroxylating heme oxygenase enzymes for which a structure is known. In pa-HO, the heme is rotated in-plane approximately 110 degrees, so the delta-meso-carbon of the major orientational isomer is located within the HO-fold in the place where the alpha-hydroxylating enzymes typically place the alpha-meso-carbon. The unusual heme seating displayed by pa-HO places the heme propionates so that these groups point in the direction of the solvent-exposed heme edge and appears to originate in large part from the absence of stabilizing interactions between the polypeptide and the heme propionates, which are typically found in alpha-hydroxylating heme oxygenase enzymes. These interactions typically involve Lys-16 and Tyr-112, in Neisseriae meningitidis HO, and Lys-16 and Tyr-134, in human and rat HO-1. The corresponding residues in pa-HO are Asn-19 and Phe-117, respectively. In agreement with this hypothesis, we found that the Asn-19 Lys/Phe-117 Tyr double mutant of pa-HO exists as a mixture of molecules exhibiting two distinct heme seatings; one seating is identical to that exhibited by wild-type pa-HO, whereas the alternative seating is very similar to that typical of alpha-hydroxylating heme oxygenase enzymes and is related to the wild-type seating by approximately 110 degrees in-plane rotation of the heme. Furthermore, each of these heme seatings in the pa-HO double mutant gives rise to a subset of two heme isomeric orientations that are related to each other by 180 degrees rotation about the alpha-gamma-meso-axis. The coexistence of these molecules in solution, in the proportions suggested by the corresponding area under the peaks in the (1)H NMR spectrum, explains the unusual regioselectivity of heme oxygenation observed with the double mutant, which we found produces alpha- (55%), delta- (35%), and beta-biliverdin (10%). Alpha-biliverdin is obtained by oxidation of the heme seated similar to that of alpha-hydroxylating enzymes, whereas beta- and delta-biliverdin are formed from the oxidation of heme seated as in wild-type pa-HO.     

Effects of a nonplanar porphyrin rings on the spin-spin interactions in low-spin ferric porphyrin radical cationst

Low-spin ferric porphyrin radical cations formed by the oxidation of chloro(meso-tetraalkylporphyrinato)iron(III) followed by the addition of bulky 2-methylimidazole show antiferromagnetic coupling, which is interpreted in terms of the interaction between porphyrin a2u and iron d(xy), orbitals caused by the S4 ruffling of the porphyrin core.     

A strategic approach for the synthesis of new porphyrin rings, attractive for heme model purpose

Novel complexes have been efficiently synthesized with a facile route using two different atropisomers of the same porphyrin. These compounds feature a tridentate binding site, a tyrosine molecule, and a proximal base, all bound to the porphyrin ring in different fashions, making them attractive for heme modeling purposes.     

A strategy for the stepwise ring annulation of all four pyrrolic rings of a porphyrin

The repeated introduction of an a-dione unit and its reaction with an arene-1,2-diamine allows the stepwise annulation of all four pyrrolic rings of a porphyrin, as is demonstrated by the synthesis of a trisquinoxalinoporphyrin, a tetrakisquinoxalinoporphyrin and the more elaborated bisporphyrin.     

The hydrogen-bonding network in heme oxygenase also functions as a modulator of enzyme dynamics: chaotic motions upon disrupting the H-bond network in heme oxygenase from Pseudomonas aeruginosa

Relaxation compensated Carr-Purcell-Meiboom-Gill (rc-CPMG) NMR experiments have been used to investigate micros-ms motions in heme oxygenase from Pseudomonas aeruginosa (pa-HO) in its ferric state, inhibited by CN- (pa-HO-CN) and N3- (pa-HO-N3), and in its ferrous state, inhibited by CO (pa-HO-CO). Comparative analysis of the data from the three forms indicates that the nature of the coordinated distal ligand affects the micros-ms conformational freedom of the polypeptide in regions of the enzyme far removed from the heme iron and distal ligand. Interpretation of the dynamical information in the context of the crystal structure of resting state pa-HO shows that residues involved in the network of structural hydrogen-bonded waters characteristic of HOs undergo micros-ms motions in pa-HO-CN, which was studied as a model of the highly paramagnetic S = 5/2 resting state form. In comparison, similar motions are suppressed in the pa-HO-CO and pa-HO-N3 complexes, which were studied as mimics of the obligatory oxyferrous and ferric hydroperoxide intermediates, respectively, in the catalytic cycle of heme degradation. These findings suggest that in addition to proton delivery to the nascent Fe(III)-OO(-) intermediate during catalysis, the hydrogen-bonding network serves two additional roles: (i) propagate the electronic state (reactive state) in each of the distinct steps of the catalytic cycle to key but remote sections of the polypeptide via small rearrangements in the network of hydrogen bonds and (ii) modulate the conformational freedom of the enzyme, thus allowing it to adapt to the demanding changes in axial coordination state and substrate transformations that take place during the catalytic cycle. This idea was probed by disrupting the hydrogen-bonding network in pa-HO by replacing R80 with L. NMR spectroscopic studies conducted with R80L-pa-HO-N3 and R80L-pa-HO-CO revealed that the mutant exhibits nearly global conformational disorder, which is absent in the equivalent complexes of the wild type enzyme. The "chaotic" disorder in the R80L mutant is likely related to its significantly lower efficiency to hydroxylate heme in the presence of H2O2, relative to the wild type enzyme.     

