Metal-ligand vibrations of cyanoferric myeloperoxidase and cyanoferric horseradish peroxidase: evidence for a constrained heme pocket in myeloperoxidase

Active Site Hydrogen Bonding Induced in Cytochrome P450cam by Effector Putidaredoxin

Cytochrome P450s are diverse and powerful catalysts that can activate molecular oxygen to oxidize a wide variety of substrates. Catalysis relies on effective uptake of two electrons and two protons. For cytochrome P450cam, an archetypal member of the superfamily, the second electron must be supplied by the redox partner putidaredoxin (Pdx). Pdx also plays an effector role beyond electron transfer, but after decades the mechanism remains under investigation. We applied infrared spectroscopy to heme-ligated CN^- to examine the influence of Pdx binding. The results indicate that Pdx induces the population of a conformation wherein the CN^- ligand forms a strong hydrogen bond to a solvent water molecule, experimentally corroborating the formation of a proposed proton delivery network. Further, characterization of T252A P450cam implicates the side chain of Thr252 in regulating the population equilibrium of hydrogen-bonded states within the P450cam/Pdx complex, which could underlie its role in directing activated oxygen toward product formation and preventing reaction uncoupling through peroxide release.

Investigation of Cyanide Ligand as an Active Site Probe of Human Heme Oxygenase

Human heme oxygenase (hHO-1) is a physiologically important enzyme responsible for free heme catabolism. The enzyme's high regiospecificity is controlled by the distal site hydrogen bond network that involves water molecules and the D140 amino acid residue. In this work, we probe the active site environment of the wild-type (WT) hHO-1 and its D140 mutants using resonance Raman (rR) spectroscopy. Cyanide ligands are more stable than dioxygen adducts and are an effective probe of active site environment of heme proteins. The inherently linear geometry of the Fe-C-N fragment can be altered by the steric, electrostatic, and H-bonding interactions imposed by the amino acid residues present in the heme distal site, resulting in a tilted or bent configuration. The WT hHO-1 and its D140A, D140N, and D140E mutants were studied in the presence of natural abundance CN^- and its isotopic analogues (¹³CN^-, C¹⁵N^-, and ¹³C¹⁵N^-). Deconvolution of spectral data revealed that the ν(Fe-CN) stretching and δ(Fe-CN) bending modes are present at 454 and 376 cm^-1, respectively. The rR spectral patterns of the CN^- adducts of WT revealed that the Fe-C-N fragment adopts a tilted conformation, with a larger bending contribution for the D140A, D140N, and D140E mutants. These studies suggest that the FeCN fragment in hHO-1 is tilted more strongly toward the porphyrin macrocycle compared to other histidine-ligated proteins, reflecting the propensity of the exogenous hHO-l ligands to position toward the α-meso-carbon, which is crucial for the HO reactivity and essential for regioselectivity.

Distinguishing Active Site Characteristics of Chlorite Dismutases with Their Cyanide Complexes

O2-evolving chlorite dismutases (Clds) efficiently convert chlorite (ClO2-) to O2 and Cl-. Dechloromonas aromatica Cld ( DaCld) is a highly active chlorite-decomposing homopentameric enzyme, typical of Clds found in perchlorate- and chlorate-respiring bacteria. The Gram-negative, human pathogen Klebsiella pneumoniae contains a homodimeric Cld ( KpCld) that also decomposes ClO2-, albeit with an activity 10-fold lower and a turnover number lower than those of DaCld. The interactions between the distal pocket and heme ligand of the DaCld and KpCld active sites have been probed via kinetic, thermodynamic, and spectroscopic behaviors of their cyanide complexes for insight into active site characteristics that are deterministic for chlorite decomposition. At 4.7 × 10-9 M, the KD for the KpCld-CN- complex is 2 orders of magnitude smaller than that of DaCld-CN- and indicates an affinity for CN- that is greater than that of most heme proteins. The difference in CN- affinity between Kp- and DaClds is predominantly due to differences in koff. The kinetics of binding of cyanide to DaCld, DaCld(R183Q), and KpCld between pH 4 and 8.5 corroborate the importance of distal Arg183 and a p Ka of ∼7 in stabilizing complexes of anionic ligands, including the substrate. The Fe-C stretching and FeCN bending modes of the DaCld-CN- (νFe-C, 441 cm-1; δFeCN, 396 cm-1) and KpCld-CN- (νFe-C, 441 cm-1; δFeCN, 356 cm-1) complexes reveal differences in their FeCN angle, which suggest different distal pocket interactions with their bound cyanide. Conformational differences in their catalytic sites are also reported by the single ferrous KpCld carbonyl complex, which is in contrast to the two conformers observed for DaCld-CO.

