Resonance Raman Spectroscopy Reveals pH-Dependent Active Site Structural Changes of Lactoperoxidase Compound 0 and Its Ferryl Heme O–O Bond Cleavage Products

The first step in the enzymatic cycle of mammalian peroxidases, including lactoperoxidase (LPO), is binding of hydrogen peroxide to the ferric resting state to form a ferric-hydroperoxo intermediate designated as Compound 0, the residual proton temporarily associating with the distal pocket His109 residue. Upon delivery of this “stored” proton to the hydroperoxo fragment, it rapidly undergoes O–O bond cleavage, thereby thwarting efforts to trap it using rapid mixing methods. Fortunately, as shown herein, both the peroxo and the hydroperoxo (Compound 0) forms of LPO can be trapped by cryoradiolysis, with acquisition of their resonance Raman (rR) spectra now permitting structural characterization of their key Fe–O–O fragments. Studies were conducted under both acidic and alkaline conditions, revealing pH-dependent differences in relative populations of these intermediates. Furthermore, upon annealing, the low pH samples convert to two forms of a ferryl heme O–O bond-cleavage product, whose ν(Fe═O) frequencies reflect substantially different Fe═O bond strengths. In the process of conducting these studies, rR structural characterization of the dioxygen adduct of LPO, commonly called Compound III, has also been completed, demonstrating a substantial difference in the strengths of the Fe–O linkage of the Fe–O–O fragment under acidic and alkaline conditions, an effect most reasonably attributed to a corresponding weakening of the trans-axial histidyl imidazole linkage at lower pH. Collectively, these new results provide important insight into the impact of pH on the disposition of the key Fe–O–O and Fe═O fragments of intermediates that arise in the enzymatic cycles of LPO, other mammalian peroxidases, and related proteins

Unveiling the Crucial Intermediates in Androgen Production

Significance: The human enzyme cytochrome P450 17A1 (CYP17A1) catalyzes the critical step in the biosynthesis of the male sex hormones, and, as such, it is a key target for the inhibition of testosterone production that is necessary for the progression of certain cancers. CYP17A1 catalyzes two distinct types of chemical transformations. The first is the hydroxylation of the steroid precursors pregnenolone and progesterone. The second is a different reaction involving carbon–carbon (C-C) bond cleavage, the mechanism of which has been actively debated in the literature. Using a combination of chemical and biophysical methods, we have been able to trap and characterize the active intermediate in this C-C lyase reaction, an important step in the potential design of mechanism-based inhibitors for the treatment of prostate cancers. Abstract: Ablation of androgen production through surgery is one strategy against prostate cancer, with the current focus placed on pharmaceutical intervention to restrict androgen synthesis selectively, an endeavor that could benefit from the enhanced understanding of enzymatic mechanisms that derives from characterization of key reaction intermediates. The multifunctional cytochrome P450 17A1 (CYP17A1) first catalyzes the typical hydroxylation of its primary substrate, pregnenolone (PREG) and then also orchestrates a remarkable C17–C20 bond cleavage (lyase) reaction, converting the 17-hydroxypregnenolone initial product to dehydroepiandrosterone, a process representing the first committed step in the biosynthesis of androgens. Now, we report the capture and structural characterization of intermediates produced during this lyase step: an initial peroxo-anion intermediate, poised for nucleophilic attack on the C20 position by a substrate-associated H-bond, and the crucial ferric peroxo-hemiacetal intermediate that precedes carbon–carbon (C-C) bond cleavage. These studies provide a rare glimpse at the actual structural determinants of a chemical transformation that carries profound physiological consequences

Resonance Raman Studies of Oxygenated Forms of Myoglobin and CYP2B4 and Their Mutants

Important oxidative heme enzymes use hydrogen peroxide or activate molecular oxygen to generate highly reactive peroxo-, hydroperoxo- and feryl intermediates resulting from heterolytic O-O bond cleavage. Members of the cytochrome P450 superfamily catalyze difficult chemical transformations, including hydroxylations and C-C bond cleavage reactions. In mammals, these enzymes function to reliably produce important steroids with the required high degree of structural precision. On the other hand, certain other mammalian P450s serve a different role, efficiently metabolizing xenobiotics, including pharmaceuticals and environmental pollutants. Though so important, the precise mechanisms involved in such transformations are incompletely understood, because of difficulties in structurally characterizing the fleeting intermediates. This dissertation exploits a unique combination of techniques to address this issue, cryoradiolytically reducing the relatively stable dioxgen adducts to generate and trap the reactive species at low temperatures, followed by resonance Raman (rR) spectroscopic interrogation to effectively characterize key molecular fragments within these crucial intermediates. One essential goal of this work is to evaluate the rR spectral response to structural variations of such species employing an accessible model that can be systematically manipulated. Myoglobin (Mb) serves this purpose, because its readily accessible site-directed mutants are useful for investigating the effects of heme site environment on the structure and function of heme proteins. In the present work, horse heart Mb and 6 site-directed mutants are employed to study the effects of active site environment on the structure and behavior of the Fe-O-O and Fe=O fragments of the peroxo-, hydroperoxo- and ferryl forms that can arise. In addition, successful efforts were made to structurally define the Fe-O-O fragment of the dioxgen adduct of the mammalian drug-metabolizing Cytochrome P450 2B4 (CYP2B4) and explore its interaction with cytochromeb5. Much effort in this work was devoted to developing effective strategies to trap the especially unstable dioxygen adduct of CYP2B4. Corresponding studies of two key CYP2B4 mutants, E301Q and F429H, were also conducted, where the former mutation alters distal pocket interactions, while the F429H variant alters the strength of the trans-axial thiolate linkage that can modify the strength of the Fe-O and O-O linkages of the Fe-O-O fragments

