Cytochrome P450cam and its complexes. Mössbauer parameters of the heme iron

Resonance Raman Characterization of O2-Binding Heme Proteins

A vast array of critical in vivo processes and pathways are dependent on a multitude of O₂-binding heme proteins which contain a diverse range of functions. Resonance Raman (rR) spectroscopy is an ideal technique for structural investigation of these proteins, providing information about the geometry of the Fe-O-O fragment and its electrostatic interactions with the distal active site. Characterization of these oxy adducts is an endeavor that is complicated by their instability for many heme proteins in solution, an obstacle which can be overcome by applying the rR technique to cryogenically frozen samples. We describe here how to measure rR spectra of heme proteins with stable oxy forms, as well as the technical adaptations required to measure unstable samples at 77 K.

Mössbauer-based molecular-level decomposition of the Saccharomyces cerevisiae ironome, and preliminary characterization of isolated nuclei

One hundred proteins in Saccharomyces cerevisiae are known to contain iron. These proteins are found mainly in mitochondria, cytosol, nuclei, endoplasmic reticula, and vacuoles. Cells also contain non-proteinaceous low-molecular-mass labile iron pools (LFePs). How each molecular iron species interacts on the cellular or systems' level is underdeveloped as doing so would require considering the entire iron content of the cell-the ironome. In this paper, Mössbauer (MB) spectroscopy was used to probe the ironome of yeast. MB spectra of whole cells and isolated organelles were predicted by summing the spectral contribution of each iron-containing species in the cell. Simulations required input from published proteomics and microscopy data, as well as from previous spectroscopic and redox characterization of individual iron-containing proteins. Composite simulations were compared to experimentally determined spectra. Simulated MB spectra of non-proteinaceous iron pools in the cell were assumed to account for major differences between simulated and experimental spectra of whole cells and isolated mitochondria and vacuoles. Nuclei were predicted to contain ∼30 μM iron, mostly in the form of [Fe4S4] clusters. This was experimentally confirmed by isolating nuclei from 57Fe-enriched cells and obtaining the first MB spectra of the organelle. This study provides the first semi-quantitative estimate of all concentrations of iron-containing proteins and non-proteinaceous species in yeast, as well as a novel approach to spectroscopically characterizing LFePs.

Isolating Fe-O2 Intermediates in Dioxygen Activation by Iron Porphyrin Complexes

Dioxygen (O₂) is an environmentally benign and abundant oxidant whose utilization is of great interest in the design of bioinspired synthetic catalytic oxidation systems to reduce energy consumption. However, it is unfortunate that utilization of O₂ is a significant challenge because of the thermodynamic stability of O₂ in its triplet ground state. Nevertheless, nature is able to overcome the spin state barrier using enzymes, which contain transition metals with unpaired d-electrons facilitating the activation of O₂ by metal coordination. This inspires bioinorganic chemists to synthesize biomimetic small-molecule iron porphyrin complexes to carry out the O₂ activation, wherein Fe-O₂ species have been implicated as the key reactive intermediates. In recent years, a number of Fe-O₂ intermediates have been synthesized by activating O₂ at iron centers supported on porphyrin ligands. In this review, we focus on a few examples of these advances with emphasis in each case on the particular design of iron porphyrin complexes and particular reaction environments to stabilize and isolate metal-O₂ intermediates in dioxygen activation, which will provide clues to elucidate structures of reactive intermediates and mechanistic insights in biological processes.

The Chemical Basis of Intracerebral Hemorrhage and Cell Toxicity With Contributions From Eryptosis and Ferroptosis

Intracerebral hemorrhage (ICH) is a particularly devastating event both because of the direct injury from space-occupying blood to the sequelae of the brain exposed to free blood components from which it is normally protected. Not surprisingly, the usual metabolic and energy pathways are overwhelmed in this situation. In this review article, we detail the complexity of red blood cell degradation, the contribution of eryptosis leading to hemoglobin breakdown into its constituents, the participants in that process, and the points at which injury can be propagated such as elaboration of toxic radicals through the metabolism of the breakdown products. Two prominent products of this breakdown sequence, hemin, and iron, induce a variety of pathologies including free radical damage and DNA breakage, which appear to include events independent from typical oxidative DNA injury. As a result of this confluence of damaging elements, multiple pathways of injury, cell death, and survival are likely engaged including ferroptosis (which may be the same as oxytosis but viewed from a different perspective) and senescence, suggesting that targeting any single cause will likely not be a sufficient strategy to maximally improve outcome. Combination therapies in addition to safe methods to reduce blood burden should be pursued.

One small step for cytochrome P450 in its catalytic cycle, one giant leap for enzymology

The intermediates operating in the cytochrome P450 catalytic cycle have been investigated for more than half a century, fascinating many enzymologists. Each intermediate has its unique role to carry out diverse oxidations. Natural time course of the catalytic cycle is quite fast, hence, not all of the reactive intermediates could be isolated during physiological catalysis. Different high-valent iron intermediates have been proposed as primary oxidants: the candidates are compound 0 (Cpd 0, [FeOOH][Formula: see text]P450) and compound I (Cpd I, Fe(IV)[Formula: see text]O por[Formula: see text]P450). Among them, the role of Cpd I in hydroxylation is fairly well understood due the discovery of the peroxide shunt. This review endeavors to put the outstanding research efforts conducted to isolate and characterize the intermediates together. In addition to spectral features of each intermediate in the catalytic cycle, the oxidizing powers of Cpd 0 and Cpd I will be discussed along with most recent scientific findings.