Investigations of ferric heme cyanide photodissociation in myoglobin and horseradish peroxidase

The photodissociation of cyanide from ferric myoglobin (MbCN) and horseradish peroxidase (HRPCN) has definitively been observed. This has implications for the interpretation of ultrafast IR (Helbing et al. Biophys. J. 2004, 87, 1881-1891) and optical (Gruia et al. Biophys. J. 2008, 94, 2252-2268) studies that had previously suggested the Fe-CN bond was photostable in MbCN. The photolysis of ferric MbCN takes place with a quantum yield of ~75%, and the resonance Raman spectrum of the photoproduct observed in steady-state experiments as a function of laser power and sample spinning rate is identical to that of ferric Mb (metMb). The data are quantitatively analyzed using a simple model where cyanide is photodissociated and, although geminate rebinding with a rate of kBA ≈ (3.6 ps)(-1) is the dominant process, some CN(-) exits from the distal heme pocket and is replaced by water. Using independently determined values for the CN(-) association rate, we find that the CN(-) escape rate from the ferric myoglobin pocket to the solution at 293 K is kout ≈ (1-2) × 10(7) s(-1). This value is very similar to, but slightly larger than, the histidine gated escape rate of CO from Mb (1.1 × 10(7) s(-1)) under the same conditions. The analysis leads to an escape probability kout/(kout + kBA) ~ 10(-4), which is unobservable in most time domain kinetic measurements. However, the photolysis is surprisingly easy to detect in Mb using cw resonance Raman measurements. This is due to the anomalously slow CN(-) bimolecular association rate (170 M(-1) s(-1)), which arises from the need for water to exchange at the ferric heme binding site of Mb. In contrast, ferric HRP does not have a heme bound water molecule and its CN(-) bimolecular association rate is larger by ~10(3), making the CN(-) photolysis more difficult to observe.

CO binding and ligand discrimination in human myeloperoxidase

Despite the fact that ferrous myeloperoxidase (MPO) can bind both O(2) and NO, its ability to bind CO has been questioned. UV/visible spectroscopy was used to confirm that CO induces small spectral shifts in ferrous MPO, and Fourier transform infrared difference spectroscopy showed definitively that these arose from formation of a heme ferrous-CO compound. Recombination rates after CO photolysis were monitored at 618 and 645 nm as a function of CO concentration and pH. At pH 6.3, k(on) and k(off) were 0.14 mM(-1) x s(-1) and 0.23 s(-1), respectively, yielding an unusually high K(D) of 1.6 mM. This affinity of MPO for CO is 10 times weaker than its affinity for O(2). The observed rate constant for CO binding increased with increasing pH and was governed by a single protonatable group with a pK(a) of 7.8. Fourier transform infrared spectroscopy revealed two different conformations of bound CO with frequencies at 1927 and 1942 cm(-1). Their recombination rate constants were identical, indicative of two forms of bound CO that are in rapid thermal equilibrium rather than two distinct protein populations with different binding sites. The ratio of bound states was pH-dependent (pK(a) approximately 7.4) with the 1927 cm(-1) form favored at high pH. Structural factors that account for the ligand-binding properties of MPO are identified by comparisons with published data on a range of other ligand-binding heme proteins, and support is given to the recent suggestion that the proximal His336 in MPO is in a true imidazolate state.

Geometries and electronic structures of cyanide adducts of the non-heme iron active site of superoxide reductases: vibrational and ENDOR studies

