Proximal ligand effects on electronic structure and spectra of compound I of peroxidases

Computational analysis of the tryptophan cation radical energetics in peroxidase Compound I

Three well-characterized heme peroxidases (cytochrome c peroxidase = CCP, ascorbate peroxidase = APX, and Leishmania major peroxidase = LMP) all have a Trp residue tucked under the heme stacked against the proximal His heme ligand. The reaction of peroxidases with H₂O₂ to give Compound I results in the oxidation of this Trp to a cationic radical in CCP and LMP but not in APX. Considerable experimental data indicate that the local electrostatic environment controls whether this Trp or the porphyrin is oxidized in Compound I. Attempts have been made to place the differences between these peroxidases on a quantitative basis using computational methods. These efforts have been somewhat limited by the approximations required owing to the computational cost of using fully solvated atomistic models with well-developed forcefields. This now has changed with available GPU computing power and the associated development of software. Here we employ thermodynamic integration and multistate Bennett acceptance ratio methods to help fine-tune our understanding on the energetic differences in Trp radical stabilization in all three peroxidases. These results indicate that the local solvent structure near the redox active Trp plays a significant role in stabilization of the cationic Trp radical.

How Does Replacement of the Axial Histidine Ligand in Cytochrome c Peroxidase by Nδ-Methyl Histidine Affect Its Properties and Functions? A Computational Study

Heme peroxidases have important functions in nature related to the detoxification of H₂O₂. They generally undergo a catalytic cycle where, in the first stage, the iron(III)-heme-H₂O₂ complex is converted into an iron(IV)-oxo-heme cation radical species called Compound I. Cytochrome c peroxidase Compound I has a unique electronic configuration among heme enzymes where a metal-based biradical is coupled to a protein radical on a nearby Trp residue. Recent work using the engineered N_δ-methyl histidine-ligated cytochrome c peroxidase highlighted changes in spectroscopic and catalytic properties upon axial ligand substitution. To understand the axial ligand effect on structure and reactivity of peroxidases and their axially N_δ-methyl histidine engineered forms, we did a computational study. We created active site cluster models of various sizes as mimics of horseradish peroxidase and cytochrome c peroxidase Compound I. Subsequently, we performed density functional theory studies on the structure and reactivity of these complexes with a model substrate (styrene). Thus, the work shows that the N_δ-methyl histidine group has little effect on the electronic configuration and structure of Compound I and little changes in bond lengths and the same orbital occupation is obtained. However, the N_δ-methyl histidine modification impacts electron transfer processes due to a change in the reduction potential and thereby influences reactivity patterns for oxygen atom transfer. As such, the substitution of the axial histidine by N_δ-methyl histidine in peroxidases slows down oxygen atom transfer to substrates and makes Compound I a weaker oxidant. These studies are in line with experimental work on N_δ-methyl histidine-ligated cytochrome c peroxidases and highlight how the hydrogen bonding network in the second coordination sphere has a major impact on the function and properties of the enzyme.

Crystal structure of the pristine peroxidase ferryl center and its relevance to proton-coupled electron transfer

The reaction of peroxides with peroxidases oxidizes the heme iron from Fe(III) to Fe(IV)=O and a porphyrin or aromatic side chain to a cationic radical. X-ray-generated hydrated electrons rapidly reduce Fe(IV), thereby requiring very short exposures using many crystals, and, even then, some reduction cannot be avoided. The new generation of X-ray free electron lasers capable of generating intense X-rays on the tenths of femtosecond time scale enables structure determination with no reduction or X-ray damage. Here, we report the 1.5-Å crystal structure of cytochrome c peroxidase (CCP) compound I (CmpI) using data obtained with the Stanford Linear Coherent Light Source (LCLS). This structure is consistent with previous structures. Of particular importance is the active site water structure that can mediate the proton transfer reactions required for both CmpI formation and reduction of Fe(IV)=O to Fe(III)-OH. The structures indicate that a water molecule is ideally positioned to shuttle protons between an iron-linked oxygen and the active site catalytic His. We therefore have carried out both computational and kinetic studies to probe the reduction of Fe(IV)=O. Kinetic solvent isotope experiments show that the transfer of a single proton is critical in the peroxidase rate-limiting step, which is very likely the proton-coupled reduction of Fe(IV)=O to Fe(III)-OH. We also find that the pKa of the catalytic His substantially increases in CmpI, indicating that this active site His is the source of the proton required in the reduction of Fe(IV)=O to Fe(IV)-OH.