Specificity and mechanism of carbohydrate demethylation by cytochrome P450 monooxygenases

Degradation of carbohydrates by bacteria represents a key step in energy metabolism that can be inhibited by methylated sugars. Removal of methyl groups, which is critical for further processing, poses a biocatalytic challenge because enzymes need to overcome a high energy barrier. Our structural and computational analysis revealed how a member of the cytochrome P450 family evolved to oxidize a carbohydrate ligand. Using structural biology, we ascertained the molecular determinants of substrate specificity and revealed a highly specialized active site complementary to the substrate chemistry. Invariance of the residues involved in substrate recognition across the subfamily suggests that they are critical for enzyme function and when mutated, the enzyme lost substrate recognition. The structure of a carbohydrate-active P450 adds mechanistic insight into monooxygenase action on a methylated monosaccharide and reveals the broad conservation of the active site machinery across the subfamily.

Synthetic Fe/Cu Complexes: Toward Understanding Heme-Copper Oxidase Structure and Function

Heme-copper oxidases (HCOs) are terminal enzymes on the mitochondrial or bacterial respiratory electron transport chain, which utilize a unique heterobinuclear active site to catalyze the 4H+/4e- reduction of dioxygen to water. This process involves a proton-coupled electron transfer (PCET) from a tyrosine (phenolic) residue and additional redox events coupled to transmembrane proton pumping and ATP synthesis. Given that HCOs are large, complex, membrane-bound enzymes, bioinspired synthetic model chemistry is a promising approach to better understand heme-Cu-mediated dioxygen reduction, including the details of proton and electron movements. This review encompasses important aspects of heme-O2 and copper-O2 (bio)chemistries as they relate to the design and interpretation of small molecule model systems and provides perspectives from fundamental coordination chemistry, which can be applied to the understanding of HCO activity. We focus on recent advancements from studies of heme-Cu models, evaluating experimental and computational results, which highlight important fundamental structure-function relationships. Finally, we provide an outlook for future potential contributions from synthetic inorganic chemistry and discuss their implications with relevance to biological O2-reduction.

The relationships between cytochromes P450 and H2O2: Production, reaction, and inhibition

In this review we address the relationship between cytochromes P450 (P450) and H2O2. This association can affect biology in three distinct ways. First, P450s produce H2O2 as a byproduct either during catalysis or when no substrate is present. This reaction, known as uncoupling, releases reactive oxygen species that may have implications in disease. Second, H2O2 is used as an oxygen-donating co-substrate in peroxygenase and peroxidase reactions catalyzed by P450s. This activity has proven to be important mainly in reactions involving prokaryotic P450s, and investigators have harnessed this reaction with the aim of adaptation for industrial use. Third, H2O2-dependent inhibition of human P450s has been studied in our laboratory, demonstrating heme destruction and also the inactivating oxidation of the heme-thiolate ligand to a sulfenic acid (-SOH). This reversible oxidative modification of P450s may have implications in the prevention of uncoupling and may give new insights into the oxidative regulation of these enzymes. Research has elucidated many of the chemical mechanisms involved in the relationship between P450 and H2O2, but the application to biology is difficult to evaluate. Further studies are needed reveal both the harmful and protective natures of reactive oxygen species in an organismal context.

[Methods for determining of cytochrome P450 isozymes functional activity]

The review is dedicated to modern methods and technologies for determining of cytochrome P450 isozymes functional activity, such as absorbance and fluorescent spectroscopy, electron paramagnetic resonance (EPR), nuclear magnetic resonance (NMR), Raman, Mossbauer, and X-ray spectroscopy, surface plasmon resonance (SPR), atomic force microscopy (AFM). Methods of molecular genetic analysis were reviewed from personalized medicine point of view. The use of chromate-mass-spectrometric methods for cytochrome P450-dependent catalytic reactions' products was discussed. The review covers modern electrochemical systems based on cytochrome P450 isozymes for their catalytic activity analysis, their use in practice and further development perspectives for experimental pharmacology, biotechnology and translational medicine.

Oxygen Activation and Radical Transformations in Heme Proteins and Metalloporphyrins

As a result of the adaptation of life to an aerobic environment, nature has evolved a panoply of metalloproteins for oxidative metabolism and protection against reactive oxygen species. Despite the diverse structures and functions of these proteins, they share common mechanistic grounds. An open-shell transition metal like iron or copper is employed to interact with O2 and its derived intermediates such as hydrogen peroxide to afford a variety of metal-oxygen intermediates. These reactive intermediates, including metal-superoxo, -(hydro)peroxo, and high-valent metal-oxo species, are the basis for the various biological functions of O2-utilizing metalloproteins. Collectively, these processes are called oxygen activation. Much of our understanding of the reactivity of these reactive intermediates has come from the study of heme-containing proteins and related metalloporphyrin compounds. These studies not only have deepened our understanding of various functions of heme proteins, such as O2 storage and transport, degradation of reactive oxygen species, redox signaling, and biological oxygenation, etc., but also have driven the development of bioinorganic chemistry and biomimetic catalysis. In this review, we survey the range of O2 activation processes mediated by heme proteins and model compounds with a focus on recent progress in the characterization and reactivity of important iron-oxygen intermediates. Representative reactions initiated by these reactive intermediates as well as some context from prior decades will also be presented. We will discuss the fundamental mechanistic features of these transformations and delineate the underlying structural and electronic factors that contribute to the spectrum of reactivities that has been observed in nature as well as those that have been invented using these paradigms. Given the recent developments in biocatalysis for non-natural chemistries and the renaissance of radical chemistry in organic synthesis, we envision that new enzymatic and synthetic transformations will emerge based on the radical processes mediated by metalloproteins and their synthetic analogs.

