Role of the Invariant Peptide Fragment Forming NH.S Hydrogen Bonds in the Active Site of Cytochrome P-450 and Chloroperoxidase: Synthesis and Properties of Cys-Containing Peptide Fe(III) and Ga(III) (Octaethylporphinato) Complexes as Models

Hijacking Chemical Reactions of P450 Enzymes for Altered Chemical Reactions and Asymmetric Synthesis

Cytochrome P450s are heme-containing enzymes capable of the oxidative transformation of a wide range of organic substrates. A protein scaffold that coordinates the heme iron, and the catalytic pocket residues, together, determine the reaction selectivity and regio- and stereo-selectivity of the P450 enzymes. Different substrates also affect the properties of P450s by binding to its catalytic pocket. Modulating the redox potential of the heme by substituting iron-coordinating residues changes the chemical reaction, the type of cofactor requirement, and the stereoselectivity of P450s. Around hundreds of P450s are experimentally characterized, therefore, a mechanistic understanding of the factors affecting their catalysis is increasingly vital in the age of synthetic biology and biotechnology. Engineering P450s can enable them to catalyze a variety of chemical reactions viz. oxygenation, peroxygenation, cyclopropanation, epoxidation, nitration, etc., to synthesize high-value chiral organic molecules with exceptionally high stereo- and regioselectivity and catalytic efficiency. This review will focus on recent studies of the mechanistic understandings of the modulation of heme redox potential in the engineered P450 variants, and the effect of small decoy molecules, dual function small molecules, and substrate mimetics on the type of chemical reaction and the catalytic cycle of the P450 enzymes.

Abiological catalysis by myoglobin mutant with a genetically incorporated unnatural amino acid

To inculcate biocatalytic activity in the oxygen-storage protein myoglobin (Mb), a genetically engineered myoglobin mutant H64DOPA (DOPA = L-3,4-dihydroxyphenylalanine) has been created. Incorporation of unnatural amino acids has already demonstrated their ability to accomplish many non-natural functions in proteins efficiently. Herein, the presence of redox-active DOPA residue in the active site of mutant Mb presumably stabilizes the compound I in the catalytic oxidation process by participating in an additional hydrogen bonding (H-bonding) as compared to the WT Mb. Specifically, a general acid-base catalytic pathway was achieved due to the availability of the hydroxyl moieties of DOPA. The reduction potential values of WT (E° = -260 mV) and mutant Mb (E° = -300 mV), w.r.t. Ag/AgCl reference electrode, in the presence of hydrogen peroxide, indicated an additional H-bonding in the mutant protein, which is responsible for the peroxidase activity of the mutant Mb. We observed that in the presence of 5 mM H2O2, H64DOPA Mb oxidizes thioanisole and benzaldehyde with a 10 and 54 folds higher rate, respectively, as opposed to WT Mb. Based on spectroscopic, kinetic, and electrochemical studies, we deduce that DOPA residue, when present within the distal pocket of mutant Mb, alone serves the role of His/Arg-pair of peroxidases.

Localized Electronic Structure of Nitrogenase FeMoco Revealed by Selenium K-Edge High Resolution X-ray Absorption Spectroscopy

The size and complexity of Mo-dependent nitrogenase, a multicomponent enzyme capable of reducing dinitrogen to ammonia, have made a detailed understanding of the FeMo cofactor (FeMoco) active site electronic structure an ongoing challenge. Selective substitution of sulfur by selenium in FeMoco affords a unique probe wherein local Fe-Se interactions can be directly interrogated via high-energy resolution fluorescence detected X-ray absorption spectroscopic (HERFD XAS) and extended X-ray absorption fine structure (EXAFS) studies. These studies reveal a significant asymmetry in the electronic distribution of the FeMoco, suggesting a more localized electronic structure picture than is typically assumed for iron-sulfur clusters. Supported by experimental small molecule model data in combination with time dependent density functional theory (TDDFT) calculations, the HERFD XAS data is consistent with an assignment of Fe2/Fe6 as an antiferromagnetically coupled diferric pair. HERFD XAS and EXAFS have also been applied to Se-substituted CO-inhibited MoFe protein, demonstrating the ability of these methods to reveal electronic and structural changes that occur upon substrate binding. These results emphasize the utility of Se HERFD XAS and EXAFS for selectively probing the local electronic and geometric structure of FeMoco.