Spectral Characterization of Cytochromes P450 Active Sites Using NMR and Resonance Raman Spectroscopy

The Cytochrome P450 (P450s) has been the subject of intense research for over six decades. An efficient approach for isotopic labeling of the prosthetic group in heme proteins was exploited to produce an analogue of the soluble bacterial cytochrome P450cam (P450cam) that contains a 13C labeled-protoheme prosthetic group. HU227 strain of E. coli, which lacks the δ-aminolevulinic acid (δ-ALA) synthase gene, was employed in the heterologous expression of P450cam harboring a prosthetic group labeled with 13C at the Cm and Cα positions by growing cells in the presence of [5-13C] δ-ALA, which was synthesized in four steps from [2-13C] glycine. NMR spectroscopy was used to confirm labelling of the hemes at the Cm and Cα positions. This system was utilized as proof of principle for the strategy of defining active site structure in cytochrome P450cam, including proton-to-proton distances on bound substrates, using NMR methods1. Such data are potentially of significant use in furnishing necessary experimental restrictions in docking routines, which are commonly employed in determining the relative affinities of drug candidates. 2D NOESY was employed and resonances assigned for the 13C labeled reference positions on heme and substrate. To confirm these resonance assignments on camphor, a substrate analogue, norcamphor was used. In another project, though it’s widely accepted that a highly reactive Fe(IV)=O π-cation radical, compound I, facilitates the oxidation of relatively inert hydrocarbons, spectroscopic characterization of this putative intermediate has eluded detection under turnover conditions, presumably due to its very short lifetime. Chemically inert substrates of P450s have been utilized in a novel approach to capture and stabilize this transient intermediate and characterize it with resonance Raman (RR) spectroscopy coupled with cryoradiolysis studies. Specifically, perfluorodecanoic acid was utilized as an inert surrogate substrate of a thermophilic cytochrome P450 designated CYP119 which was reported to possess a stable compound 12. Clearly, the presence of an inert substrate at low temperatures may prolong the lifetime of Compound I, allowing characterization by UV-visible and possibly RR and cryoradiolysis methods

Capture and Characterization of Dioxygen Reactive Intermediates in CYP51 Catalysis

The cytochromes P450 (CYPs) are a superfamily of biological catalysts that are ubiquitous throughout the biological domain. CYPs are heme-b containing monooxygenases which oxidize substrates with the help of accessory redox partners. CYP substrates include endogenous compounds required for many biological functions and homeostasis, such as steroids, as well as the majority of clinically used drugs and environmental xenobiotics. The majority of studies that have been performed to date are on P450cam (CYP101) from Pseudomonas putida. Of the numerous reactions catalyzed by CYPs, unactivated carbon-carbon bond cleavage, is one of particular versatility. Being unique in their catalytic mechanisms, the C-C bond cleaving enzymes and in particular CYP51 from Mycobacterium tuberculosis are though to be capable of utilizing multiple reactive oxygen intermediates. During the process of C-C bond cleavage, CYP51 catalyzes two classical hydroxylation reactions. The final reaction culminates in an enigmatic third step which cleaves a C-C bond, liberates formate, and installs a 14,15 double bond within its steroid substrate. The mechanism of CYP51s final step is still unclear and the exact activated oxygen species has yet to be observed. CYP51 is also distinct from most CYPs owing to the fact that the acid functionality of the conserved active site “acid-alcohol pair” found in most CYPs, is replaced by a histidine. This study aimed to trap and characterize dioxygen reactive intermediates, and elucidate the role of the unique acid-alcohol pair in the formation and stabilization of these intermediates. This study demonstrates our success in generating, stabilizing, and spectroscopically characterizing reactive dioxygen intermediates in Mtb CYP51. As the life-time of the oxyferrous intermediate in Mtb CYP51 is extremely short at ambient temperatures, this work has shown the laboratory’s expertise in being able to generate reduced oxyferrous intermediates at cryogenic temperatures. These intermediates have only been generated in a handful of cytochromes P450 and as such this work adds critical information to the small body of work currently reported