Spectroscopic studies of the cytochrome P450 reaction mechanisms

The cytochrome P450 monooxygenases (P450s) are thiolate heme proteins that can, often under physiological conditions, catalyze many distinct oxidative transformations on a wide variety of molecules, including relatively simple alkanes or fatty acids, as well as more complex compounds such as steroids and exogenous pollutants. They perform such impressive chemistry utilizing a sophisticated catalytic cycle that involves a series of consecutive chemical transformations of heme prosthetic group. Each of these steps provides a unique spectral signature that reflects changes in oxidation or spin states, deformation of the porphyrin ring or alteration of dioxygen moieties. For a long time, the focus of cytochrome P450 research was to understand the underlying reaction mechanism of each enzymatic step, with the biggest challenge being identification and characterization of the powerful oxidizing intermediates. Spectroscopic methods, such as electronic absorption (UV-Vis), electron paramagnetic resonance (EPR), nuclear magnetic resonance (NMR), electron nuclear double resonance (ENDOR), Mössbauer, X-ray absorption (XAS), and resonance Raman (rR), have been useful tools in providing multifaceted and detailed mechanistic insights into the biophysics and biochemistry of these fascinating enzymes. The combination of spectroscopic techniques with novel approaches, such as cryoreduction and Nanodisc technology, allowed for generation, trapping and characterizing long sought transient intermediates, a task that has been difficult to achieve using other methods. Results obtained from the UV-Vis, rR and EPR spectroscopies are the main focus of this review, while the remaining spectroscopic techniques are briefly summarized. This article is part of a Special Issue entitled: Cytochrome P450 biodiversity and biotechnology, edited by Erika Plettner, Gianfranco Gilardi, Luet Wong, Vlada Urlacher, Jared Goldstone.

Catalytic strategy for carbon-carbon bond scission by the cytochrome P450 OleT

OleT is a cytochrome P450 that catalyzes the hydrogen peroxide-dependent metabolism of Cn chain-length fatty acids to synthesize Cn-1 1-alkenes. The decarboxylation reaction provides a route for the production of drop-in hydrocarbon fuels from a renewable and abundant natural resource. This transformation is highly unusual for a P450, which typically uses an Fe(4+)-oxo intermediate known as compound I for the insertion of oxygen into organic substrates. OleT, previously shown to form compound I, catalyzes a different reaction. A large substrate kinetic isotope effect (≥8) for OleT compound I decay confirms that, like monooxygenation, alkene formation is initiated by substrate C-H bond abstraction. Rather than finalizing the reaction through rapid oxygen rebound, alkene synthesis proceeds through the formation of a reaction cycle intermediate with kinetics, optical properties, and reactivity indicative of an Fe(4+)-OH species, compound II. The direct observation of this intermediate, normally fleeting in hydroxylases, provides a rationale for the carbon-carbon scission reaction catalyzed by OleT.

A complete volume profile for the reversible binding of camphor to cytochrome P450(cam)

The effect of pressure on the kinetics and thermodynamics of the reversible binding of camphor to cytochrome P450(cam) was studied as a function of the K(+) concentration. The determination of the reaction and activation volumes enabled the construction of the first complete volume profile for the reversible binding of camphor to P450(cam). Although the volume profiles constructed for the reactions conducted at low and high K(+) concentrations are rather similar, and both show a drastic volume increase on going from the reactant to the transition state and a relatively small volume change on going from the transition to the product state, the position of the transition state is largely affected by the K(+) concentration in solution. Similarly, the activation volume determined for the dissociation of camphor is influenced by the presence of K(+), which reflects changes in the ease of water entering the active site of camphor-bound P450(cam) that depends on the K(+) concentration. Careful analysis of the components that contribute to the observed volume changes allowed the estimation of the total number of water molecules expelled to the bulk solvent during the binding of camphor to P450(cam) and the subsequent spin transition. The results are discussed in reference to other studies reported in the literature that deal with the kinetics and thermodynamics of the binding of camphor to P450(cam) under various reaction conditions.

A review of mechanistic studies on aromatase (CYP19) and 17α-hydroxylase-17,20-lyase (CYP17)

In the conventional P-450 dependent hydroxylation reaction, the Fe(III) resting state of the enzyme, by a single electron transfer, is reduced to Fe(II), which reacts with O(2) to produce a Fe(III)-O-O intermediate. The latter following the transfer of another electron furnishes a ferric-peroxyanion, Fe(III)-O-O(-), which after protonation leads to the fission of the O-O bond resulting in the formation of Fe(V)O, the key player in the hydroxylation process. Certain members of the P-450 family, including CYP17 and CYP19, catalyze, at the same active site, not only the hydroxylation process but also an acyl-carbon bond cleavage reaction which has been interpreted to involve the nucleophilic attack of the ferric-peroxyanion, Fe(III)-O-O(-), on the acyl carbon to furnish a tetrahedral intermediate which fragments, leading to acyl-carbon cleavage. Evidence is presented to show that in the case of CYP17 the attack of Fe(III)-O-O(-) on the target carbon is promoted by cytochrome b(5), which acts as a conformational regulator of CYP17. It is this regulation of CYP17 that provides a safety mechanism which ensures that during corticoid biosynthesis, which involves 17α-hydroxylation by CYP17, androgen formation is avoided. Finally, a brief account is presented of the inhibitors, of the two enzymes, which have been designed on the basis of their mechanism of action. Article from the Special issue on 'Targeted Inhibitors'.