How the Proximal Pocket May Influence the Enantiospecificities of Chloroperoxidase-Catalyzed Epoxidations of Olefins

Chloroperoxidase-catalyzed enantiospecific epoxidations of olefins are of significant biotechnological interest. Typical enantiomeric excesses are in the range of 66%-97% and translate into free energy differences on the order of 1 kcal/mol. These differences are generally attributed to the effect of the distal pocket. In this paper, we show that the influence of the proximal pocket on the electron transfer mechanism in the rate-limiting event may be just as significant for a quantitatively accurate account of the experimentally-measured enantiospecificities.

Chloroperoxidase-Catalyzed Epoxidation of Cis-β-Methylstyrene: NH-S Hydrogen Bonds and Proximal Helix Dipole Change the Catalytic Mechanism and Significantly Lower the Reaction Barrier

Proximal hydrogen bonding of the axial sulfur with the backbone amides (NH-S) is a conserved feature of heme-thiolate enzymes such as chloroperoxidase (CPO) and cytochrome P450 (P450). In CPO, the effect of NH-S bonds is amplified by the dipole moment of the proximal helix. Our gas-phase DFT studies show that the proximal pocket effect significantly enhances CPO's reactivity toward the epoxidation of olefinic substrates. Comparison of models with and without proximal pocket residues shows that with them, the barrier for Cβ-O bond formation is lowered by about ∼4.6 kcal/mol, while Cα-O-Cβ ring closure becomes barrierless. The dipole moment of the proximal helix was estimated to contribute 1/3 of the decrease, while the rest is attributed to the effect of NH-S bonds. The decrease of the reaction barrier correlates with increased electron density transfer to residues of the proximal pocket. The effect is most pronounced on the doublet spin surface and involves a change in the electron-transfer mechanism. A full enzyme QMMM study on the doublet spin surface gives about the same barrier as the gas-phase DFT study. The free-energy barrier was estimated to be in agreement with the experimental results for the CPO-catalyzed epoxidation of styrene.

Significantly shorter Fe-S bond in cytochrome P450-I is consistent with greater reactivity relative to chloroperoxidase

Cytochrome P450 (P450) and chloroperoxidase (CPO) are thiolate ligated heme proteins that catalyze the activation of carbon hydrogen bonds. The principal intermediate in these reactions is a ferryl radical species called compound I. P450 compound I (P450-I) is significantly more reactive than CPO-I, which only cleaves activated C-H bonds. To provide insight into the differing reactivities of these intermediates, we examined CPO-I and P450-I with variable temperature Mössbauer and X-ray absorption spectroscopies. These measurements indicate that the Fe-S bond is significantly shorter in P450-I than in CPO-I. This difference in Fe-S bond lengths can be understood in terms of variations in hydrogen bonding patterns within the “cys-pocket” (a portion of the proximal helix that encircles the thiolate ligand). Weaker hydrogen bonding in P450-I results in a shorter Fe-S bond, which enables greater electron donation from the axial-thiolate ligand. This observation may in part explain P450's greater propensity for C-H bond activation.

Heterobimetallic Complexes with MIII-(μ-OH)-MII Cores (MIII = Fe, Mn, Ga; MII = Ca, Sr, and Ba): Structural, Kinetic, and Redox Properties