Active Site Structures of CYP11A1 in the Presence of Its Physiological Substrates and Alterations upon Binding of Adrenodoxin

The rate-limiting step in the steroid synthesis pathway is catalyzed by CYP11A1 through three sequential reactions. The first two steps involve hydroxylations at positions 22 and 20, generating 20(R),22(R)-dihydroxycholesterol (20R,22R-DiOHCH), with the third stage leading to a C20–C22 bond cleavage, forming pregnenolone. This work provides detailed information about the active site structure of CYP11A1 in the resting state and substrate-bound ferric forms as well as the CO-ligated adducts. In addition, high-quality resonance Raman spectra are reported for the dioxygen complexes, providing new insight into the status of Fe–O–O fragments encountered during the enzymatic cycle. Results show that the three natural substrates of CYP11A1 have quite different effects on the active site structure, including variations of spin state populations, reorientations of heme peripheral groups, and, most importantly, substrate-mediated distortions of Fe–CO and Fe–O2 fragments, as revealed by telltale shifts of the observed vibrational modes. Specifically, the vibrational mode patterns observed for the Fe–O–O fragments with the first and third substrates are consistent with H-bonding interactions with the terminal oxygen, a structural feature that tends to promote O–O bond cleavage to form the Compound I intermediate. Furthermore, such spectral data are acquired for complexes with the natural redox partner, adrenodoxin (Adx), revealing protein–protein-induced active site structural perturbations. While this work shows that Adx has an only weak effect on ferric and ferrous CO states, it has a relatively stronger impact on the Fe–O–O fragments of the functionally relevant oxy complexes

Redox and Spectroscopic Properties of Iron Porphyrin Nitroxyl in the Presence of Weak Acids

The spectroelectrochemistry and voltammetry of Fe(OEP) (NO) in the presence of substituted phenols was studied. Cyclic voltammetry showed that two closely spaced waves were observed for the reduction of Fe(OEP) (NO) in the presence of substituted phenols. The first wave was a single electron reduction under voltammetric conditions. The second wave was kinetically controlled, multielectron process. Visible spectroelectrochemistry of Fe(OEP) (NO) in the presence of substituted phenols showed that three species were present during the electrolysis. Additional spectroscopic studies indicated that the two reduction species were Fe(OEP) (HNO) and Fe(OEP)(H2NOH). The Fe(OEP) (HNO) species, which can be generated chemically, was stable over a period of hours. Additional acid did not lead to further protonation. Proton NMR spectroscopy confirmed the Fe(OEP) (HNO) species could be deprotonated under basic conditions. The third species, Fe(OEP)(H2NOH), was generated by the further reduction of the chemically generated Fe(OEP) (HNO) complex. Both the Fe(OEP) (HNO) and Fe(OEP)(H2NOH) complexes could be slowly oxidized back to Fe(OEP) (NO). At millimolar concentrations of Fe(OEP) (HNO), there was no evidence for the disproportionation of Fe(OEP) (HNO) to Fe(OEP) (NO) and H2 in the presence of substituted phenols. Nor was there evidence for the generation of N2O. The FTIR spectroelectrochemistry showed changes in the infrared spectra in the presence of substituted phenols, but no isotopic sensitive bands were observed for the reduced species between 1450 and 1200 cm–1. This may be because the νNO band shifted into a region (1500–1450 cm–1) where it would be difficult to observe

Resonance Raman Characterization of the Peroxo and Hydroperoxo Intermediates in Cytochrome P450

Resonance Raman (RR) studies of intermediates generated by cryoreduction of the oxyferrous complex of the D251N mutant of cytochrome P450cam (CYP101) are reported. Owing to the fact that proton delivery to the active site is hindered in this mutant, the unprotonated peroxo-ferric intermediate is observed as the primary species after radiolytic reduction of the oxy-complex in frozen solutions at 77 K. In as much as previous EPR and ENDOR studies have shown that annealing of this species to ∼180 K results in protonation of the distal oxygen atom to form the hydroperoxo intermediate, this system has been exploited to permit direct RR interrogation of the changes in the Fe−O and O−O bonds caused by the reduction and subsequent protonation. Our results show that the ν(O−O) mode decreases from a superoxo-like frequency near ∼1130 cm−1 to 792 cm−1 upon reduction. The latter frequency, as well as its lack of sensitivity to H/D exchange, is consistent with heme-bound peroxide formulation. This species also exhibits a ν(Fe−O) mode, the 553 cm−1 frequency of which is higher than that observed for the nonreduced oxy P450 precursor (537 cm−1), implying a strengthened Fe−O linkage upon reduction. Upon subsequent protonation, the resulting Fe−O−OH fragment exhibits a lowered ν(O−O) mode at 774 cm−1, whereas the ν(Fe−O) increases to 564 cm−1. Both modes exhibit a downshift upon H/D exchange, as expected for a hydroperoxo-ferric formulation. These experimental RR data are compared with those previously acquired for the wild-type protein, and the shifts observed upon reduction and subsequent protonation are discussed with reference to theoretical predictions