Interactions of cytochrome P450s with their ligands

Cytochrome P450s (CYPs) are heme-containing monooxygenases that contribute to an enormous range of enzymatic function including biosynthetic and detoxification roles. This review summarizes recent studies concerning interactions of CYPs with ligands including substrates, inhibitors, and diatomic heme-ligating molecules. These studies highlight the complexity in the relationship between the heme spin state and active site occupancy, the roles of water in directing protein-ligand and ligand-heme interactions, and the details of interactions between heme and gaseous diatomic CYP ligands. Both kinetic and thermodynamic aspects of ligand binding are considered.

Spectroscopic features of cytochrome P450 reaction intermediates

Cytochromes P450 constitute a broad class of heme monooxygenase enzymes with more than 11,500 isozymes which have been identified in organisms from all biological kingdoms [1]. These enzymes are responsible for catalyzing dozens chemical oxidative transformations such as hydroxylation, epoxidation, N-demethylation, etc., with very broad range of substrates [2,3]. Historically these enzymes received their name from 'pigment 450' due to the unusual position of the Soret band in UV-vis absorption spectra of the reduced CO-saturated state [4,5]. Despite detailed biochemical characterization of many isozymes, as well as later discoveries of other 'P450-like heme enzymes' such as nitric oxide synthase and chloroperoxidase, the phenomenological term 'cytochrome P450' is still commonly used as indicating an essential spectroscopic feature of the functionally active protein which is now known to be due to the presence of a thiolate ligand to the heme iron [6]. Heme proteins with an imidazole ligand such as myoglobin and hemoglobin as well as an inactive form of P450 are characterized by Soret maxima at 420nm [7]. This historical perspective highlights the importance of spectroscopic methods for biochemical studies in general, and especially for heme enzymes, where the presence of the heme iron and porphyrin macrocycle provides rich variety of specific spectroscopic markers available for monitoring chemical transformations and transitions between active intermediates of catalytic cycle.

Trapping and spectroscopic characterization of an FeIII-superoxo intermediate from a nonheme mononuclear iron-containing enzyme

Fe(III)-O(2)*(-) intermediates are well known in heme enzymes, but none have been characterized in the nonheme mononuclear Fe(II) enzyme family. Many steps in the O(2) activation and reaction cycle of Fe(II)-containing homoprotocatechuate 2,3-dioxygenase are made detectable by using the alternative substrate 4-nitrocatechol (4NC) and mutation of the active site His200 to Asn (H200N). Here, the first intermediate (Int-1) observed after adding O(2) to the H200N-4NC complex is trapped and characterized using EPR and Mössbauer (MB) spectroscopies. Int-1 is a high-spin (S(1) = 5/2) Fe(III) antiferromagnetically (AF) coupled to an S(2) = 1/2 radical (J ≈ 6 cm(-1) in ). It exhibits parallel-mode EPR signals at g = 8.17 from the S = 2 multiplet, and g = 8.8 and 11.6 from the S = 3 multiplet. These signals are broadened significantly by hyperfine interactions (A((17)O) ≈ 180 MHz). Thus, Int-1 is an AF-coupled species. The experimental observations are supported by density functional theory calculations that show nearly complete transfer of spin density to the bound O(2). Int-1 decays to form a second intermediate (Int-2). MB spectra show that it is also an AF-coupled Fe(III)-radical complex. Int-2 exhibits an EPR signal at g = 8.05 arising from an S = 2 state. The signal is only slightly broadened by (< 3% spin delocalization), suggesting that Int-2 is a peroxo-Fe(III)-4NC semiquinone radical species. Our results demonstrate facile electron transfer between Fe(II), O(2), and the organic ligand, thereby supporting the proposed wild-type enzyme mechanism.

Glutamate–haem ester bond formation is disfavoured in flavocytochrome P450 BM3: characterization of glutamate substitution mutants at the haem site of P450 BM3

Bacillus megaterium flavocytochrome P450 BM3 (CYP102A1) is a biotechnologically important cytochrome P450/P450 reductase fusion enzyme. Mutants I401E, F261E and L86E were engineered near the haem 5-methyl group, to explore the ability of the glutamate carboxylates to form ester linkages with the methyl group, as observed for eukaryotic CYP4 relatives. Although no covalent linkage was detected, mutants displayed marked alterations in substrate/inhibitor affinity, with L86E and I401E mutants having lower Kd values for arachidonic acid and dodecanoic (lauric) acid than WT (wild-type) BM3. All mutations induced positive shifts in haem Fe(III)/Fe(II) potential, with substrate-free I401E (−219 mV) being >170 mV more positive than WT BM3. The elevated potential stimulated FMN-to-haem electron transfer ~2-fold (to 473 s−1) in I401E, and resulted in stabilization of Fe(II)O2 complexes in the I401E and L86E P450s. EPR demonstrated some iron co-ordination by glutamate carboxylate in L86E and F261E mutants, indicating structural plasticity in the haem domains. The Fe(II)O2 complex is EPR-silent, probably resulting from antiferromagnetic coupling between Fe(III) and bound superoxide in a ferric superoxo species. Structural analysis of mutant haem domains revealed modest rearrangements, including altered haem propionate interactions that may underlie the thermodynamic perturbations observed. The mutant flavocytochromes demonstrated WT-like hydroxylation of dodecanoic acid, but regioselectivity was skewed towards ω−3 hydroxydodecanoate formation in F261E and towards ω−1 hydroxydodecanoate production in I401E. Our data point strongly to a likelihood that glutamate–haem linkages are disfavoured in this most catalytically efficient P450, possibly due to the absence of a methylene radical species during catalysis.