The effects of redox-inactive metal ions on dioxygen activation were explored using a new FeII complex containing a tripodal ligand with 3 sulfonamido groups. This iron complex exhibited a faster initial rate for the reduction of O2 than its MnII analog. Increases in initial rates were also observed in the presence of group 2 metal ions for both the FeII and MnII complexes, which followed the trend NMe4+ < BaII < CaII = SrII. These studies led to the isolation of heterobimetallic complexes containing FeIII-(μ-OH)-MII cores (MII = Ca, Sr, and Ba) and one with a [SrII(OH)MnIII]+ motif. The analogous [CaII(OH)GaIII]+ complex was also prepared and its solid state molecular structure is nearly identical to that of the [CaII(OH)FeIII]+ system. Nuclear magnetic resonance studies indicated that the diamagnetic [CaII(OH)GaIII]+ complex retained its structure in solution. Electrochemical measurements on the heterobimetallic systems revealed similar one-electron reduction potentials for the [CaII(OH)FeIII]+ and [SrII(OH)FeIII]+ complexes, which were more positive than the potential observed for [BaII(OH)FeIII]+. Similar results were obtained for the heterobimetallic MnII complexes. These findings suggest that Lewis acidity is not the only factor to consider when evaluating the effects of group 2 ions on redox processes, including those within the oxygen-evolving complex of Photosystem II.

The conserved Trp-Cys hydrogen bond dampens the "push effect" of the heme cysteinate proximal ligand during the first catalytic cycle of nitric oxide synthase

Residues surrounding and interacting with the heme proximal ligand are important for efficient catalysis by heme proteins. The nitric oxide synthases (NOSs) are thiolate-coordinated enzymes that catalyze the hydroxylation of l-Arg in the first of the two catalytic cycles needed to synthesize nitric oxide. In NOSs, the indole NH group of a conserved tryptophan [W56 of the bacterial NOS-like protein from Staphylococcus aureus (saNOS)] forms a hydrogen bond with the heme proximal cysteinate ligand. The purpose of this study was to determine the impact of increasing (W56F and W56Y variants) or decreasing (W56H variant) the electron density of the proximal cysteinate ligand on molecular oxygen (O(2)) activation using saNOS as a model. We show that the removal of the indole NH···S(-) bond for W56F and W56Y caused an increase in the electron density of the cysteinate. This was probed by the decrease of the midpoint reduction potential (E(1/2)) along with weakened σ-bonding and strengthened π-backbonding with distal ligands (CO and O(2)). On the other hand, the W56H variant showed stronger Fe-OO and Fe-CO bonds (strengthened σ-bonding) along with an elevated E(1/2), which is consistent with the formation of a strong NH···S(-) hydrogen bond from H56. We also show here that changing the electron density of the proximal thiolate controls its "push effect"; whereas the rates of both O(2) activation and autoxidation of the Fe(II)O(2) complex increase with the stronger push effect created by removing the indole NH···S(-) hydrogen bond (W56F and W56Y variants), the W56H variant showed an increased stability of the complex against autoxidation and a slower rate of O(2) activation. These results are discussed with regard to the roles played by the conserved tryptophan-cysteinate interaction in the first catalytic cycle of NOS.

Elucidating the role of the proximal cysteine hydrogen-bonding network in ferric cytochrome P450cam and corresponding mutants using magnetic circular dichroism spectroscopy

Although extensive research has been performed on various cytochrome P450s, especially Cyt P450cam, there is much to be learned about the mechanism of how its functional unit, a heme b ligated by an axial cysteine, is finely tuned for catalysis by its second coordination sphere. Here we study how the hydrogen-bonding network affects the proximal cysteine and the Fe-S(Cys) bond in ferric Cyt P450cam. This is accomplished using low-temperature magnetic circular dichroism (MCD) spectroscopy on wild-type (wt) Cyt P450cam and on the mutants Q360P (pure ferric high-spin at low temperature) and L358P where the "Cys pocket" has been altered (by removing amino acids involved in the hydrogen-bonding network), and Y96W (pure ferric low-spin). The MCD spectrum of Q360P reveals fourteen electronic transitions between 15200 and 31050 cm(-1). Variable-temperature variable-field (VTVH) saturation curves were used to determine the polarizations of these electronic transitions with respect to in-plane (xy) and out-of-plane (z) polarization relative to the heme. The polarizations, oscillator strengths, and TD-DFT calculations were then used to assign the observed electronic transitions. In the lower energy region, prominent bands at 15909 and 16919 cm(-1) correspond to porphyrin (P) → Fe charge transfer (CT) transitions. The band at 17881 cm(-1) has distinct sulfur S(π) → Fe CT contributions. The Q band is observed as a pseudo A-term (derivative shape) at 18604 and 19539 cm(-1). In the case of the Soret band, the negative component of the expected pseudo A-term is split into two features due to mixing with another π → π* and potentially a P → Fe CT excited state. The resulting three features are observed at 23731, 24859, and 25618 cm(-1). Most importantly, the broad, prominent band at 28570 cm(-1) is assigned to the S(σ) → Fe CT transition, whose intensity is generated through a multitude of CT transitions with strong iron character. For wt, Q360P, and L358P, this band occurs at 28724, 28570, and 28620 cm(-1), respectively. The small shift of this feature upon altering the hydrogen bonds to the proximal cysteine indicates that the role of the Cys pocket is not primarily for electronic fine-tuning of the sulfur donor strength but is more for stabilizing the proximal thiolate against external reactants (NO, O(2), H(3)O(+)), and for properly positioning cysteine to coordinate to the iron center. This aspect is discussed in detail.