We have added cyanide to oxidized 1Fe and 2Fe superoxide reductase (SOR) as a surrogate for the putative ferric-(hydro)peroxo intermediate in the reaction of the enzymes with superoxide and have used vibrational and ENDOR spectroscopies to study the properties of the active site paramagnetic iron center. Addition of cyanide changes the active site iron center in oxidized SOR from rhombic high-spin ferric (S = 5/2) to axial-like low-spin ferric (S = 1/2). Low-temperature resonance Raman and ENDOR data show that the bound cyanide adopts three distinct conformations in Fe(III)-CN SOR. On the basis of 13CN, C15N, and 13C15N isotope shifts of the Fe-CN stretching/Fe-C-N bending modes, resonance Raman studies of 1Fe-SOR indicate one near-linear conformation (Fe-C-N angle approximately 175 degrees) and two distinct bent conformations (Fe-C-N angles <140 degrees). FTIR studies of 1Fe-SOR at ambient temperatures reveals three bound C-N stretching frequencies in the oxidized (ferric) state and one in the reduced (ferrous) state, indicating that the conformational heterogeneity in cyanide binding is a characteristic of the ferric state and is not caused by freezing-in of conformational substates at low temperature. 13C-ENDOR spectra for the 13CN-bound ferric active sites in both 1Fe- and 2Fe-SORs also show three well-resolved Fe-C-N conformations. Analysis of the 13C hyperfine tensors for the three substates of the 2Fe-SOR within a simple heuristic model for the Fe-C bonding gives values for the Fe-C-N angles in the three substates of ca. 123 degrees (C3) and 133 degrees (C2), taking a reference value from vibrational studies of 175 degrees (C1 species). Resonance Raman and ENDOR studies of SOR variants, in which the conserved glutamate and lysine residues in a flexible loop above the substrate binding pocket have been individually replaced by alanine, indicate that the side chains of these two residues are not involved in direct interaction with bound cyanide. The implications of these results for understanding the mechanism of SOR are discussed.

Active site structure and catalytic mechanisms of human peroxidases

Myeloperoxidase (MPO), eosinophil peroxidase, lactoperoxidase, and thyroid peroxidase are heme-containing oxidoreductases (EC 1.7.1.11), which bind ligands and/or undergo a series of redox reactions. Though sharing functional and structural homology, reflecting their phylogenetic origin, differences are observed regarding their spectral features, substrate specificities, redox properties, and kinetics of interconversion of the relevant redox intermediates ferric and ferrous peroxidase, compound I, compound II, and compound III. Depending on substrate availability, these heme enzymes path through the halogenation cycle and/or the peroxidase cycle and/or act as poor (pseudo-)catalases. Based on the published crystal structures of free MPO and its complexes with cyanide, bromide and thiocyanate as well as on sequence analysis and modeling, we critically discuss structure-function relationships. This analysis highlights similarities and distinguishing features within the mammalian peroxidases and intents to provide the molecular and enzymatic basis to understand the prominent role of these heme enzymes in host defense against infection, hormone biosynthesis, and pathogenesis.

The structures of prostaglandin endoperoxide H synthases-1 and -2

Despite the marked differences in their physiological roles, the structures and catalytic functions of the prostaglandin H2 endoperoxide synthases-1 and -2 (PGHS-1 and -2) are almost completely identical. These integral membrane proteins catalyze the conversion of arachidonic acid to PGG2 and finally to PGH2. The crystal structures of PGHS-1 and -2 provide new insights into the catalytic mechanism for fatty acid oxygenation. Moreover, a clearer picture emerges to explain how a handful of amino acid substitutions can give rise to subtle differences in ligand binding between the two isoforms. These "small" alterations of isozyme structure are sufficient to allow the design of new, isoform-selective drugs.

Elucidation of the differences between the 430- and 455-nm absorbing forms of P450-isocyanide adducts by resonance Raman spectroscopy

Alkylisocyanide adducts of microsomal P450 exist in two interconvertible forms, each giving the Soret maximum around 430 or 455 nm. This is demonstrated with a rabbit liver P450 2B4. Resonance Raman spectra of the 430- and 455-nm forms were examined for typical P450s of the two types as well as for P450 2B4 because the 430-nm form of P450 2B4 is liable to change into P420. P450cam and P450nor were selected as a model of the 430- and 455-nm forms, respectively. For the n-butyl isocyanide (CNBu) adduct, the Fe(II)-CNBu stretching band was observed for the first time at 480/467 cm(-1) for P450cam and at 471/459 cm(-1) for P450nor with their (12)CNBu/(13)CNBu derivatives. For P450cam, but not P450nor, other (13)C isotope-sensitive bands were observed at 412/402, 844/835, and 940/926 cm(-1). The C-N stretching mode was identified by Fourier transform IR spectroscopy at 2116/2080 cm(-1) for P450cam and at 2148/2108 cm(-1) for P450nor for the (12)C/(13)C derivatives. These findings suggest that the binding geometry of isocyanide differs between the two forms-bent and linear structures for P450cam-CNBu and P450nor-CNBu, respectively. In contrast, in the ferric state, the Raman (13)C isotopic frequency shifts, and the IR C-N stretching frequencies (2213/2170 and 2215/2172 cm(-1)) were similar between P450cam and P450nor, suggesting similar bent structures for both.

