Converting Cytochrome c into a Peroxidase-Like Metalloenzyme by Molecular Design

Effects of naturally occurring S47F/A mutations on the structure and function of human cytochrome c

The sequence and structure of human cytochrome c (hCyt c) exhibit evolutionary conservations, with only a limited number of naturally occurring mutations in humans. Herein, we investigated the effects of the naturally occurring S47F/A mutations on the structure and function of hCyt c in the oxidized form. Although the naturally occurring S47F/A mutations did not largely alter the protein structure, the S47F and S47A variants exhibited a small fraction of high-spin species. Kinetic studies showed that the peroxidase activity of the variants was enhanced by ∼2.5-fold under neutral pH conditions, as well as for the rate in reaction with H₂O₂, when compared to those of wild-type hCyt c. In addition, we evaluated the interaction between hCyt c and human neuroglobin (hNgb) by isothermal titration calorimetry (ITC) studies, which revealed that the binding constant was reduced by ∼8-fold as result of the mutation of the hydrophilic Ser to the hydrophobic Phe/Ala. These findings provide valuable insights into the role of Ser47 in Ω-loop C in sustaining the structure and function of hCyt c.

Converting cytochrome c into a DyP-like metalloenzyme

Dye-decolorizing peroxidase (DyP), which can degrade anthraquinone dyes using H₂O₂, is an attractive prospect for potential biotechnological applications for environmental purification. We previously designed an artificial DyP with an optimal pH for reactive blue 19 (RB19) degradation shifting from pH 4.5 to 6.5. We then attempted to degrade RB19 using Escherichia coli expressing this mutant, but RB19 was degraded equally compared with bacteria expressing wild-type (WT) DyP because most DyP was expressed in a heme-free form. In this study, we attempted to design an artificial peroxidase based on cytochrome c (cyt c), whose heme is covalently bound to the protein. We found that cyt c can degrade RB19, but its ability at pH 7.0 was ∼60% of that of DyP from Vibrio cholerae at pH 4.5. To enhance this activity we constructed several mutants using three approaches. Initially, to improve reactivity with H₂O₂, Met80 was replaced with a noncoordinating residue, Ala or Val, but catalytic efficiency (k_cat/K_m) was increased by only ∼1.5-fold. To enhance the substrate binding affinity we introduced an additional Trp by replacing Pro76 (P76W). The catalytic efficiency of this mutant was ∼3-fold greater than that of WT cyt c. Finally, to form a hydrogen bond to axial histidine Gly29 was replaced with Asp (G29D). This mutant exhibited an ∼80-fold greater dye-decolorizing activity. Escherichia coli expressing the G29D mutant was unable to degrade RB19 in solution due to degradation of heme itself, but this study provides new insights into the design of artificial DyPs.

Designing Artificial Metalloenzymes by Tuning of the Environment beyond the Primary Coordination Sphere

Metalloenzymes catalyze a variety of reactions using a limited number of natural amino acids and metallocofactors. Therefore, the environment beyond the primary coordination sphere must play an important role in both conferring and tuning their phenomenal catalytic properties, enabling active sites with otherwise similar primary coordination environments to perform a diverse array of biological functions. However, since the interactions beyond the primary coordination sphere are numerous and weak, it has been difficult to pinpoint structural features responsible for the tuning of activities of native enzymes. Designing artificial metalloenzymes (ArMs) offers an excellent basis to elucidate the roles of these interactions and to further develop practical biological catalysts. In this review, we highlight how the secondary coordination spheres of ArMs influence metal binding and catalysis, with particular focus on the use of native protein scaffolds as templates for the design of ArMs by either rational design aided by computational modeling, directed evolution, or a combination of both approaches. In describing successes in designing heme, nonheme Fe, and Cu metalloenzymes, heteronuclear metalloenzymes containing heme, and those ArMs containing other metal centers (including those with non-native metal ions and metallocofactors), we have summarized insights gained on how careful controls of the interactions in the secondary coordination sphere, including hydrophobic and hydrogen bonding interactions, allow the generation and tuning of these respective systems to approach, rival, and, in a few cases, exceed those of native enzymes. We have also provided an outlook on the remaining challenges in the field and future directions that will allow for a deeper understanding of the secondary coordination sphere a deeper understanding of the secondary coordintion sphere to be gained, and in turn to guide the design of a broader and more efficient variety of ArMs.