Quantum mechanical modeling: a tool for the understanding of enzyme reactions

Most enzyme reactions involve formation and cleavage of covalent bonds, while electrostatic effects, as well as dynamics of the active site and surrounding protein regions, may also be crucial. Accordingly, special computational methods are needed to provide an adequate description, which combine quantum mechanics for the reactive region with molecular mechanics and molecular dynamics describing the environment and dynamic effects, respectively. In this review we intend to give an overview to non-specialists on various enzyme models as well as established computational methods and describe applications to some specific cases. For the treatment of various enzyme mechanisms, special approaches are often needed to obtain results, which adequately refer to experimental data. As a result of the spectacular progress in the last two decades, most enzyme reactions can be quite precisely treated by various computational methods.

New insight into the electronic structure of iron(IV)-oxo porphyrin compound I. A quantum chemical topological analysis

The electronic structure of iron-oxo porphyrin π-cation radical complex Por(·+) Fe(IV)=O (S-H) has been studied for doublet and quartet electronic states by means of two methods of the quantum chemical topology analysis: electron localization function (ELF) η(r) and electron density ρ(r). The formation of this complex leads to essential perturbation of the topological structure of the carbon-carbon bonds in porphyrin moiety. The double C=C bonds in the pyrrole anion subunits, represented by pair of bonding disynaptic basins V(i=1,2)(C,C) in isolated porphyrin, are replaced by single attractor V(C,C)(i=1-20) after complexation with the Fe cation. The iron-nitrogen bonds are covalent dative bonds, N→Fe, described by the disynaptic bonding basins V(Fe,N)(i=1-4), where electron density is almost formed by the lone pairs of the N atoms. The nature of the iron-oxygen bond predicted by the ELF topological analysis, shows a main contribution of the electrostatic interaction, Fe(δ+)···O(δ-), as long as no attractors between the C(Fe) and C(O) core basins were found, although there are common surfaces between the iron and oxygen basines and coupling between iron and oxygen lone pairs, that could be interpreted as a charge-shift bond. The Fe-S bond, characterized by the disynaptic bonding basin V(Fe,S), is partially a dative bond with the lone pair donated from sulfur atom. The change of electronic state from the doublet (M = 2) to quartet (M = 4) leads to reorganization of spin polarization, which is observed only for the porphyrin skeleton (-0.43e to 0.50e) and S-H bond (-0.55e to 0.52e).

Symmetry states of metalloporphyrin π-cation radicals, models for peroxidase compound I

Oxoferryl porphyrin π-cation radical active sites of compound I intermediates which are found in enzymes such as peroxidases and catalases have been extensively modeled by oxidized synthetic metalloporphyrins. The electronic symmetry states of these compounds were initially assigned on the basis of electronic absorption data. In recent years new experimental and theoretical results have become available which have led to a re-evaluation and modification of the original assignments. A historical perspective of these developments is provided in the context of recent NMR, resonance Raman, and other spectroscopic data and theoretical calculations for the synthetic models and enzymatic systems.

The Poulos-Kraut mechanism of Compound I formation in horseradish peroxidase: a QM/MM study

QM/MM calculations are used to elucidate the Poulos-Kraut (Poulos, T. L.; Kraut, J. J. Biol. Chem. 1980, 255, 8199-8205) mechanism of O-O bond activation and Compound I (Cpd I) formation in HRP, in conditions corresponding to neutral to basic pH. Attempts to generate Compound I directly from the Fe(H2O2) complex by migrating the proton from the proximal oxygen to the distal one (1,2- proton shift) result in high barriers. The lowest energy mechanism was found to involve initial deprotonation of ferric hydrogen peroxide complex (involving spin crossover from the quartet to the doublet state) by His42 to form ferric-hydroperoxide (Cpd 0). Subsequently, the distal OH group of Cpd 0 is pulled by Arg38 and reprotonated by His42(H+) to form Cpd I and a water molecule that bridges the two residues. The structures of the intermediate and the transition state reveal the manner by which the Arg-His residues promote cooperatively the electronic reorganization that is required to attend the heterolytic O-O cleavage.