Probing the electronic structure of the hemoglobin active center in physiological solutions

Soft-x-ray absorption spectroscopy at the L_{2,3} edge of the iron center in bovine hemoglobin and hemin under physiological conditions is reported for the first time. Spectra of the same compounds in solid form are presented for comparison. Striking differences in the electronic structure of the metalloporphyrin are observed between the liquid and solid compounds. We unambiguously show that hemoglobin and hemin are in a high-spin ferric state in solution, and that the 2p spin-orbit coupling decreases for hemin compared to the hemoglobin, while this is not the case in solids. The spectra were simulated using ligand field multiplet theory, in good agreement with the experiment, allowing quantification of the amount of charge transfer between the porphyrin and Fe3+ ion in hemoglobin and in hemin.

Swapping metals in Fe- and Mn-dependent dioxygenases: evidence for oxygen activation without a change in metal redox state

Biological O(2) activation often occurs after binding to a reduced metal [e.g., M(II)] in an enzyme active site. Subsequent M(II)-to-O(2) electron transfer results in a reactive M(III)-superoxo species. For the extradiol aromatic ring-cleaving dioxygenases, we have proposed a different model where an electron is transferred from substrate to O(2) via the M(II) center to which they are both bound, thereby obviating the need for an integral change in metal redox state. This model is tested by using homoprotocatechuate 2,3-dioxygenases from Brevibacterium fuscum (Fe-HPCD) and Arthrobacter globiformis (Mn-MndD) that share high sequence identity and very similar structures. Despite these similarities, Fe-HPCD binds Fe(II) whereas Mn-MndD incorporates Mn(II). Methods are described to incorporate the nonphysiological metal into each enzyme (Mn-HPCD and Fe-MndD). The x-ray crystal structure of Mn-HPCD at 1.7 A is found to be indistinguishable from that of Fe-HPCD, while EPR studies show that the Mn(II) sites of Mn-MndD and Mn-HPCD, and the Fe(II) sites of the NO complexes of Fe-HPCD and Fe-MndD, are very similar. The uniform metal site structures of these enzymes suggest that extradiol dioxygenases cannot differentially compensate for the 0.7-V gap in the redox potentials of free iron and manganese. Nonetheless, all four enzymes exhibit nearly the same K(M) and V(max) values. These enzymes constitute an unusual pair of metallo-oxygenases that remain fully active after a metal swap, implicating a different way by which metals are used to promote oxygen activation without an integral change in metal redox state.

Combined quantum mechanical/molecular mechanical study on the pentacoordinated ferric and ferrous cytochrome P450cam complexes

The pentacoordinated ferric and ferrous cytochrome P450(cam) complexes have been investigated by combined quantum mechanical/molecular mechanical (QM/MM) calculations in the presence of a protein/solvent environment and by QM calculations on the isolated QM regions with use of density functional theory. The B3LYP functional has been found more reliable than the BLYP and BHLYP functionals for estimating the relative state energies. The B3LYP/CHARMM calculations with an all-electron basis set for iron give high-spin ground states for the title complexes, in agreement with experiment. The comparison of the B3LYP/CHARMM results of the entire protein system with the B3LYP calculations on the naked QM regions shows that the amount of stabilization by the protein environment is largest for the intermediate-spin states, followed by the high-spin states of the complexes. The calculation of Mössbauer parameters in the presence of the enzyme environment confirms the double occupation of the d(xz) orbital in the quintet spin state of the ferrous complex, consistent with the computed QM/MM energies in the enzyme environment, while the d(x)2(-)(y)2 orbital is doubly occupied in the gas-phase quintet state.

Reaction of cytochrome P450BM3 and peroxynitrite yields nitrosyl complex

Peroxynitrite has come into the spotlight in recent years. Its effects on proteins have been implicated in several diseases such as acute lung injury, rheumatoid arthritis, implant rejection, artherosclerosis, Parkinson's disease, and Alzheimer's disease. Peroxynitrite is thought to inactivate a variety of proteins including thiolate-ligated heme proteins such as cytochrome P450 2B1 and PGI2 synthase, through the nitration of tyrosine residues. In previous studies it was reported that thiolate-ligated heme enzymes react with peroxynitrite to form a ferryl intermediate. In an effort to spectroscopically characterize this species in P450BM3, we discovered that the peroxynitrite-generated intermediate is not an FeIVoxo, but rather an iron-nitrosyl [FeNO]6 complex. We present density functional calculations as well as Mössbauer and stopped-flow spectroscopic characterizations of the peroxynitrite-generated intermediate in P450BM3.

Fe L-edge X-ray absorption spectroscopy of low-spin heme relative to non-heme Fe complexes: delocalization of Fe d-electrons into the porphyrin ligand

Hemes (iron porphyrins) are involved in a range of functions in biology, including electron transfer, small-molecule binding and transport, and O2 activation. The delocalization of the Fe d-electrons into the porphyrin ring and its effect on the redox chemistry and reactivity of these systems has been difficult to study by optical spectroscopies due to the dominant porphyrin pi-->pi(*) transitions, which obscure the metal center. Recently, we have developed a methodology that allows for the interpretation of the multiplet structure of Fe L-edges in terms of differential orbital covalency (i.e., differences in mixing of the d-orbitals with ligand orbitals) using a valence bond configuration interaction (VBCI) model. Applied to low-spin heme systems, this methodology allows experimental determination of the delocalization of the Fe d-electrons into the porphyrin (P) ring in terms of both P-->Fe sigma and pi-donation and Fe-->P pi back-bonding. We find that pi-donation to Fe(III) is much larger than pi back-bonding from Fe(II), indicating that a hole superexchange pathway dominates electron transfer. The implications of the results are also discussed in terms of the differences between heme and non-heme oxygen activation chemistry.