Naturally Occurring I81N Mutation in Human Cytochrome c Regulates Both Inherent Peroxidase Activity and Interactions with Neuroglobin

Human cytochrome c (hCyt c) is a crucial heme protein and plays an indispensable role in energy conversion and intrinsic apoptosis pathways. The sequence and structure of Cyt c were evolutionarily conserved and only a few naturally occurring mutants were detected in humans. Among those variable sites, position 81 was proposed to act as a peroxidase switch in the initiation stages of apoptosis. In this study, we show that Ile81 not only suppresses the intrinsic peroxidase activity but also is essential for Cyt c to interact with neuroglobin (Ngb), a potential protein partner. The kinetic assays showed that the peroxidase activity of the naturally occurring variant I81N was enhanced up to threefold under pH 5. The local stability of the Ω-loop D (residues 70-85) in the I81N variant was decreased. Moreover, the Alphafold2 program predicted that Ile81 forms stable contact with human Ngb. Meanwhile, the Ile81 to Asn81 missense mutation abolishes the interaction interface, resulting in a ∼40-fold decrease in binding affinity. These observations provide an insight into the structure-function relationship of the conserved Ile81 in vertebrate Cyt c.

Electrocatalysis by Heme Enzymes—Applications in Biosensing

Heme proteins take part in a number of fundamental biological processes, including oxygen transport and storage, electron transfer, catalysis and signal transduction. The redox chemistry of the heme iron and the biochemical diversity of heme proteins have led to the development of a plethora of biotechnological applications. This work focuses on biosensing devices based on heme proteins, in which they are electronically coupled to an electrode and their activity is determined through the measurement of catalytic currents in the presence of substrate, i.e., the target analyte of the biosensor. After an overview of the main concepts of amperometric biosensors, we address transduction schemes, protein immobilization strategies, and the performance of devices that explore reactions of heme biocatalysts, including peroxidase, cytochrome P450, catalase, nitrite reductase, cytochrome c oxidase, cytochrome c and derived microperoxidases, hemoglobin, and myoglobin. We further discuss how structural information about immobilized heme proteins can lead to rational design of biosensing devices, ensuring insights into their efficiency and long-term stability.

Early modification of cytochrome c by hydrogen peroxide triggers its fast degradation

Cytochrome c (cyt c), in addition to its function as an electron shuttle in respiratory chain, is able to perform as a pseudo-peroxidase with a critical role during apoptosis. Incubation of cyt c with an excess of hydrogen peroxide leads to a suicide inactivation of the protein, which is accompanied by heme destruction and covalent modification of numerous amino acid residues. Although steady-state reactions of cyt c with an excess of hydrogen peroxide represent non-physiological conditions, they might be used for analysis of the first-modified amino acid in in vivo. Here, we observed oxidation of tyrosine residues 67 and 74 and heme as the first modifications found upon incubation with hydrogen peroxide. The positions of the oxidized tyrosines suggest a possible migration pathway of hydrogen peroxide-induced radicals from the site of heme localization to the protein surface. Analysis of a size of folded fraction of cyt c upon limited incubation with hydrogen peroxide indicates that the early oxidation of amino acids triggers an accelerated destruction of cyt c. Position of channels from molecular dynamics simulation structures of cyt c points to a location of amino acid residues exposed to reactive oxidants that are thus more prone to covalent modification.

Hemoglobins from Scapharca subcrenata (Bivalvia: Arcidae) likely play an bactericidal role through their peroxidase activity

