Designer Heme Proteins: Achieving Novel Function with Abiological Heme Analogues

Tetraquinolines; four linked quinoline units or porphyrinoids

Tetraquinolines (TEQs) have been recently synthesized and proposed to be a new member of the porphyrinoid family with highly distorted, nonplanar, geometries. In this contribution by studying several molecules, closely related to TEQs, we have suggested that the origin of the nonplanarity of TEQs and their counterparts is a combination of steric strain and the propensity of the molecules to avoid antiaromaticity. The tendency of TEQs to coordinate with doubly charged metal ions can be interpreted in terms of their transition from potential antiaromaticity to nonaromaticity. Even metal-coordinated TEQs do not sustain diatropic ring currents. Although full planarization is not possible because of steric strain, doubly oxidized TEQs and their counterparts sustain moderate global diatropic ring currents and partially planarize. The nature of current density in the molecules is studied in the light of Steiner-Fowler selection rules.

Atomic-level design of metalloenzyme-like active pockets in metal-organic frameworks for bioinspired catalysis

Natural metalloenzymes with astonishing reaction activity and specificity underpin essential life transformations. Nevertheless, enzymes only operate under mild conditions to keep sophisticated structures active, limiting their potential applications. Artificial metalloenzymes that recapitulate the catalytic activity of enzymes can not only circumvent the enzymatic fragility but also bring versatile functions into practice. Among them, metal-organic frameworks (MOFs) featuring diverse and site-isolated metal sites and supramolecular structures have emerged as promising candidates for metalloenzymes to move toward unparalleled properties and behaviour of enzymes. In this review, we systematically summarize the significant advances in MOF-based metalloenzyme mimics with a special emphasis on active pocket engineering at the atomic level, including primary catalytic sites and secondary coordination spheres. Then, the deep understanding of catalytic mechanisms and their advanced applications are discussed. Finally, a perspective on this emerging frontier research is provided to advance bioinspired catalysis.

An engineered thermally tolerant apo-cytochrome scaffold for metal-less incorporation of heme derivative

Cytochrome c552 from Thermus thermophilus is one of the hot topics for creating smart biomaterials as it possesses remarkable stability, is tolerant to multiple mutations and has therefore been recently reported for a number of functionalizations upon substitution of the original prosthetic group with an artificial prosthetic group. However, all of the substitutions were driven by the coordination through the axial ligands followed by complete reconstitution with a metal-porphyrin complex. This limits the scope of the cytochrome c for incorporating a metal-less non-natural heme species that could improve the versatility of cytochrome c for a new generation of engineered cytochrome proteins for further enhancement in their functionalities such as biocatalysts. In this connection, a new variant of Cytochrome c (rC552 C14A) from Thermus thermophilus was reported, where an easy approach to remove the original prosthetic group was achieved, followed by the incorporation of a number of metal-PPIX derivatives that ultimately led to the formation of artificial c-type cytochromes through covalent bonding. The apo-cytochrome was found to be thermally tolerant and to possess a distinctive overall structure as that of the wild type, as was evident from the corresponding CD spectra, which ultimately encouraged reconstitution with a metal-less protoporphyrin derivative for better understanding the role of axial ligands in the reconstitution process. Successful reconstitution was achieved, resulting in a new type of Cytochrome b-type artificial protein without the metal in its active site, indicating the non-involvement of the axial ligand. In order to prove the non-involvement of the axial ligand, a subsequent double mutant (C14A/M69A) was constructed, replacing the methionine at 69 position with non-coordinating alanine residue. Accordingly, the apo-C14A/M69A was prepared and found to be extremely stable as the earlier mutants and the WT showed no signs of denaturation, even at the elevated temperature of 98°C. Subsequently, heme b was successfully incorporated into the apo-C14A/M69A, which demonstrated itself as a highly thermally tolerant protein scaffold for incorporating a metal-less artificial prosthetic group in the absence of the axial ligand. Further improvement in the reconstitution process is achieved by replacing the methionine at 69 position with phenyl alanine (C14A/M69F mutant), resulting in further stabilization of heme species, possibly through non-covalent π-interactions, as corroborated by molecular docking.

