Oxygen Activation by Axial Ligand Mutants of Mitochondrial Cytochrome b5: Oxidation of Heme to Verdoheme and Biliverdin

Hydrogen-bonded organic framework biomimetic entrapment allowing non-native biocatalytic activity in enzyme

Nature programs the structural folding of an enzyme that allows its on-demand biofunctionality; however, it is still a long-standing challenge to manually modulate an enzyme’s conformation. Here, we design an exogenous hydrogen-bonded organic framework to modulate the conformation of cytochrome c, and hence allow non-native bioactivity for the enzyme. The rigid hydrogen-bonded organic framework, with net-arranged carboxylate inner cage, is in situ installed onto the native cytochrome c. The resultant hydrogen-bonded nano-biointerface changes the conformation to a previously not achieved catalase-like species within the reported cytochrome c-porous organic framework systems. In addition, the preserved hydrogen-bonded organic framework can stabilize the encapsulated enzyme and its channel-like pores also guarantee the free entrance of catalytic substrates. This work describes a conceptual nanotechnology for manoeuvring the flexible conformations of an enzyme, and also highlights the advantages of artificial hydrogen-bonded scaffolds to modulate enzyme activity.

Heme units are immobilised in diverse heme enzymes for oxidation, and have been immobilised also in hydrogen-bonded organic frameworks. Here, the authors show the use of hydrogen-bonded organic framework to modulate the enzyme’s conformation and show different biofunction from the original.

Ligand accessibility to heme cytochrome b5 coordinating sphere and enzymatic activity enhancement upon tyrosine ionization

Recently, we observed that at extreme alkaline pH, cytochrome b₅ (Cb₅) acquires a peroxidase-like activity upon formation of a low spin hemichrome associated with a non-native state. A functional characterization of Cb₅, in a wide pH range, shows that oxygenase/peroxidase activities are stimulated in alkaline media, and a correlation between tyrosine ionization and the attained enzymatic activities was noticed, associated with an altered heme spin state, when compared to acidic pH values at which the heme group is released. In these conditions, a competitive assay between imidazole binding and Cb₅ endogenous heme ligands revealed the appearance of a binding site for this exogenous ligand that promotes a heme group exposure to the solvent upon ligation. Our results shed light on the mechanism behind Cb₅ oxygenase/peroxidase activity stimulation in alkaline media and reveal a role of tyrosinate anion enhancing Cb₅ enzymatic activities on the distorted protein before maximum protein unfolding.

Peroxidase-like activity of cytochrome b5 is triggered upon hemichrome formation in alkaline pH

In alkaline media (pH12) a catalytic peroxidase activity of cytochrome b₅ was found associated to a different conformational state. Upon incubation at this pH, cytochrome b₅ electronic absorption spectrum was altered, with disappearance of characteristic bands of cytochrome b₅ at pH7.0. The appearance of new electronic absorption bands and EPR measurements support the formation of a cytochrome b₅ class B hemichrome with an acquired ability to bind polar ligands. This hemichrome is characterized by a negative formal redox potential and the same folding properties than cytochrome b₅ at pH7. The acquired peroxidase-like activity of cytochrome b₅ found at pH12, driven by a hemichrome formation, suggests a role of this protein in peroxidation products propagation.

Rational heme protein design: all roads lead to Rome

Heme proteins are among the most abundant and important metalloproteins, exerting diverse biological functions including oxygen transport, small molecule sensing, selective C-H bond activation, nitrite reduction, and electron transfer. Rational heme protein designs focus on the modification of the heme-binding active site and the heme group, protein hybridization and domain swapping, and de novo design. These strategies not only provide us with unique advantages for illustrating the structure-property-reactivity-function (SPRF) relationship of heme proteins in nature but also endow us with the ability to create novel biocatalysts and biosensors.

Heme uptake and metabolism in bacteria

All but a few bacterial species have an absolute need for heme, and most are able to synthesize it via a pathway that is highly conserved among all life domains. Because heme is a rich source for iron, many pathogenic bacteria have also evolved processes for sequestering heme from their hosts. The heme biosynthesis pathways are well understood at the genetic and structural biology levels. In comparison, much less is known about the heme acquisition, trafficking, and degradation processes in bacteria. Gram-positive and Gram-negative bacteria have evolved similar strategies but different tactics for importing and degrading heme, likely as a consequence of their different cellular architectures. The differences are manifested in distinct structures for molecules that perform similar functions. Consequently, the aim of this chapter is to provide an overview of the structural biology of proteins and protein-protein interactions that enable Gram-positive and Gram-negative bacteria to sequester heme from the extracellular milieu, import it to the cytosol, and degrade it to mine iron.