Cyanide binding and active site structure in heme-copper oxidases: normal coordinate analysis of iron-cyanide vibrations of a3(2+)CN- complexes of cytochromes ba3 and aa3

The cyanide isotope-sensitive low-frequency vibrations of ferrous cyano complexes of cytochrome a3 are studied for cytochrome ba3 from Thermus thermophilus and cytochrome aa3 from bovine heart. Cyanide complexes of ba3 display three isotope sensitive frequencies at 512, 485, and 473 cm-1. The first is primarily an Fe-C stretching motion, whereas the lower wavenumber modes are bending motions. These iron-cyanide vibrations are independent of the redox levels of the other metal centers in the protein. On the other hand, the fully reduced bovine derivative complexed with cyanide gives rise to a bending vibration at 503 cm-1 and a stretching vibration at 469 cm-1. That is, the ordering of the stretching and bending frequencies is reversed from that of the bacterial protein. These results are analyzed by normal coordinate calculations to obtain comparative models for the binuclear O2 reducing site of the two proteins. We find that the observed frequencies are consistent with a linear Fe-C-N group and larger Fe-C stretching force constant (2.558 mdyn/A) for ba3 and a slightly bent Fe-C-N group (angle approximately 170 degrees) and a smaller Fe-C stretching force constant (2.335 mdyn/A) for aa3. Thus, there are significant differences in the interaction of cyanide with ferrous a3 in the two proteins that are most likely caused by a weaker proximal histidine interaction and stronger peripheral heme electron withdrawing effects in ba3. Possible sources of these protein-induced effects are discussed. Using the analysis developed here, comparison of the FeCN stretching and bending frequencies of the ferrous bovine a3-CN complex to those obtained from the ferric a3-CN complex suggests that upon conversion of the resting to the fully reduced protein, a conformational change occurs that constrains the ligand binding site.

Vibrational Analysis of a Molecular Heme-Copper Assembly with a Nearly Linear Fe(III)-CN-Cu(II) Bridge: Insight into Cyanide Binding to Fully Oxidized Cytochrome c Oxidase

The complete vibrational analysis of [(1-MeIm)Fe(OEP)-CN-Cu(Me(6)tren)](2+) (1), which has been constructed as a model for the cyanide-ligated binuclear center in the respiratory protein cytochrome c oxidase, has been carried out. The resonance Raman spectra (lambda(exc) = 647 nm) and the mid-infrared spectra display three cyanide isotope-dependent vibrational modes. Two vibrations showed monotonic decreases with increasing mass of the cyanide ligand (2182-2137-2146-2101 cm(-)(1) and 535-526-526-520 cm(-)(1), respectively, for the (12)C(14)N-(13)C(14)N-(12)C(15)N-(13)C(15)N isotopomers), and could thus be assigned to the C&tbd1;N and Fe-CN-Cu stretching vibrations, respectively. The third vibration, detected with resonance Raman, showed a zigzag-type behavior (495-487-493-485 cm(-)(1) with the set of isotopomers above) with the frequency being more sensitive to (13)C labeling of the cyanide ligand than with (15)N labeling. This pattern of isotopic dependence is characteristic of a bending vibration. Additionally, with the same laser excitation frequency, the C&tbd1;N stretching mode was observed, which is the first time that this vibration has been detected in the resonance Raman spectrum of a synthetic heme-cyanide complex. The normal coordinate analysis showed marked differences between bridged and unbridged heme-cyanide complexes. Internal coordinates that are orthogonal in unbridged systems are significantly mixed in the bridged model, despite the overall linearity of the Fe-CN-Cu moiety. These measurements strengthen the proposal that cyanide bridges the two metal atoms in the cyanide-ligated, oxidized binuclear center of cytochrome c oxidase. A quantitative consideration of the vibrational characteristics of cyanide bound to the resting enzyme, in light of our model compound results, strongly suggests that the binuclear center is flexible and can undergo structural rearrangement to accommodate exogenous ligands. This is likely to be of mechanistic importance in both dioxygen reduction and proton translocation.