Diversifying the functions of heme proteins with non-porphyrin cofactors

Heme proteins perform diverse biochemical functions using a single iron porphyrin cofactor. This versatility makes them attractive platforms for the development of new functional proteins. While directed evolution and metal substitution have expanded the properties, reactivity, and applications of heme proteins, the incorporation of porphyrin analogs remains an underexplored approach. This review discusses the replacement of heme with non-porphyrin cofactors, such as porphycene, corrole, tetradehydrocorrin, phthalocyanine, and salophen, and the attendant properties of these conjugates. While structurally similar, each ligand exhibits distinct optical and redox properties, as well as unique chemical reactivity. These hybrids serve as model systems to elucidate the effects of the protein environment on the electronic structure, redox potentials, optical properties, or other features of the porphyrin analog. Protein encapsulation can confer distinct chemical reactivity or selectivity of artificial metalloenzymes that cannot be achieved with the small molecule catalyst alone. Additionally, these conjugates can interfere with heme acquisition and uptake in pathogenic bacteria, providing an inroad to innovative antibiotic strategies. Together, these examples illustrate the diverse functionality that can be achieved by cofactor substitution. The further expansion of this approach will access unexplored chemical space, enabling the development of superior catalysts and the creation of heme proteins with emergent properties.

Heterologous expression, purification and structural features of native Dictyostelium discoideum dye-decolorizing peroxidase bound to a natively incorporated heme

The Dictyostelium discoideum dye-decolorizing peroxidase (DdDyP) is a newly discovered peroxidase, which belongs to a unique class of heme peroxidase family that lacks homology to the known members of plant peroxidase superfamily. DdDyP catalyzes the H2O2-dependent oxidation of a wide-spectrum of substrates ranging from polycyclic dyes to lignin biomass, holding promise for potential industrial and biotechnological applications. To study the molecular mechanism of DdDyP, highly pure and functional protein with a natively incorporated heme is required, however, obtaining a functional DyP-type peroxidase with a natively bound heme is challenging and often requires addition of expensive biosynthesis precursors. Alternatively, a heme in vitro reconstitution approach followed by a chromatographic purification step to remove the excess heme is often used. Here, we show that expressing the DdDyP peroxidase in ×2 YT enriched medium at low temperature (20°C), without adding heme supplement or biosynthetic precursors, allows for a correct native incorporation of heme into the apo-protein, giving rise to a stable protein with a strong Soret peak at 402 nm. Further, we crystallized and determined the native structure of DdDyP at a resolution of 1.95 Å, which verifies the correct heme binding and its geometry. The structural analysis also reveals a binding of two water molecules at the distal site of heme plane bridging the catalytic residues (Arg239 and Asp149) of the GXXDG motif to the heme-Fe(III) via hydrogen bonds. Our results provide new insights into the geometry of native DdDyP active site and its implication on DyP catalysis.

Study on enhancement of hemoglobin antitoxic ability modified with chromium and ruthenium

Hemoglobin is essential for carrying oxygen (O₂) in the blood. However, its ability to bind excessively to carbon monoxide (CO) makes it susceptible to CO poisoning. To reduce the risk of CO poisoning, Cr-based heme and Ru-based heme were selected from among many transition metal-based hemes based on their characteristics of adsorption conformation, binding intensity, spin multiplicity, and electronic properties. The results showed that hemoglobin modified by Cr-based heme and Ru-based heme had strong anti-CO poisoning abilities. The Cr-based heme and Ru-based heme exhibited much stronger affinity for O₂ (-190.67 kJ/mol and -143.18 kJ/mol, respectively) than Fe-based heme (-44.60 kJ/mol). Moreover, Cr-based heme and Ru-based heme exhibited much weaker affinity for CO (-121.50 kJ/mol and -120.88 kJ/mol, respectively) than their affinity for O₂, suggesting that they were less likely to cause CO poisoning. The electronic structure analysis also supported this conclusion. Additionally, molecular dynamics analysis showed that hemoglobin modified by Cr-based heme and Ru-based heme was stable. Our findings offer a novel and effective strategy for enhancing the reconstructed hemoglobin's ability to bind O₂ and reduce its potential for CO poisoning.

Chimeric Biocatalyst Combining Peptidic and Nucleic Acid Components Overcomes the Performance and Limitations of the Native Horseradish Peroxidase

Chimeric peptide-DNAzyme (CPDzyme) is a novel artificial peroxidase that relies on the covalent assembly of DNA, peptides, and an enzyme cofactor in a single scaffold. An accurate control of the assembly of these different partners allows for the design of the CPDzyme prototype G4-Hemin-KHRRH, found to be >2000-fold more active (in terms of conversion number k_cat) than the corresponding but non-covalent G4/Hemin complex and, more importantly, >1.5-fold more active than the corresponding native peroxidase (horseradish peroxidase) when considering a single catalytic center. This unique performance originates in a series of gradual improvements, thanks to an accurate selection and arrangement of the different components of the CPDzyme, in order to benefit from synergistic interactions between them. The optimized prototype G4-Hemin-KHRRH is efficient and robust as it can be used under a wide range of non-physiologically relevant conditions [organic solvents, high temperature (95 °C), and in a wide range of pH (from 2 to 10)], thus compensating for the shortcomings of the natural enzymes. Our approach thus opens broad prospects for the design of ever more efficient artificial enzymes.