The Cytoplasmic Heme-binding Protein (PhuS) from the Heme Uptake System of Pseudomonas aeruginosa Is an Intracellular Heme-trafficking Protein to the δ-Regioselective Heme Oxygenase

The uptake and utilization of heme as an iron source is a receptor-mediated process in bacterial pathogens and involves a number of proteins required for internalization and degradation of heme. In the following report we provide the first in-depth spectroscopic and functional characterization of a cytoplasmic heme-binding protein PhuS from the opportunistic pathogen Pseudomonas aeruginosa. Spectroscopic characterization of the heme-PhuS complex at neutral pH indicates that the heme is predominantly six-coordinate low spin. However, the resonance Raman spectra and global fit analysis of the UV-visible spectra show that at all pH values between 6 and 10 three distinct species are present to varying degrees. The distribution of the heme across multiple spin states and coordination number highlights the flexibility of the heme environment. We provide further evidence that the cytoplasmic heme-binding proteins, contrary to previous reports, are not heme oxygenases. The degradation of the heme-PhuS complex in the presence of a reducing agent is a result of H2O2 formed by direct reduction of molecular oxygen and does not yield biliverdin. In contrast, the heme-PhuS complex is an intracellular heme trafficking protein that specifically transfers heme to the previously characterized iron-regulated heme oxygenase pa-HO. Surface plasmon resonance experiments confirm that the transfer of heme is driven by a specific protein-protein interaction. This data taken together with the spectroscopic characterization is consistent with a protein that functions to shuttle heme within the cell.

Voltammetric studies of Zn and Fe complexes of EDTA: Evidence for the push mechanism

The 'push' hypothesis for the antioxidant action of Zn2+ is based on its displacement of iron from a low molecular weight pro-oxidant complex. In this study, the chemical plausibility of that proposed function is investigated by cyclic voltammetry. As a model for a pro-oxidative low molecular weight iron complex the Fe(II/III)/EDTA couple was examined. This complex was selected for its well-defined electrochemical, iron stability constants, and similarity to other low molecular weight chelates in physiological fluids in terms of logical binding sites, i.e. amino, and carboxylate groups. Also investigated were iron complexes of nitrilotriacetic acid and DL-glutamic acid. Results demonstrate that approximately 90% of the cyclic voltammetric peak current for Fe(III)EDTA reduction and the EC' current for the mediated reduction of H2O2 by Fe(II/III)EDTA (Fenton Reaction) are lost when Zn2+ is introduced to a 1:1 molar ratio relative to iron. All experiments were conducted in HEPES buffered solutions at pH 7.4. Iron (II/III) complexes of nitrilotriacetic acid and DL-glutamic acid followed the same trends. Cyclic voltammetric experiments indicate that Zn2+ displaces Fe(III) from EDTA despite the much larger stability constant for the iron complex (10(25.1)) versus zinc (10(16.50)). The hydrolysis aided displacement of Fe(III) from EDTA by Zn2+ is considered by the equilibria modeling program, HySS. With Fe(III) hydrolysis products included, Zn2+ is able to achieve 90% displacement of iron from EDTA, a result consistent with cyclic voltammetric observations.

A hypothesis for the basis of the pro-oxidant nature of calcium ions

A new hypothesis describing the role of the redox inactive Ca2+ ion in the expression of physiological oxidative damage is described. The hypothesis is based on the optimization of the chelation characteristics of iron complexes for pro-oxidant activity. In a previous investigation it was found that an excess of ligand kinetically hindered the Fenton reaction activity of the FeII/III EDTA complex (Bobier et al. 2003). EDTA, citrate, NTA, and glutamate were selected as models for the coordination sites likely encountered by mobile iron, i.e. proteins. The optimal [EDTA]:[FeIII] ratio for Fenton reaction activity as measured by electrocatalytic voltammetry in a solution was found to be 1:1. An excess of EDTA in the amount of 10:1 [ligand]: [metal] suppresses the Fenton reaction activity to nearly the control. It is expected that the physiological coordination characteristics of mobile Fe would have a very large excess of [ligand]:[metal] and thus not be optimized for the Fenton reaction. Introduction of Ca2+ in to a ratio of 10:10:1 [Ca2+]:[EDTA]:[FeIII] to the system reinvigorated the Fenton reaction activity to nearly the value of the optimal 1:1 [EDTA] :[FeIII] complex. The pH distribution diagrams of Ca2+ in the presence of EDTA and FeII/III indicate that Ca2+ has the ability to uptake excess EDTA without displacing either FeII of FeIII from their respective complexed forms. The similarity in the presence for hard ligand sites albeit with a lower binding constant for Ca2+ accounts for this action.