Thermal degradation mechanism of poly(arylene sulfone)s by stepwise Py‐GC/MS

The thermal degradation of poly(ether sulfone) (PES) and polysulfone (PSF) was studied with a combination of thermogravimetric analysis and stepwise pyrolysis–gas chromatography/mass spectrometry techniques with consecutive heating of the samples at fixed temperature intervals (100 °C) to achieve narrow‐temperature pyrolysis conditions. The individual mass chromatograms of various pyrolysates were correlated with pyrolysis temperatures to elucidate the pyrolysis mechanism. The major mechanism for both PES and PSF was a one‐stage pyrolysis involving main‐chain random scission and carbonization. The major products SO₂ and phenol were released from the sulfone and ether groups in PES. The major products SO₂, phenol, and 1‐methyl‐4‐phenoxybenzene were released from the sulfone, ether, and isopropylene groups in PSF. In the PES, the thermal stability of the sulfone and ether groups was identical to the maximum thermogravimetric loss rate. In the PSF, the thermal stability was in the following order: sulfone < ether < isopropylene. The temperature of the maximum thermogravimetric loss rate was similar to the maximum evolution of phenol. However, there was a considerable difference in the thermal behavior of both polymers; the correlation of the polymer structure to the degradation mechanism is discussed. © 2000 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 38: 583–593, 2000     

Evaluation of degradation mechanism of chlorhexidine by means of Density Functional Theory calculations

Chlorhexidine (CHD), a germicidal drug, has degradation products that can be hemotoxic and carcinogenic. However, there is no consensus in literature about the degradation pathway. In order to shed light on that mechanism, we have employed Density Functional Theory to study reactants, in different protonation states, products and intermediates involved in the different pathways. Based on free energy values comparison and frontier molecular orbital analysis, we have obtained the most stable structures in each protonation state. CHD in saturated form has HOMO localized in one p-chloroaniline, and, due to molecule’s symmetry, HOMO-1 has contributions from the other side of the molecule, but mainly from the biguanide portion of the molecule, instead of from the p-chloroaniline. For the saturated form, we have studied two possible degradation pathways, starting from the monoprotonated structure, and three pathways starting from the neutral structure. We found out that the mechanisms proposed in literature, whose pathways lead to p-chloroaniline (PCA) formation in a smaller number of steps, are more likely than the mechanisms with more intermediate steps or pathways that do not predict PCA formation. Also, based on free energy results, we have found that the formation of another sub-product (PBG-AU) is favorable as well.     

13C NMR spectroscopy of core heme carbons as a simple tool to elucidate the coordination state of ferric high-spin heme proteins

Evidence is presented demonstrating that the magnitudes of the 13C chemical shifts originating from heme meso carbons provide a straightforward diagnostic tool to elucidate the coordination state of high-spin heme proteins and enzymes. Pentacoordinate high-spin heme centers exhibit 13C meso shifts centered at approximately 250 ppm, whereas their hexacoordinate counterparts exhibit 13C shifts centered at approximately -80 ppm. The relatively small spectral window (400 to -100 ppm) covering the meso-13C shifts, the relatively narrow lines of these resonances, and the availability of biosynthetic methods to prepare 13C-labeled heme (Rivera, M.; Walker, F. A. Anal. Biochem. 1995, 230, 295-302) make this approach practical. The theoretical basis for the distinct chemical shifts observed for meso carbons from hexacoordinate high-spin hemes relative to their pentacoordinate counterparts are now well understood (Cheng, R.-J.; Chen, P. Y.; Lovell, T.; Liu, T.; Noodleman, L.; Case, D. A. J. Am. Chem. Soc. 2003, 125, 6774-6783), which indicates that the magnitude of the meso-carbon chemical shifts can be used as a simple and reliable diagnostic tool for determining the coordination state of the heme active sites, independent of the nature of the proximal ligand. Proof of the principle for the 13C NMR spectroscopic approach is demonstrated using hexa- and pentacoordinate myoglobin. Subsequently, 13C NMR spectroscopy has been used to unambiguously determine that a recently discovered heme protein from Shigella dysenteriae (ShuT) is pentacoordinate.     