Hemoglobin (Hb) is an iron-containing respiratory protein present in all vertebrates and some invertebrates. The blood clam Scapharca subcrenata is one of the few invertebrates that have Hb-containing red hemocytes. In this study, we purified Hb (Ss-Hb), including Ss-HbI and Ss-HbII, from S. subcrenata hemocytes using gel chromatography with a recovery rate of 70.71%, and then characterized their peroxidase activities. Both Ss-Hbs possessed peroxidase activity with high affinity to the substrates guaiacol and H₂O₂. Moreover, both Ss-Hbs had structural similarities, such as type b heme, proximal histidine (His), distal His, and heme pocket arginine (Arg), with other peroxidases. The optimal peroxidase activity of both Ss-Hbs was at pH 5 and 35 °C, but this was inhibited in the presence of Cu²⁺ and Fe²⁺. Ss-Hbs produced [Formula: see text] in the presence of H₂O₂. β-phenylethylamine, a substrate of peroxidase, increased the [Formula: see text] generation, while Cu²⁺, an inhibitor of peroxidase, inhibited this reaction. These results indicated that the peroxidase cycle of Ss-Hb was involved in the production of [Formula: see text] . A large amount of [Formula: see text] may be generated by the peroxidase cycle if the substrate is sufficient. During the incubation of Ss-Hbs with Bacillus subtilis, it was speculated that trace H₂O₂, probably from autoxidation of Ss-Hbs or generated by B. subtilis, started the peroxidase cycle of Ss-Hb. and produced a large amount of [Formula: see text] in the presence of sufficient substrate in the culture medium. It is therefore reasonable to assume that Ss-Hbs played an antibacterial role owing to their peroxidase activity, which produced [Formula: see text] .

Lysine carbonylation is a previously unrecognized contributor to peroxidase activation of cytochrome c by chloramine-T

The peroxidase activity of cytochrome c (cyt c) plays a key role during apoptosis. Peroxidase catalysis requires a vacant Fe coordination site, i.e., cyt c must undergo an activation process involving structural changes that rupture the native Met80-Fe contact. A common strategy for dissociating this bond is the conversion of Met80 to sulfoxide (MetO). It is widely believed that this MetO formation in itself is sufficient for cyt c activation. This notion originates from studies on chloramine-T-treated cyt c (CT-cyt c) which represents a standard model for the peroxidase activated state. CT-cyt c is considered to be a "clean" species that has undergone selective MetO formation, without any other modifications. Using optical, chromatographic, and mass spectrometry techniques, the current work demonstrates that CT-induced activation of cyt c is more complicated than previously thought. MetO formation alone results in only marginal peroxidase activity, because dissociation of the Met80-Fe bond triggers alternative ligation scenarios where Lys residues interfere with access to the heme. We found that CT causes not only MetO formation, but also carbonylation of several Lys residues. Carbonylation is associated with -1 Da mass shifts that have gone undetected in the CT-cyt c literature. Proteoforms possessing both MetO and Lys carbonylation exhibit almost fourfold higher peroxidase activity than those with MetO alone. Carbonylation abrogates the capability of Lys to coordinate the heme, thereby freeing up the distal site as required for an active peroxidase. Previous studies on CT-cyt c may have inadvertently examined carbonylated proteoforms, potentially misattributing effects of carbonylation to solely MetO formation.

Structure, electrocatalysis and dynamics of immobilized cytochrome PccH and its microperoxidase

Geobacter sulfurreducens cells have the ability to exchange electrons with conductive materials, and the periplasmic cytochrome PccH plays an essential role in the direct electrode-to-cell electron transfer in this bacterium. It has atypically low redox potential and unique structural features that differ from those observed in other c-type cytochromes. We report surface enhanced resonance Raman spectroscopic and electrochemical characterization of the immobilized PccH, together with molecular dynamics simulations that allow for the rationalization of experimental observations. Upon attachment to electrodes functionalized with partially or fully hydrophobic self-assembled monolayers, PccH displays a distribution of native and non-native heme spin configurations, similar to those observed in horse heart cytochrome c. The native structural and thermodynamic features of PccH are preserved upon attachment mixed hydrophobic (-CH₃/-NH₂) surfaces, while pure -OH, -NH₂ and -COOH surfaces do not provide suitable platforms for its adsorption, indicating that its still unknown physiological redox partner might be membrane integrated. Neither of the employed immobilization strategies results in electrocatalytically active PccH capable of the reduction of hydrogen peroxide. Pseudoperoxidase activity is observed in immobilized microperoxidase, which is enzymatically produced from PccH and spectroscopically characterized. Further improvement of PccH microperoxidase stability is required for its application in electrochemical biosensing of hydrogen peroxide.