Spectroscopic characterization of iron-oxygen intermediates in human aromatase (CYP19A1)

CYP19A1 or aromatase, is a human steroidogenic P450 important for estrogen biosynthesis in humans. Over activation of aromatase results in malignancies of the breast tissue, especially in post menopausal women. In fact, aromatase inhibitors constitute the front line therapy for estrogen receptor positive (ER+) breast cancer in post-menopausal women which accounts for over 70% of all breast cancer cases in the United States. Starting with its androgenic substrates, testosterone and androstenedione, CYP19A1 forms estradiol and estrone utilizing one molecule of atmospheric oxygen and two reducing equivalents in the form of NADPH. This is accomplished in a three-step process one of which involves a carbon-carbon bond scission and aromatization. The catalytic mechanism of P450s has been long studied and it is well known that an oxo-ferryl π-cation radical, known as “Compound 1” in P450 chemistry is the reactive intermediate that catalyzes most of the reactions of P450s. The identity of the reaction intermediate that catalyzes the terminal step estrogen biosynthesis by CYP19A1 is still a mystery. There is evidence in the literature suggesting the involvement of Compound 1 via a hydrogen abstraction that initiates deformylation and subsequent aromatization. There is also suggestion of the peroxo-anion or “Compound 0” acting as a nucleophile, attacking the electrophilic carbonyl carbon of 19-oxo-androstenedione forming a peroxide adduct that then fragments to produce acyl-carbon cleavage. Owing to the interesting chemistry CYP19A1 catalyzes and its role in human health I focused my attention towards elucidating the mechanism of this critical enzyme with the hope that a detailed picture of the workings of CYP19A1 will help guide efforts to make more specific inhibitors and improve breast cancer prognosis. CYP19A1 is a membrane-bound hemeprotein with a rich spectroscopic landscape thus affording an opportunity to apply a repertoire of biophysical approaches to help piece together a reaction mechanism. I used the Nanodisc technology to stabilize CYP19A1 in its native membrane-like environment to obtain a mono-disperse, stable and homogenous enzyme preparation that is amicable to the optical, resonance Raman (rR) and electron paramagnetic resonance (EPR) spectroscopy and also, cryoradiolysis and cryospectroscopy. The approach I have applied in this project has been that of characterizing the individual fate of reaction intermediates on their way from substrates to products thereby catching them ‘in action’. My cryospectroscopy, EPR, rR and steady state kinetics efforts outlined in this doctoral thesis all implicate “Compound 1” as the reactive intermediate that is responsible for the carbon-carbon scission reactivity of CYP19A1

Spectral Characterization of Cytochromes P450 Active Site and Catalytic Intermediates

Cytochromes P450 (P450s) have been the subject of intense research for over six decades. Though it is widely accepted that a highly reactive Fe(IV)=O π-cation radical, or the so called compound I, facilitates the oxidation of relatively inert hydrocarbons, spectroscopic characterization of this putative intermediate has eluded detection under turnover conditions, presumably due to its very short lifetime. In this work, chemically inert substrates of P450s have been utilized in a new approach to capture and stabilize this transient intermediate and characterize it with resonance Raman (RR) spectroscopy, which is a well established tool for studying heme proteins. Specifically, perfluorodecanoic acid has been utilized as an inert surrogate substrate of a thermophilic cytochrome P450 designated CYP119 and RR and cryoradiolysis methods were employed to characterize the enzymatic intermediates under turnover conditions. In a separate project, a recent and more efficient approach for the isotopic labeling of the prosthetic group in heme proteins has been exploited to produce a 13C labeled analogue of the soluble bacterial cytochrome P450cam (P450cam). Briefly, the HU227 strain of E. coli that lacks the δ-aminolevulinic acid (δ-ALA) synthase gene was employed in the heterologous expression of P450cam harboring a prosthetic group labeled with 13C at the Cm and Cα positions by growing cells in the presence of [5-13C] δ-ALA, which was synthesized in four steps from [2-13C] glycine. This system has been utilized as proof of principle for the strategy of defining active site structure in mammalian cytochromes P450 using NMR methods to furnish necessary experimental restrictions in docking routines, which are commonly employed in determining the relative affinities of drug candidates. Noting that few crystal structures of substrate bound complexes of drug metabolizing P450s exist, a truncated CYP2D6 gene has been designed following a recently published procedure and efforts were made to heterologously express a selectively13C enriched analogue of this important drug metabolizing enzyme