Kinetics and mechanism of alkane hydroperoxidation with tert-butyl hydroperoxide catalysed by a vanadate anion

tert-Butyl hydroperoxide oxidizes alkanes in acetonitrile at 60 degrees C if the soluble vanadium(v) salt, n-Bu4NVO3, is used as a catalyst. Alkyl hydroperoxides are formed as main products which decompose during the course of the reaction to produce the more stable corresponding alcohols and ketones. Turnover numbers (ie. numbers of moles of products per one mole of a catalyst) attained 250. The kinetics and selectivity of the reaction have been studied. The mechanism proposed involves the formation of a complex between the V(V) species and t-BuOOH (K5 was estimated to be 5 dm3 mol(-1)) followed by decomposition of this complex (k6 = 0.2 s(-1)). The generated V(IV) species reacts with another t-BuOOH molecule to produce an active t-BuO* radical which attacks the hydrocarbon.     

Proton delivery to ferryl heme in a heme peroxidase: enzymatic use of the Grotthuss mechanism

We test the hypothesized pathway by which protons are passed from the substrate, ascorbate, to the ferryl oxygen in the heme enzyme ascorbate peroxidase (APX). The role of amino acid side chains and bound solvent is demonstrated. We investigated solvent kinetic isotope effects (SKIE) for the wild-type enzyme and several site-directed replacements of the key residues which form the proposed proton path. Kinetic constants for H(2)O(2)-dependent enzyme oxidation to Compound I, k(1), and subsequent reduction of Compound II, k(3), were determined in steady-state assays by variation of both H(2)O(2) and ascorbate concentrations. A high value of the SKIE for wild type APX ((D)k(3) = 4.9) as well as a clear nonlinear dependence on the deuterium composition of the solvent in proton inventory experiments suggest the simultaneous participation of several protons in the transition state for proton transfer. The full SKIE and the proton inventory data were modeled by applying Gross-Butler-Swain-Kresge theory to a proton path inferred from the known structure of APX. The model has been tested by constructing and determining the X-ray structures of the R38K and R38A variants and accounts for their observed SKIEs. This work confirms APX uses two arginine residues in the proton path. Thus, Arg38 and Arg172 have dual roles, both in the formation of the ferryl species and binding of ascorbate respectively and to facilitate proton transfer between the two.     

Models of the low-spin iron(III) hydroperoxide intermediate of heme oxygenase: magnetic resonance evidence for thermodynamic stabilization of the d(xy) electronic state at ambient temperatures

The (13)C pulsed ENDOR and NMR study of [meso-(13)C-TPPFe(OCH(3))(OO(t)Bu)](-) performed in this work shows that although the unpaired electron in low-spin ferrihemes containing a ROO(-) ligand resides in a d(pi) orbital at 8 K, the d(xy) electron configuration is favored at physiological temperatures. The variable temperature NMR spectra indicate a dynamic situation in which a heme with a d(pi) electron configuration and planar porphyrinate ring is in equilibrium with a d(xy) electron configuration that has a ruffled porphyrin ring. Because of the similarity in the EPR spectra of the hydroperoxide complexes of heme oxygenase, cytochrome P450, and the model heme complex reported herein, it is possible that these two electron configurations and ring conformations may also exist in equilibrium in the enzymatic systems. The ruffled porphyrinate ring would aid the attack of the terminal oxygen of the hydroperoxide intermediate of heme oxygenase (HO) on the meso-carbon, and the large spin density at the meso-carbons of a d(xy) electron configuration heme suggests the possibility of a radical mechanism for HO. The dynamic equilibrium between the ruffled (d(xy)) and planar (d(pi)) conformers observed in the model complexes also suggests that a flexible heme binding cavity may be an important structural motif for heme oxygenase activity.