How axial ligands control the reactivity of high-valent iron(IV)–oxo porphyrin π-cation radicals in alkane hydroxylation: A computational study

The push effect of anionic axial ligands of high-valent iron(IV)-oxo porphyrin pi-cation radicals, (Porp)(+.)Fe(IV)(O)(X) (X=OH(-), AcO(-), Cl(-), and CF(3)SO(3)(-)), in alkane hydroxylation is investigated by B3LYP DFT calculations. The electron-donating ability of anionic axial ligands influences the activation energy for the alkane hydroxylation by the iron(IV)-oxo intermediates and the Fe-O bond distance of the iron-oxo species in transition state.

Resonance Raman spectroscopy of oxoiron(IV) porphyrin π-cation radical and oxoiron(IV) hemes in peroxidase intermediates

The catalytic cycle intermediates of heme peroxidases, known as compounds I and II, have been of long standing interest as models for intermediates of heme proteins, such as the terminal oxidases and cytochrome P450 enzymes, and for non-heme iron enzymes as well. Reports of resonance Raman signals for compound I intermediates of the oxo-iron(IV) porphyrin pi-cation radical type have been sometimes contradictory due to complications arising from photolability, causing compound I signals to appear similar to those of compound II or other forms. However, studies of synthetic systems indicated that protein based compound I intermediates of the oxoiron(IV) porphyrin pi-cation radical type should exhibit vibrational signatures that are different from the non-radical forms. The compound I intermediates of horseradish peroxidase (HRP), and chloroperoxidase (CPO) from Caldariomyces fumago do in fact exhibit unique and characteristic vibrational spectra. The nature of the putative oxoiron(IV) bond in peroxidase intermediates has been under discussion in the recent literature, with suggestions that the Fe(IV)O unit might be better described as Fe(IV)-OH. The generally low Fe(IV)O stretching frequencies observed for proteins have been difficult to mimic in synthetic ferryl porphyrins via electron donation from trans axial ligands alone. Resonance Raman studies of iron-oxygen vibrations within protein species that are sensitive to pH, deuteration, and solvent oxygen exchange, indicate that hydrogen bonding to the oxoiron(IV) group within the protein environment contributes to substantial lowering of Fe(IV)O frequencies relative to those of synthetic model compounds.

Effect of the axial cysteine ligand on the electronic structure and reactivity of high-valent iron(IV) oxo-porphyrins (Compound I): A theoretical study

The effect of axial ligands on the reactivity of high-valent iron(IV) oxo-porphyrins (Compound I) was investigated using the B3LYP hybrid density functional method. We studied alkane hydroxylation using four models: Compound I with thiolate, imidazole, phenolate, and chloride anions as axial ligands. The first three ligands were employed as models for cysteinate, histidine, and tyrosinate, respectively. Our calculations show that anionic ligands and neutral ligands favor different electronic states for stationary points in the reaction coordinate, and the calculated energy barrier and energy of several reaction intermediates show similar values. A remarkable effect of axial ligands was found in the final product release step. Our calculations show that the thiolate ligand weakens a bond between heme and an alcohol. In contrast, the imidazole ligand significantly increases the interaction between heme and an alcohol, which causes the catalytic cycle to be less efficient.

The protonation status of compound II in myoglobin, studied by a combination of experimental data and quantum chemical calculations: quantum refinement