Common system setup for the entire catalytic cycle of cytochrome P450cam in quantum mechanical/molecular mechanical studies

We describe a system setup that is applicable to all species in the catalytic cycle of cytochrome P450(cam). The chosen procedure starts from the X-ray coordinates of the ferrous dioxygen complex and follows a protocol that includes the careful assignment of protonation states, comparison between different conceivable hydration schemes, and system preparation through a series of classical minimizations and molecular dynamics (MD) simulations. The resulting setup was validated by quantum mechanical/molecular mechanical (QM/MM) calculations on the resting state, the pentacoordinated ferric and ferrous complexes, Compound I, the transition state and hydroxo intermediate of the C--H hydroxylation reaction, and the product complex. The present QM/MM results are generally consistent with those obtained previously with individual setups. Concerning hydration, we find that saturating the protein interior with water is detrimental and leads to higher structural flexibility and catalytically inefficient active-site geometries. The MD simulations favor a low water density around Asp251 that facilitates side chain rotation of protonated Asp251 during the conversion of Compound 0 to Compound I. The QM/MM results for the two preferred hydration schemes (labeled SE-1 and SE-4) are similar, indicating that slight differences in the solvation close to the active site are not critical as long as camphor and the crystallographic water molecules preserve their positions in the experimental X-ray structures.

Models of the membrane-bound cytochromes: mössbauer spectra of crystalline low-spin ferriheme complexes having axial ligand plane dihedral angles ranging from 0 degree to 90 degrees

Crystalline samples of four low-spin Fe(III) octaalkyltetraphenylporphyrinate and two low-spin Fe(III) tetramesitylporphyrinate complexes, all of which are models of the bis-histidine-coordinated cytochromes of mitochondrial complexes II, III, and IV and chloroplast complex b(6)f, and whose molecular structures and EPR spectra have been reported previously, have been investigated in detail by Mössbauer spectroscopy. The six complexes and the dihedral angles between axial ligand planes of each are [(TMP)Fe(1-MeIm)(2)]ClO(4) (0 degree), paral-[(OMTPP)Fe(1-MeIm)(2)]Cl (19.5 degrees), paral-[(TMP)Fe(5-MeHIm)(2)]ClO(4) (26 degrees, 30 degrees for two molecules in the unit cell whose EPR spectra overlap), [(OETPP)Fe(4-Me(2)NPy)(2)]Cl (70 degrees), perp-[(OETPP)Fe(1-MeIm)(2)]Cl (73 degrees), and perp-[(OMTPP)Fe(1-MeIm)(2)]Cl (90 degrees). Of these, the first three have been shown to exhibit normal rhombic EPR spectra, each with three clearly resolved g-values, while the last three have been shown to exhibit "large g(max)" EPR spectra at 4.2 K. It is found that the hyperfine coupling constants of the complexes are consistent with those reported previously for low-spin ferriheme systems, with the largest-magnitude hyperfine coupling constant, A(zz), being considerably smaller for the "parallel" complexes (400-540 kG) than for the strictly perpendicular complex (902 kG), A(xx) being negative for all six complexes, and A(zz) and A(xx) being of similar magnitude for the "parallel" complexes (for example, for [(TMP)Fe(1-MeIm)(2)]Cl, A(zz) = 400 kG, A(xx) = -400 kG). In all cases, A(yy) is small but difficult to estimate with accuracy. With results for six structurally characterized model systems, we find for the first time qualitative correlations of g(zz), A(zz), and DeltaE(Q) with axial ligand plane dihedral angle Deltavarphi.

Evidence for Two Ferryl Species in Chloroperoxidase Compound II

Using a combination of density functional calculations and Mössbauer spectroscopy, we have examined chloroperoxidase compound II (CPO-II). The Mössbauer spectrum of CPO-II suggests the presence of two distinct ferryl species in an approximately 70:30 ratio. Density functional calculations and cryogenic reduction and annealing experiments allow us to assign the major species as an Fe(IV)OH intermediate. The Mössbauer parameters of the minor component are indicative of an authentic iron(IV)oxo species, but we have found the 70:30 ratio to be pH invariant. The unchanging ratio of component concentrations is in agreement with CPO-II's visible absorption spectrum, which shows no change over the enzyme's range of pH stability.

Two States and Two More in the Mechanisms of Hydroxylation and Epoxidation by Cytochrome P450

Past studies have shown that oxidation reactions by P450 Compound I (Cpd I) can be described by two competing quartet and doublet spin states, which possess three unpaired electrons, hence tri-radicals. One electron excitation from the delta orbital to sigma* xy generates two states that possess five unpaired electrons, so-called penta-radicals, in sextet and quartet situations, and which were shown by theory to lie only approximately 12-14 kcal/mol higher in energy than the tri-radical ground states (ref 7). The present study focuses on the C-H hydroxylation and C=C epoxidation of propene by these penta-radical states. It is shown that the initial energy differences, between the penta-radical and tri-radical states, diminish along the reaction pathway, due to the favorable and cumulative exchange stabilization of the more open-shell species. Furthermore, theory suggests that hydrogen bonding to the thiolate ligand, and general polarity of the environment, reduce these gaps further, thereby making the penta-radical states accessible to ground-state reactivity. The interconversion between the tri-radical and penta-radical states along the reaction coordinate will depend on the dynamics of spin-flips and energy barriers between the states. Especially interesting should be the region of the reaction intermediates; for both epoxidation and hydroxylation, this region is typified by a dense manifold of spin states and electromeric states (that differ by the oxidation state of iron), such that the total reactivity would be expected to reflect the interplay of these states, giving rise to multistate reactivity.