Probing nitric oxide signaling using molecular MRI

Wide field measurements of nitric oxide (NO) signaling could help understand and diagnose the many physiological processes in which NO plays a key role. Magnetic resonance imaging (MRI) can support particularly powerful approaches for this purpose if equipped with molecular probes sensitized to NO and NO-associated targets. In this review, we discuss the development of MRI-detectable probes that could enable studies of nitrergic signaling in animals and potentially human subjects. Major families of probes include contrast agents designed to capture and report integrated NO levels directly, as well as molecules that respond to or emulate the activity of nitric oxide synthase enzymes. For each group, we outline the relevant molecular mechanisms and discuss results that have been obtained in vitro and in animals. The most promising in vivo data described to date have been acquired using NO capture-based relaxation agents and using engineered nitric oxide synthases that provide hemodynamic readouts of NO signaling pathway activation. These advances establish a beachhead for ongoing efforts to improve the sensitivity, specificity, and clinical applicability of NO-related molecular MRI technology.

Ratiometric Oxygen Sensing with H-NOX Protein Conjugates

Ratiometric sensors are self-referencing constructs that are functional in cells and tissues, and the read-out is independent of sensor concentration. One strategy for ratiometric sensing is to utilize two-color emission, where one component possesses analyte-dependent emission and the other is independent of analyte concentration, serving as an internal standard. In this way, the intensity ratio of the two components is a quantitative measure of the analyte. In this study, protein-based ratiometric oxygen sensors are prepared using the heme nitric oxide/oxygen-binding protein (H-NOX) from the thermophilic bacterium Caldanaerobacter subterraneus. The native heme cofactor is replaced with a Pd(II) or Pt(II) porphyrin as the oxygen-responsive phosphor. Mutagenesis is performed to incorporate a cysteine residue on the protein surface for thiol/maleimide coupling of the oxygen-insensitive dye, which serves as a Förster resonance energy transfer (FRET) donor for the porphyrin. While both Pd(II)- and Pt(II)-based sensors are responsive over biologically relevant ranges, the Pd sensor exhibits greater sensitivity at lower oxygen concentrations. Together, these sensors represent a new class of protein-based ratiometric oxygen sensors, and the modular platform allows the oxygen sensitivity to be tailored for a specific application. This proof-of-principle study has identified the key considerations and optimal methodologies to develop and subsequently refine protein-based ratiometric oxygen sensors.

Phosphorus(V) tetrapyrazinocorrolazines bearing axial aryloxy groups as pH-sensitive fluorophores and photosensitizers

Phosphorus(V) complexes of octaphenyltetrapyrazinocorrolazine bearing two aryloxy groups in the axial position, [TPyzCAP(OAr)₂] (2a-c, Ar = phenyl (2a), 4-dimethylaminophenyl (2b), and 4-hydroxyphenyl (2c)), were prepared using a one-pot procedure by consecutive treatment of the dihydroxidophosphorus(V) derivative, [TPyzCAP(OH)₂] (1), with SOCl₂ and then with the corresponding phenol ArOH. Complex 2a containing axial PhO groups is fluorescent in all studied solvents (toluene, CH₂Cl₂, THF, and DMSO, Φ_F ∼ 0.16-0.31) and is efficient to generate singlet oxygen (Φ_Δ = 0.55 (THF), 0.68 (toluene)). The introduction of NMe₂ and OH groups in the para-position of the axial ArO ligands strongly affects the fluorescence parameters and photosensitizing properties due to the appearance of the solvent-sensitive and pH-switchable effects of photoinduced electron transfer (PET). The PET effect of NMe₂ groups completely quenches the excited state of 2b in all solvents, but it is switched-OFF upon their protonation, and in the presence of acid traces, the fluorescence of 2b becomes bright and singlet oxygen generation is strongly enhanced. The PET effect of the OH group is increased upon its deprotonation and in the presence of base 2c as well as 1 becomes non-fluorescent. Specific solvation in THF and DMSO increases the ionic character of the OH bonds, and the fluorescence and photosensitizing properties of 1 and 2c are strongly decreased in these solvents. According to the results of DFT calculations performed using the B3LYP functional with the cc-pVDZ basis set and cyclic voltammetric studies, the molecular orbitals localized on aryloxy ligands are destabilized upon the introduction of OH and especially NMe₂ groups and their close position to the HOMO of corrolazine macrocycle (above HOMO in 2b and between HOMO and HOMO-1 in 2c) leads to the appearance of the PET effect.

Corrole–protein interactions in H-NOX and HasA

Mutagenesis was utilised to reveal corrole–protein interactions in H-NOX and HasA. The key interaction is a hydrogen bond between the PO unit of the corrole and a protonated histidine residue.