Oxidative Verdoheme Formation and Stabilization by Axial Isocyanide Ligation

The effect of isocyanides as axial ligands on the formation and stability of verdoheme by oxidation has been examined. The reaction of [Fe(III)(OEPO)]2 with t-butyl isocyanide under dioxygen-free conditions results in the formation of (t-BuNC)2Fe(II)(OEPO*) with an electron paramagnetic resonance at g=2.009 with a peak-to-peak separation of 23.5 G at 4 K. (OEPO is the trianion of octaethyloxophlorin and OEPO* is the radical dianion obtained from OEPO by one-electron oxidation.) Exposure of chloroform solutions of either (2,6-xylylNC)2Fe(II)(OEPO*) or (t-BuNC)2Fe(II)(OEPO*) to dioxygen followed by the addition of ammonium hexafluorophosphate results in their transformation into the diamagnetic verdohemes, [(2,6-xylylNC)2Fe(II)(OEOP)](PF6) and [(t-BuNC)2Fe(II)(OEOP)](PF6), yields 68 and 70%, respectively. (OEOP is the anion of octaethyl-5-oxaporphyrin.) The oxidation reactions of (2,6-xylylNC)2Fe(II)(OEPO*) and (t-BuNC)2Fe(II)(OEPO*) have also been monitored by 1H NMR spectroscopy. No resonances due to paramagnetic products could be detected, the reactions appear to result only in the formation of the diamagnetic verdohemes, and the products are not susceptible to further oxidation.

Metallobiliverdin radicals--DFT studies

Several aspects of the molecular and electronic structure of biliverdin derivatives have been studied using density functional theory (DFT). The calculations have been performed for complexes of trianion (BvO2)3- and dianion [BvO(OH)]2-, derived from two tautomeric forms of biliverdin, BvO2H3 and [BvO(OH)]H2, with redox innocent metal ions: lithium(I), zinc(II), and gallium(III). One-electron-oxidized and reduced forms of each complex (cation and anion radicals) have been also considered. The molecular structures of all species investigated are characterized by a helical arrangement of tetrapyrrolic ligands with the metal ion lying in the plane formed by the two central pyrrole rings. The spin density distribution in four types of metallobiliverdin radicals--[(BvO2.)Mn+]n-2,[[BvO(OH).]Mn+]n-1 (cation radicals),[(BvO2.)Mn+]n-4,[[BvO(OH).]Mn+]n-3 (anion radicals)--has been investigated. In general, the absolute values of spin density on meso carbon atoms were larger than for the beta-carbon atoms. Sign alteration of spin density has been found for meso positions, and also for the beta-carbon atoms of at least two pyrrole rings. The calculated spin density maps accounted for the essential NMR spectroscopic features of iron biliverdin derivatives, including the considerable isotropic shifts detected for the meso resonances and shift alteration at the meso and beta-positions.

Coupled oxidation vs heme oxygenation: insights from axial ligand mutants of mitochondrial cytochrome b5

Mutation of His-39, one of the axial ligands in rat outer mitochondrial membrane cytochrome b(5) (OM cyt b(5)), to Val produces a mutant (H39V) capable of carrying out the oxidation of heme to biliverdin when incubated with hydrazine and O(2). The reaction proceeds via the formation of an oxyferrous complex (Fe(II)(-)O(2)) that is reduced by hydrazine to a ferric hydroperoxide (Fe(III)(-)OOH) species. The latter adds a hydroxyl group to the porphyrin to form meso-hydroxyheme. The observation that catalase does not inhibit the oxidation of the heme in the H39V mutant is consistent with the formation of a coordinated hydroperoxide (Fe(III)(-)OOH), which in heme oxygenase is the precursor of meso-hydroxyheme. By comparison, mutation of His-63, the other axial ligand in OM cyt b(5), to Val results in a mutant (H63V) capable of oxidizing heme to verdoheme in the absence of catalase. However, the oxidation of heme by H63V is completely inhibited by catalase. Furthermore, whereas the incubation of Fe(III)(-)H63V with H(2)O(2) leads to the nonspecific degradation of heme, the incubation of Fe(II)(-)H63V with H(2)O(2) results in the formation of meso-hydroxyheme, which upon exposure to O(2) is rapidly converted to verdoheme. These findings revealed that although meso-hydroxyheme is formed during the degradation of heme by the enzyme heme oxygenase or by the process of coupled oxidation of model hemes and hemoproteins not involved in heme catabolism, the corresponding mechanisms by which meso-hydroxyheme is generated are different. In the coupled oxidation process O(2) is reduced to noncoordinated H(2)O(2), which reacts with Fe(II)-heme to form meso-hydroxyheme. In the heme oxygenation reaction a coordinated O(2) molecule (Fe(II)(-)O(2)) is reduced to a coordinated peroxide molecule (Fe(III)(-)OOH), which oxidizes heme to meso-hydroxyheme.