Preparation and characterization of mononuclear Co, Ni, and Zn complexes of dinucleating macrocyclic hexaaza-dithiophenolate ligands and their open-chain derivatives

The preparation and characterization of mononuclear complexes of the dinucleating 24-membered hexazadithiophenolate macrocycles H2L2 and H2L3 and their open-chain N3S2 analogues H2L4 and H2L5 are reported. The highly crystalline compounds [Ni(L4)] (4), [Ni(L5)] (5), [Co(L5)] (6), [NiH2(L2)]2+ (7), [ZnH2(L2)]2+ (8), and [NiH2(L3)]2+ (9) could be readily prepared by stoichiometric complexation reactions of the hydrochlorides of the free ligands with the corresponding metal(II) dichlorides and NEt3 in methanolic solution. All complexes were characterized by X-ray crystallography. Monometallic complexes 4-6 of the pentadentate ligands H2L4 and H2L5 feature distorted square pyramidal MN3S2 structures (tau = 0.01 to 0.44). Similar coordination geometries are observed for the macrocyclic complexes 7-9 of the octadentate ligands H2L2 and H2L3. The two hydrogen atoms in 7-9 are attached to the noncoordinating benzylic amine functions and are hydrogen bonded to the metal-bound thiophenolate functions. A comparison of the structures of 4-9 reveals that the macrocycles L2 and L3 have a rather flexible ligand backbone that do not confer unusual coordination geometries on the metal ions. We also report on the ability of the monometallic complexes 7 and 8 to serve as starting materials for the preparation of dinuclear complexes.

Gallium(III) complexes of methyl pyropheophorbide-a as synthetic models for investigation of diastereomerically controlled axial ligation towards chlorophylls

Gallium(III) chlorins possessing a series of axial ligands were synthesized as model compounds of natural chlorophylls. A pair of diastereomers arising from the fifth axial coordination onto the asymmetric chlorin pi-macrocycle could be discriminated in a solution by both (1)H- and (13)C NMR spectroscopies.

Effects of the Intramolecular NH···S Hydrogen Bond in Mononuclear Platinum(II) and Palladium(II) Complexes with 2,2‘-Bipyridine and Benzenethiol Derivatives

A series of complexes, [M(bpy)(SAr)2] (M = platinum(II) or palladium(II), bpy = 2,2'-bipyridine, SAr = 2- or 4-(acylamino)benzenethiolate, or 2-(alkylcarbamoyl)benzenethiolate), were synthesized and characterized on the basis of 1H NMR, IR, and electrochemical properties. The structures of [Pt(bpy)(S-2-Ph3CCONHC6H4)2] (1) and [Pt(bpy)(S-2-t-BuNHCOC6H4)2] (3) were determined by X-ray analysis. The complexes have intramolecular NH...S hydrogen bonds between the amide NH group and the sulfur atom. A weak NH...S hydrogen bond in these complexes and [Pd(bpy)(S-2-Ph3CCONHC6H4)2] (4) is detected from the 1H NMR spectra and the IR spectra in chloroform and in the solid state. [Pt(bpy)(S-2-Ph3CCONHC6H4)2] (1) exhibits a remarkably high-energy-shifted lowest-energy band in UV-visible spectra and has a positively shifted oxidation potential. The blue-shift of 42 nm and the positive shift of +0.24 V, as compared to those of [Pt(bpy)(SC6H5)2), are due to the effect of the NH...S hydrogen bond.