Hunting oxygen complexes of nitric oxide synthase at low temperature and high pressure

The reaction of nitric oxide synthase (NOS) with oxygen is fast and takes place within several steps, separated by ephemeral intermediates. The use of extreme experimental conditions, such as low temperature and high pressure, associated to rapid kinetic analysis, has proven to be a convenient tool to study this complex reaction. Stopped-flow experiments under high pressure indicated that oxygen binding occurred in more than one step. This was further corroborated by the detection of two short-lived oxy-compounds, differing in their spectral and electronic properties. Oxy-I resembles the ferrous oxygen complex known for cytochrome P450, whereas oxy-II appears to be locked in the superoxide form. Subzero temperature spectroscopy, together with an analytical separation method, revealed that the subsequent one-electron reduction of the oxygen complex is carried out by the NOS cofactor tetrahydrobiopterin (BH4). The low-temperature stabilized oxidation product of BH4 was found to be a protonated BH3 radical. Finally, work in the presence of a BH4 analog indicated that proton transfer to the activated oxygen complex is a second essential function of BH4.

Crystal Structure of the Cytochrome P450cam Mutant That Exhibits the Same Spectral Perturbations Induced by Putidaredoxin Binding

The cytochrome P450cam active site is known to be perturbed by binding to its redox partner, putidaredoxin (Pdx). Pdx binding also enhances the camphor monooxygenation reaction (Nagano, S., Shimada, H., Tarumi, A., Hishiki, T., Kimata-Ariga, Y., Egawa, T., Suematsu, M., Park, S.-Y., Adachi, S., Shiro, Y., and Ishimura, Y. (2003) Biochemistry 42, 14507-14514). These effects are unique to Pdx because nonphysiological electron donors are unable to support camphor monooxygenation. The accompanying 1H NMR paper (Tosha, T., Yoshioka, S., Ishimori, K., and Morishima, I. (2004) J. Biol. Chem. 279, 42836-42843) shows that the conformation of active site residues, Thr-252 and Cys-357, and the substrate in the ferrous (Fe(II)) CO complex of the L358P mutant mimics that of the wild-type enzyme complexed to Pdx. To explore how these changes are transmitted from the Pdx-binding site to the active site, we have solved the crystal structures of the ferrous and ferrous-CO complex of wild-type and the L358P mutant. Comparison of these structures shows that the L358P mutation results in the movement of Arg-112, a residue known to be important for putidaredoxin binding, toward the heme. This change could optimize the Pdx-binding site leading to a higher affinity for Pdx. The mutation also pushes the heme toward the substrate and ligand binding pocket, which relocates the substrate to a position favorable for regio-selective hydroxylation. The camphor is held more firmly in place as indicated by a lower average temperature factor. Residues involved in the catalytically important proton shuttle system in the I helix are also altered by the mutation. Such conformational alterations and the enhanced reactivity of the mutant oxy complex with non-physiological electron donors suggest that Pdx binding optimizes the distal pocket for monooxygenation of camphor.

Evidence of Two Distinct Oxygen Complexes of Reduced Endothelial Nitric Oxide Synthase

Oxygen binding to the oxygenase domain of reduced endothelial nitric oxide synthase (eNOS) results in two distinct species differing in their Soret and visible absorbance maxima and in their capacity to exchange oxygen by CO. At 7 degrees C, heme-oxy I (with maxima at 420 and 560 nm) is formed very rapidly (k(on) approximately 2.5.10(6) m(-1).s(-1)) in the absence of substrate but in the presence of pterin cofactor. It is capable of exchanging oxygen with CO at -30 degrees C. Heme-oxy II is formed more slowly (k(on) approximately equal to 3.10(5) m(-1).s(-1)) in the presence of substrate, regardless of the presence of pterin. It is also formed in the absence of both substrate and pterin. In contrast to heme-oxy I, it cannot exchange oxygen with CO at cryogenic temperature. In the presence of arginine, heme-oxy II is characterized by absorbance maxima near 432, 564, and 597 nm. When arginine is replaced by N-hydroxyarginine, and also in the absence of both substrate and pterin, its absorbance maxima are blue-shifted to 428, 560, and 593 nm. Heme-oxy I seems to resemble the ferrous dioxygen complex observed in many hemoproteins, including cytochrome P450. Heme-oxy II, which is the oxygen complex competent for product formation, appears to represent a distinct conformation in which the electronic configuration is essentially locked in the ferric superoxide complex.

Steady-State Kinetic Investigation of Cytochrome P450cam: Interaction with Redox Partners and Reaction with Molecular Oxygen

Cytochrome P450cam (CYP101) is a prokaryotic monooxygenase that requires two proteins, putidaredoxin reductase (PdR) and putidaredoxin (Pdx), to supply electrons from NADH. This study addresses the mechanism by which electrons are transported from PdR to P450cam through Pdx and used to activate O(2) at the heme of P450cam. It is shown that k(cat)/Km(O2) is independent of the PdR concentration and hyperbolically dependent on Pdx. The phenomenon of saturation of reaction rates with either P450cam or PdR at high ratios of one enzyme to the other is investigated and shown to be consistent with a change in the rate limiting step. Either the reduction of Pdx by PdR (high P450) or the reduction of P450 by Pdx (high PdR) determines the rate. These data support a mechanism where Pdx acts as a shuttle for transport of electrons from PdR to P450cam, effectively ruling out the formation of a kinetically significant PdR/Pdx/P450cam complex.