Hemoglobins Likely Function as Peroxidase in Blood Clam Tegillarca granosa Hemocytes

Hemoglobins are a group of respiratory proteins principally functioning in transport of oxygen and carbon dioxide in red blood cells of all vertebrates and some invertebrates. The blood clam T. granosa is one of the few invertebrates that have hemoglobin-containing red hemocytes. In the present research, the peroxidase activity of T. granosa hemoglobins (Tg-Hbs) was characterized and the associated mechanism of action was deciphered via structural comparison with other known peroxidases. We detected that purified Tg-Hbs catalyzed the oxidation of phenolic compounds in the presence of exogenous H₂O₂. Tg-Hbs peroxidase activity reached the maximum at pH 5 and 35°C and was inhibited by Fe²⁺, Cu²⁺, SDS, urea, and sodium azide. Tg-Hbs shared few similarities in amino acid sequence and overall structural characteristics with known peroxidases. However, the predicted structure at their heme pocket was highly similar to that of horseradish peroxidase (HRP) and myeloperoxidase (MPO). This research represented the first systemic characterization of hemoglobin as a peroxidase.

Magnetic Nano-Sponges for High-Capacity Protein Enrichment and Immobilization

On the basis of the gel effect of the living RAFT (Reversible Addition-Fragmentation Chain Transfer) polymerization, magnetic nano-sponges with ultrasoft PAA net-like shells are prepared and then used for enriching the entire proteins from real biological samples with ultrahigh capacity. In addition, the immobilized enzyme Cyt c or HRP surprisingly show much higher catalytic activity than free enzymes.

Regulating the coordination state of a heme protein by a designed distal hydrogen-bonding network

Heme coordination state determines the functional diversity of heme proteins. Using myoglobin as a model protein, we designed a distal hydrogen-bonding network by introducing both distal glutamic acid (Glu29) and histidine (His43) residues and regulated the heme into a bis-His coordination state with native ligands His64 and His93. This resembles the heme site in natural bis-His coordinated heme proteins such as cytoglobin and neuroglobin. A single mutation of L29E or F43H was found to form a distinct hydrogen-bonding network involving distal water molecules, instead of the bis-His heme coordination, which highlights the importance of the combination of multiple hydrogen-bonding interactions to regulate the heme coordination state. Kinetic studies further revealed that direct coordination of distal His64 to the heme iron negatively regulates fluoride binding and hydrogen peroxide activation by competing with the exogenous ligands. The new approach developed in this study can be generally applicable for fine-tuning the structure and function of heme proteins.

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.

Cytochrome c(552) from Thermus thermophilus engineered for facile substitution of prosthetic group

The facile replacement of heme c in cytochromes c with non-natural prosthetic groups has been difficult to achieve due to two thioether linkages between cysteine residues and the heme. Fee et al. demonstrated that cytochrome c(552) from Thermus thermophilus, overproduced in the cytosol of E. coli, has a covalent linkage cleavable by heat between the heme and Cys11, as well as possessing the thioether linkage with Cys14 [Fee, J. A. (2004) Biochemistry 43, 12162-12176]. Prompted by this result, we prepared a C14A mutant, anticipating that the heme species in the mutant was bound to the polypeptide solely through the thermally cleavable linkage; therefore, the removal of the heme would be feasible after heating the protein. Contrary to this expectation, C14A immediately after purification (as-purified C14A) possessed no covalent linkage. An attempt to extract the heme using a conventional acid-butanone method was unsuccessful due to rapid linkage formation between the heme and polypeptide. Spectroscopic analyses suggested that the as-purified C14A possessed a heme b derivative where one of two peripheral vinyl groups had been replaced with a group containing a reactive carbonyl. A reaction of the as-purified C14A with [BH(3)CN](-) blocked the linkage formation on the carbonyl group, allowing a quantitative yield of heme-free apo-C14A. Reconstitution of apo-C14A was achieved with ferric and ferrous heme b and zinc protoporphyrin. All reconstituted C14As showed spontaneous covalent linkage formation. We propose that C14A is a potential source for the facile production of an artificial cytochrome c, containing a non-natural prosthetic group.

Peroxidase activity enhancement of horse cytochrome c by dimerization

The peroxidase activity of horse cytochrome c was enhanced by its dimerization, where its Compound III (oxy-form) and Compound I (oxoferryl porphyrin π-cation radical) species were detected in the reactions with hydrogen peroxide and meta-chloroperbenzoic acid, respectively. These results show that oligomeric cytochrome c can contribute as a proapoptotic conformer by the increased peroxidase activity.