Treatment of met-myoglobin (FeIII) with H2O2 gives rise to ferryl myoglobin, which is closely related to compound II in peroxidases. Experimental studies have given conflicting results for this species. In particular, crystallographic and extended x-ray absorption fine-structure data have shown either a short (approximately 170 pm) or a longer (approximately 190 pm) Fe-O bond, indicating either a double or a single bond. We here present a combined experimental and theoretical investigation of this species. In particular, we use quantum refinement to re-refine a crystal structure with a long bond, using 12 possible states of the active site. The states differ in the formal oxidation state of the iron ion and in the protonation of the oxygen ligand (O2-, OH-, or H2O) and the distal histidine residue (with a proton on Ndelta1, Nepsilon2, or on both atoms). Quantum refinement is essentially standard crystallographic refinement, where the molecular-mechanics potential, normally used to supplement the experimental data, is replaced by a quantum chemical calculation. Thereby, we obtain an accurate description of the active site in all the different protonation and oxidation states, and we can determine which of the 12 structures fit the experimental data best by comparing the crystallographic R-factors, electron-density maps, strain energies, and deviation from the ideal structure. The results indicate that FeIII OH- and FeIV OH- fit the experimental data almost equally well. These two states are appreciably better than the standard model of compound II, FeIV O2-. Combined with the available spectroscopic data, this indicates that compound II in myoglobin is protonated and is best described as FeIV OH-. It accepts a hydrogen bond from the distal His, which may be protonated at low pH.

UV optical absorption by protein radicals in cytochrome c oxidase

The UV properties of key oxygen intermediates of cytochrome c oxidase have been investigated by transient absorption spectroscopy. The temporal behavior of P(m) species upon aerobic incubation with CO or in the reaction with H(2)O(2) is closely concurred by a new optical shift at 290/260 nm. In the acid-induced conversion of P(m) to F(*), it is replaced by another shift at 323/288 nm. The wavelength and intensity of the UV signal observed in F(*) match closely the properties of model Trp? in agreement with results of ENDOR studies on this species. The UV spectrum of Tyr* gives the closest match with the 290/260 nm signal observed in P(m). On the basis of analysis of possible UV chromophores in CcO and similarity to Tyr*, the 290/260 nm signal is proposed to originate from the H(240)-Y(244)* site. Possible effects of local environment on UV properties of this site are discussed.

Quantum Mechanical/Molecular Mechanical Investigation of the Mechanism of C−H Hydroxylation of Camphor by Cytochrome P450cam: Theory Supports a Two-State Rebound Mechanism

The stereospecific cytochrome P450-catalyzed hydroxylation of the C(5)-H((5-exo)) bond in camphor has been studied theoretically by a combined quantum mechanical/molecular mechanical (QM/MM) approach. Density functional theory is employed to treat the electronic structure of the active site (40-100 atoms), while the protein and solvent environment (ca. 24,000 atoms) is described by the CHARMM force field. The calculated energy profile of the hydrogen-abstraction oxygen-rebound mechanism indicates that the reaction takes place in two spin states (doublet and quartet), as has been suggested earlier on the basis of calculations on simpler models ("two-state reactivity"). While the reaction on the doublet potential energy surface is nonsynchronous, yet effectively concerted, the quartet pathway is truly stepwise, including formation of a distinct intermediate substrate radical and a hydroxo-iron complex. Comparative calculations in the gas phase demonstrate the effect of the protein environment on the geometry and relative stability of intermediates (in terms of spin states and redox electromers) through steric constraints and electronic polarization.

On the role of the axial ligand in heme proteins: a theoretical study

We present a systematic investigation of how the axial ligand in heme proteins influences the geometry, electronic structure, and spin states of the active site, and the energies of the reaction cycles. Using the density functional B3LYP method and medium-sized basis sets, we have compared models with His, His+Asp, Cys, Tyr, and Tyr+Arg as found in myoglobin and hemoglobin, peroxidases, cytochrome P450, and heme catalases, respectively. We have studied 12 reactants and intermediates of the reaction cycles of these enzymes, including complexes with H(2)O, OH(-), O(2-), CH(3)OH, O(2), H(2)O(2), and HO(2)(-) in various formal oxidation states of the iron ion (II to V). The results show that His gives ~0.6 V higher reduction potentials than the other ligands. In particular, it is harder to reduce and protonate the O(2) complex with His than with the other ligands, in accordance with the O(2) carrier function of globins and the oxidative chemistry of the other proteins. For most properties, the trend Cys<Tyr<Tyr+Arg<His+Asp<His is found, reflecting the donor capacity of the various ligands. Thus, it is easier to reduce compound I with a His+Asp ligand than with a Cys ligand, in accordance with the one-electron chemistry of peroxidases and the hydroxylation reactions of cytochromes P450. However, the Tyr complexes have an unusually low affinity for all neutral ligands, giving them a slightly enhanced driving force in the oxidation of H(2)O(2) by compound I.