Resonance Raman investigation of cyanide ligated beef liver and Aspergillus niger catalases

Resonance Raman spectroscopy has been used to investigate the properties of cyanide-bound beef liver catalase (BLC) and Aspergillus niger catalase (ANC) in the pH range 4.9-11.5. Evidence has been obtained for the binding of cyanide to both BLC and ANC in two binding geometries. The first conformer, exhibiting the nu[Fe-CN] stretching mode at a higher frequency than the delta[Fe-C-N] bending mode, exists as an essentially linear Fe-C-N linkage. For both BLC-CN and ANC-CN, the nu[Fe-CN] and delta[Fe-C-N] frequencies of this conformer were practically identical and observed at approximately 434 and approximately 413 cm-1, respectively. The second conformer exhibits a nu[Fe-CN] mode at lower frequency than the delta[Fe-C-N] mode, and is thus characteristic of a bent Fe-C-N linkage. The nu[Fe-CN] and delta[Fe-C-N] modes were identified at 349 and 445 cm-1, respectively, for BLC-CN, and at 350 and 456 cm-1, respectively, for ANC-CN. The two conformers persist in the pH range 4.9-11.5. Furthermore, upon raising the pH to 11.5, the nu[Fe-CN] mode of the linear conformer of BLC-CN downshifts to 429 cm-1 while that of the bent conformer remains unchanged. The observed pH-dependent shift is attributed to the deprotonation of a distal-side amino acid residue, probably a distal histidine. The Fe-C-N axial vibrations of the two conformers identified for ANC-CN did not show any significant pH-dependent shifts, indicating a more stable hydrogen bonding interaction relative to BLC-CN.

Distinct heme active-site structure in lactoperoxidase revealed by resonance Raman spectroscopy

Low-frequency resonance Raman spectra of the cyanide and carbon monoxide adducts of lactoperoxidase are obtained with Soret excitation. The nu(Fe-CN) and delta(Fe-C-N) modes are detected at 360 and 453 cm-1, respectively. Upon the isotopic substitution of 13C14N, 12C15N, and 13C15N, the band at 453 cm-1 in the natural abundance adduct shifts to 448, 452, and 445 cm-1, while the 360-cm-1 peak shifts to 358, 357, and 356 cm-1, respectively. The 360-cm-1 band is shifted to 355 cm-1 when the pH is changed from 7.0 to 10.5. On the basis of a previous normal-mode analysis of the cyanoferric adduct of myeloperoxidase, a bent Fe-C-N linkage is suggested for the cyanide adduct of lactoperoxidase. The nu(Fe-CN) (374 cm-1) and delta(Fe-C-N) (480 cm-1) modes are observed for the cyanide adduct of reduced lactoperoxidase. For the carbon monoxide adduct, the nu(Fe-CO) (533 cm-1) and delta(Fe-C-O) (578 cm-1) modes at pH 7.0 are observed to shift to 498 and 570 cm-1 as the pH is raised from 7.0 to 10.0. The strong intensity of delta(Fe-C-O) at both acid and alkaline pHs, along with a suggested bent structure of the Fe-C-N moiety, implies a narrow heme pocket for lactoperoxidase.

Reaction of cyanide with cytochrome ba3 from Thermus thermophilus: spectroscopic characterization of the Fe(II)a3-CN.Cu(II)B-CN complex suggests four 14N atoms are coordinated to CuB

Cytochrome ba3 from Thermus thermophilus reacts slowly with excess HCN at pH 7.4 to create a form of the enzyme in which CuA, cytochrome b, and CuB remain oxidized, while cytochrome a3 is reduced by one electron, presumably with the formation of cyanogen. We have examined this form of the enzyme by UV-visible, resonance Raman, EPR, and electron nuclear double resonance spectroscopies in conjunction with permutations of 13C- and 15N-labeled cyanide. The results support a model in which one CN- binds through the carbon atom to ferrous a3, supporting a low-spin (S = 0) configuration on the Fe; bridging by this cyanide to the CuB is weak or absent. Four 14N atoms, presumably donated by histidine residues of the protein, provide a strong equatorial ligand field about CuB; a second CN- is coordinated through the carbon atom to CuB in an axial position.

Interaction of halides with the cyanide complex of myeloperoxidase: a model for substrate binding to compound I

EPR spectra of the low-spin cyanide complex of myeloperoxidase have been measured in the absence and presence of halide substrates; chloride, bromide and iodide. Halide-dependent spectral changes are found at acidic pH. The electronic structure of the low-spin ferric iron in cyanide complex appears to be modulated by halide binding to a protonated amino acid in the distal heme cavity. These findings suggest halide substrates can interact with ferryl oxygen in compound I during enzyme catalysis to form hypohalous acid.