Stabilization of calcium- and terbium-carboxylate bonds by NH...O hydrogen bonds in a mononuclear complex: a functional model of the active site of calcium-binding proteins

Novel benzoic acid ligands with bulky amide groups at the ortho position, 2,6-(MeCONH)(2)C(6)H(3)CO(2)H (1) and 2,6-(t-BuCONH)(2)C(6)H(3)CO(2)H (2), and their tris- and tetrakis(carboxylate) complexes with Ca(II) and Tb(III) ions, (NEt(4))(2)[Ca(II)[O(2)C-2,6-(t-BuCONH)(2)C(6)H(3)](4)] (4), [Tb[O(2)C-2,6-(t-BuNHCO)(2)C(6)H(3)](3)(H(2)O)(3)]] (5), and (NMe)(4)[Tb[O(2)C-2,6-(t-BuNHCO)(2)C(6)H(3)](4)(thf)] (6), were synthesized. The formation of the NH...O hydrogen bonds between the amide NH and carboxylate for 2, (NEt(4))[2,6-(t-BuCONH)(2)C(6)H(3)CO(2)] (3), and 4 was determined by (1)H NMR spectroscopy in solution and in the solid state (CRAMPS, IR). The ligand exchange reactions were attempted between 4 and a large excess of 2,4,6- Me(3)C(6)H(3)CO(2)H in chloroform-d solution; however, exchange reaction did not take place, indicating that the Ca(II) ions bound strongly to the carboxylate in 4. The Ca(II) ion binding properties with the benzoate derivatives were also examined using Tb(III) ion as a fluorescence probe. These results indicate that the NH...O hydrogen bonding between the amide NH and the oxygen atom of the carboxylate contributes to strong Ca(II) binding and prevents the dissociation of the calcium-carboxylate bond. The X-ray structural analyses of these complexes revealed that the NH.O hydrogen-bonded carboxylate ligands prefer the chelate-type coordination and create a mononuclear [Ca(O(2)CR)(4)](2)(-) or [Tb(O(2)CR)(4)](-) core with anionic charge, which is known only in the active site of calcium-binding proteins.

Roles of the proximal hydrogen bonding network in cytochrome P450cam-catalyzed oxygenation

Structural and functional roles of the hydrogen bonding network that surrounds the heme-thiolate coordination of P450(cam) from Pseudomonas putida were investigated. A hydrogen bond between the side chain amide of Gln360 and the carbonyl oxygen of the axial Cys357 was removed in Q360L. The side chain hydrogen bond and the electrostatic interaction between the polypeptide amide proton of Gln360 and the sulfur atom of Cys357 were simultaneously removed in Q360P. The increased electron donation of the axial thiolate in Q360L and Q360P was evidenced by negative shifts of their reduction potentials by 45 and 70 mV, respectively. Together with the results on L358P in which the amide proton at position 358 was removed (Yoshioka, S., Takahashi, S., Ishimori, K., Morishima, I. J. Inorg. Biochem. 2000, 81, 141-151), we propose that the side chain hydrogen bond and the electrostatic interaction of the amide proton with the thiolate ligand cause approximately 45 and approximately 35 mV of positive shifts, respectively, of the redox potential of the heme in P450(cam). The resonance Raman spectra of the ferrous-CO form of the Q360 mutants showed a downshifted Fe-CO stretching mode at 482 approximately 483 cm(-)(1) compared with that of wild-type P450(cam) at 484 cm(-)(1). The Q360 mutants also showed the upshift by 4 approximately 5 cm(-)(1) of the Fe-NO stretching mode in the ferrous-NO form. These Raman results indicate the increase in the sigma-electron donation of the thiolate ligand in the reduced state of the Q360 mutants and were in contrast to the increased pi-back-donation of the thiolate in L358P having an upshifted Fe-CO stretching mode at 489 cm(-)(1). The catalytic activities of the Q360 mutants for the unnatural substrates were similar to those of the wild-type enzyme, indicating that the increased sigma-electron donation does not promote the O-O bond heterolysis in the Q360 mutants, although the increased pi-electron donation in L358P promoted the heterolysis of the O-O bond. We conclude that the functions of the proximal hydrogen bonding network in P450(cam) are to stabilize the heme-thiolate coordination, and to regulate the redox potential of the heme iron. Furthermore, we propose that the pi-electron donation, not the sigma-electron donation, of the thiolate ligand promotes the heterolysis of the O-O bond of dioxygen.