What Factors Affect the Regioselectivity of Oxidation by Cytochrome P450? A DFT Study of Allylic Hydroxylation and Double Bond Epoxidation in a Model Reaction

Epoxidation (C=C) vis-à-vis allylic hydroxylation (C-H) reactions of propene with a model compound I (Cpd I) of the enzyme cytochrome P450 were studied using B3LYP density functional theory. Potential energy profiles and kinetic isotope effects (KIE) were calculated. The interactions in the protein pocket were mimicked by adding two external NH- - -S hydrogen bonds to the thiolate ligand and by introducing a nonpolar medium (with a dielectric constant, epsilon = 5.7) that can exert a polarization effect on the reacting species. A two-state reactivity (TSR) with high-spin (HS) and low-spin (LS) states were located for both processes (Ogliaro, F.; Harris, N.; Cohen, S.; Filatov, M.; de Visser, S. P.; Shaik, S. J. Am. Chem. Soc. 2000, 122, 8977-8989. de Visser, S. P.; Ogilaro, F.; Harris, N.; Shaik, S. J. Am. Chem. Soc. 2001, 123, 3037-3047). The HS processes were found to be stepwise, whereas the LS processes were characterized as nonsynchronous but effectively concerted pathways. The computed KIE for C-H hydroxylation with and without tunneling corrections are large (>7), and they support the assignment of the corresponding transition states as hydrogen-abstraction species (Groves, J. T.; Han, Y.-Z. In Cytochrome P450: Structures, Mechanism and Biochemistry, 2nd ed.; Ortiz de Montellano, P. R., Ed.; Plenum Press: New York, 1995; Chapter 1; pp 3-48). In the gas phase, epoxidation is energetically favorable by 3.4 kcal mol(-1). Inclusion of zero-point energy reduces this difference but still predicts C=C/C-H > 1. Environmental effects were found to have major impact on the C=C/C-H ratio as well as on the stereoselectivity of the processes. Thus, two NH- - -S hydrogen bonds away from the reaction center reverse the regioselectivity and prefer hydroxylation, namely, C=C/C-H <1. The polarity of the medium further accentuates the trend and leads to a change by 2 orders of magnitude in the regioselectivity, C=C/C-H << 1. Furthermore, since the environmental interactions prefer the LS over the HS reactions, both hydroxylation and epoxidation processes are rendered more stereoselective, again by 2 orders of magnitude. It follows, therefore, that Cpd I is a chameleon oxidant (Ogliaro, F.; Cohen, S.; de Visser, S. P.; Shaik, S. J. Am. Chem. Soc. 2000, 122, 12892-12893; Ogliaro, F.; de Visser, S. P.; Cohen, S.; Kaneti, J.; Shaik, S. Chembiochem. 2001, 2, 848-851; Ogliaro, F.; de Visser, S. P.; Groves, J. T.; Shaik, S. Angew. Chem., Int. Ed. 2001, 40, 2874-2878) that tunes its reactivity and selectivity patterns in response to the protein environment in which it is accommodated. A valence bond (VB) model, akin to "redox mesomerism" (Bernadou, J.; Fabiano, A.-S.; Robert, A.; Meunier, B. J. Am. Chem. Soc. 1994, 116, 9375-9376), is constructed and enables the description of a chameleon transition state. It shows that the good donor ability of the thiolate ligand and the acceptor ability of the iron porphyrin create mixed-valent situations that endow the transition state with a great sensitivity to external perturbations as in the protein pocket. The model is used to discuss the computed results and to relate them to experimental findings.

High-valent intermediates of heme proteins and model compounds

Recent computational and experimental probes of high-valent intermediates in heme proteins and model compounds reveal a rich spectrum of chemical behavior that is dependent on the nature of the proximal ligand, metal center, distal- and proximal-binding site environment, porphyrin macrocycle architecture, and consequent electronic structure. The results of such studies reveal an underlying complexity, which is simply understood once one is cognizant of the 'chameleon'-like behavior of such intermediates is determined by the high-valent intermediate environment.