Of spherical cows, cloudy crystal balls, and proteins

Although proteins perform a vast multitude of tasks in living organisms, perhaps the most fascinating and least well understood is the nanoengine aspect of protein action, where chemical energy is turned into mechanical motion. In order for this to happen a protein must change chemical bond energy into physical displacement via some sort of a conformational change of the protein. The critical first step of this process must be the transient storage (self-trapping) of chemical energy into some metastable strained conformation of the protein. We discuss how the early work of Irwin C. "Gunny" Gunsalus with Hans Frauenfelder and Peter Debrunner led to insights into the picosecond dynamics of proteins, the initial functionally important motions.

Models of the bis-histidine-coordinated ferricytochromes: Mössbauer and EPR spectroscopic studies of low-spin iron(III) tetrapyrroles of various electronic ground states and axial ligand orientations

The EPR and magnetic Mössbauer spectra of a series of axial ligand complexes of tetrakis(2,6-dimethoxyphenyl)porphyrinatoiron(III), [(2,6-(OMe)(2))(4)TPPFeL(2)](+), where L= N-methylimidazole, 2-methylimidazole, or 4-(dimethylamino)pyridine, of one axial ligand complex of tetraphenylporphyrin, the bis(4-cyanopyridine) complex [TPPFe(4-CNPy)(2)](+), and of one axial ligand complex of tetraphenylchlorin, [TPCFe(ImH)(2)](+), where ImH=imidazole, have been investigated and compared to those of low-spin Fe(III) porphyrinates and ferriheme proteins reported in the literature. On the basis of this and previous complementary spectroscopic investigations, three types of complexes have been identified: those having (d(xy))(2)(d(xz),d(yz))(3) electronic ground states with axial ligands aligned in perpendicular planes (Type I), those having (d(xy))(2)(d(xz),d(yz))(3) electronic ground states with axial ligands aligned in parallel planes (Type II), and those having the novel (d(xz),d(yz))(4)(d(xy))(1) electronic ground state (Type III). A subset of the latter type, with planar axial ligands aligned parallel to each other or strong macrocycle asymmetry that yield rhombic EPR spectra, cannot be created using the porphyrinate ligand. Type I centers are characterized by "large g(max)" EPR spectra with g>3.2 and well-resolved, widely spread magnetic Mössbauer spectra having A(zz)/ g(N)mu(N)>680 kG, with A(xx) negative in sign but much smaller in magnitude than A(zz), while Type II centers have well-resolved rhombic EPR spectra with g(zz)=2.4-3.1 and also less-resolved magnetic Mössbauer spectra, and usually have A(zz)/ g(Nmu(N) in the range of 440-660 kG (but in certain cases as small as 180 kG) and A(xx) again negative in sign but only somewhat smaller (but occasionally larger in magnitude) than A(zz), and Type III centers have axial EPR spectra with g( upper left and right quadrants ) approximately 2.6 or smaller and g( vertical line )<1.0-1.95, but often not resolved, and less-resolved magnetic Mössbauer spectra having A(zz)/ g(N)mu(N) in the range of 270-400 kG, and A(xx) again negative in sign but much smaller in magnitude than A(zz). An exception to this rule is [TPPFe(4-CNPy)(2)](+), which has A(xx)/ g(N)mu(N)=-565 kG, A(yy)/ g(N)mu(N)=629 kG, and A(zz)/ g(N)mu(N)=4 kG. A subset of Type II complexes (Type II') have rhombicities ( V/Delta) much greater than 0.67 and A(zz)/ g(N)mu(N) ranging from 320 to 170 kG, with A(xx) also negative but with the magnitude of A(xx) significantly larger than that of A(zz). These classifications are also observed for a variety of ferriheme proteins, and they lead to linear correlations between A(zz) and either A(xx), g(zz), or V/Delta for Types I and II (but not for A(zz) versus V/Delta for Type II'). Not enough data are yet available on Type III complexes to determine what, if any, correlations may be observed.

A Mössbauer study of the interaction of chitosan and D-glucosamine with iron and its relevance to other metalloenzymes

The interaction of iron with water-soluble polymer chitosan and monomer d-glucosamine is investigated by Mössbauer spectroscopy. The 4.2 K Mössbauer spectrum of Fe-water-soluble chitosan complex indicates the presence of a magnetic pattern and a quadrupole doublet, and analysis of the spectral data leads to the conclusion that an Fe(II) state is partially stabilized in this system. Fe-glucosamine (monomer of chitosan) complex, on the other hand, clearly stabilizes the Fe(II) state in the acidic pH range as evidenced from the isomer shift extracted from the Mössbauer spectra. The oxidation state of the metal ion in the complex is found to be pH dependent. Indirect evidence supporting the involvement of amino group in the bonding with the metal ion is discussed. From the analysis of the experimental data under varying experimental conditions, it is concluded that the metal ion in the complex is at least tetracoordinated and at most hexacoordinated with O/N ligands of the polymer or monomer and thus corroborates the bonding scheme proposed earlier.

Mechanistic enzymology of oxygen activation by the cytochromes P450

The P450 cytochromes represent a universal class of heme-monooxygenases. The detailed mechanistic understanding of their oxidative prowess is a critical theme in the studies of metabolism of a wide range of organic compounds including xenobiotics. Integral to the O2 bond cleavage mechanism by P450 is the enzyme's concerted use of protein and solvent-mediated proton transfer events to transform reduced dioxygen to a species capable of oxidative chemistry. To this end, a wide range of kinetic, structural, and mutagenesis data has been accrued. A critical role of conserved acid-alcohol residues in the P450 distal pocket, as well as stabilized waters, enables the enzyme to catalyze effective monooxygenation chemistry. In this review, we discuss the detailed mechanism of P450 dioxygen scission utilizing the CYP101 hydroxylation of camphor as a model system. The application of low-temperature radiolytic techniques has enabled a structural and spectroscopic analysis of the nature of critical intermediate states in the reaction.