Discontinuum between a thiolate and a thiol ligand

The effect of H-bond donation to the thiolate ligand of (eta(5)-C(5)H(5))Fe(CO)(2)SR (1) to give H-bond adducts (1 small middle dotHX) and eventually protonation to give [(eta(5)-C(5)H(5))Fe(CO)(2)(HSR)](+) (1H(+)()) has been investigated experimentally and computationally. The electronic structures of 1(R = Me), several derivatives of 1(R = Me) small middle dotHX, and 1(R = Me)H(+)() have been investigated using DFT (density functional theory) computational methods. As previously suggested, these calculations indicate the HOMO of 1 is Fedpi-Sppi antibonding and largely sulfur in character. The calculations indicate the electronic structure of 1 is not altered markedly by H-bond donation to the S center, but protonation results in a reorganization of the electronic structure of 1H(+)() and a HOMO that is largely metal in character. The reduction of Fe-S distances upon protonation of 1(R = Ph) to give 1(R = Ph)H(+)() small middle dotBF(4)()(-)() (2.282(2) and 2.258(2) A, respectively), as determined by single-crystal X-ray crystallography, also indicates diminished Fedpi-Sppi antibonding. Using the carbonyl stretching frequencies as a gauge of the donor ability of the thiolate ligand, we conclude that H-bonding has a continuous effect on the donor properties of the thiolate ligand of 1 (i.e., is a function of the pK(a) of the H-bond donor). A discontinuous effect results when the pK(b) of 1 is reached and the complex is protonated. For our study of 1, the maximal effect of H-bonding is about 30% of protonation. Because the position of acid-base equilibrium depends on the relative basicities of the thiolate ligand and the conjugate base of the H-bond donor (and the relative heats of solvation of the acids and their conjugate bases), a true continuum of effects can be anticipated only for systems that are pK-matched in their given environments. Thus, when the conjugate base of the H-bond donor is a stronger base than the thiolate ligand (as in the present case), H-bond donation has a relatively small effect, but protonation triggers a large, discontinuous effect on the electronic structure of 1.

Roles of the axial push effect in cytochrome P450cam studied with the site-directed mutagenesis at the heme proximal site

To examine the roles of the axial thiolate in cytochrome P450-catalyzed reactions, a mutant of cytochrome P450cam, L358P, was prepared to remove one of the conserved amide protons that are proposed to neutralize the negative charge of the thiolate sulfur. The increased push effect of the thiolate in L358P was evidenced by the reduced reduction potential of the heme. The 15N-NMR and resonance Raman spectra of the mutant in the ferric-CN and in the ferrous-CO forms, respectively, also supported the increased push effect. The maintenance of stereo- and regioselectivities for d-camphor hydroxylation by the mutant suggests the minimum structural change at the distal site. The heterolysis/homolysis ratios of cumene hydroperoxide were the same for wild-type and L358P. However, we observed the enhanced monooxygenations of the unnatural substrates using dioxygen and electrons supplied from the reconstituted system, which indicate the significant role of the push effect in dioxygen activation. We interpret that the enhanced push effect inhibits the protonation of the inner oxygen atom and/or promotes the protonation of the outer oxygen atom in the putative iron-hydroperoxo intermediate (Fe3+ -O-OH) of P450cam. This work is the first experimental indication of the significance of the axial cysteine for the P450 reactivity.