Evidence for nonhydrogen bonded compound II in cyclic reaction of hemoglobin I from Lucina pectinata with hydrogen peroxide

Studies that elucidate the behavior of the hemoglobins (Hbs) and myoglobins upon reaction with hydrogen peroxide are essential to the development of oxygen carrier substitutes. Stopped-flow kinetics and resonance Raman data show that the reaction between hydrogen peroxide and oxygenated and deoxygenated ferric Hb I (oxy- and deoxy-HbI) from Lucina pectinata produce compound I and compound II ferryl species. The rate constants ratio (k23/k41) between the formation of compound II from compound I (k23) and the oxidation of the ferrous HbI (k41, i.e., 25 M(-1) s(-1)) of 12 x 10(-4) M suggests that HbI has a peroxidative capacity for removing H2O2 from solution. Resonance Raman presents the formation of both, met-aquo-HbI and compound II ferryl species in the cyclic reaction of HbI with H2O2. The ferric HbI species is maintained by the presence of H2O2; it can produce HbI compound I, or it can be reduced to a deoxy-HbI derivative to form HbI compound II upon reaction with H2O2. The compound II ferryl vibration frequency appears at 805 and 769 cm(-1) for HbIFe(IV)=(16)O and HbIFe(IV)=(18)O species, respectively. This ferryl mode indicates the absence of hydrogen bonding between the carbonyl group of the distal Q64 and the HbIFe(IV)=O ferryl moiety. The observation suggests that both the trans-ligand effect and the polarizabilty of the HbI heme pocket are responsible for the observed ferryl oxo vibrational energy. The vibrational mode also suggests that the carbonyl group of the distal Q64 is oriented toward the iron of the heme group, increasing the distal pocket electron density.

Solution NMR determination of the seating(s) of meso-nitro-etioheme-1 in myoglobin: implications for steric constraints to meso position access in heme degradation by coupled oxidation

The highly stereoselective cleavage of hemin in myoglobin by coupled oxidation has been attributed to steric barriers that leave more space near the alpha- than the other meso-positions. The steric barriers near meso positions in myoglobin have been investigated by establishing the thermodynamics and dynamics of possible seatings in the pocket of horse myoglobin of a four-fold symmetric etioheme I modified with a bulky nitro group at a single meso position. The cyanomet complex of this reconstituted myoglobin exhibits three sets of (1)H NMR resonances that are linked dynamically and occur in approximate populations ratios of 0.82:0.10:0.08. Two dimensional (1)H NMR has been used to assign the hemin and heme pocket resonances in the major isomer in solution and to determine that the hemin is oriented with the nitro group at the canonical gamma-meso position of native hemin. The dominance of this isomer is attributed to the solvent exposure of this portion of the hemin which stabilizes the highly polar nitro group. Using a combination of magnetization transfer among methyl groups of the three isomers due to "hopping" of the hemin about its normal, the assigned resonances of an isoelectronic, bis-cyano complex of meso-nitro-etioheme I, and the known essentially constant rhombic perturbation of heme pocket sites on the hyperfine shifts of heme methyl (Kolczak, U.; Hauksson, J. B.; Davis, N. L.; Pande, U.; de Ropp, J. S.; Langry, K. C.; Smith, K. M.; LaMar, G. N. J. Am. Chem. Soc. 1999, 121, 835-843); the two minor isomers are shown to place their bulky nitro group at the canonical delta-meso (8%) and alpha-meso positions (10%). The comparable population of the isomers with nitro groups at the hydrophobic alpha- and delta-meso positions dictates that, while the static crystal structure finds more room near the alpha-meso position, the deformation at minimal energetic expense near the alpha- and delta-meso positions is comparable. These results argue that factors other than simple steric influences control the selectivity of the ring cleavage in myoglobin.