82 publications
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A "Broad Spectrum" Carbene Transferase for Synthesis of Chiral α-Trifluoromethylated Organoborons
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ACS Cent. Sci. 2019, 5, 206-208, 10.1021/acscentsci.9b00015
Directed evolution generated an enzyme for the enantioselective synthesis of α-trifluoromethylated organoborons—potentially attractive synthons for fluorinated compounds.
Metal: FeLigand type: PorphyrinHost protein: Cytochrome cAnchoring strategy: NativeOptimization: GeneticNotes: ---
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Achiral Cyclopentadienone Iron Tricarbonyl Complexes Embedded in Streptavidin: An Access to Artificial Iron Hydrogenases and Application in Asymmetric Hydrogenation
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Catal. Lett. 2016, 146, 564-569, 10.1007/s10562-015-1681-6
We report on the synthesis of biotinylated (cyclopentadienone)iron tricarbonyl complexes, the in situ generation of the corresponding streptavidin conjugates and their application in asymmetric hydrogenation of imines and ketones.
Metal: FeHost protein: Streptavidin (Sav)Anchoring strategy: SupramolecularOptimization: ChemicalNotes: ---
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Active Site Topology of Artificial Peroxidase-like Hemoproteins Based on Antibodies Constructed from a Specifically Designed Ortho-carboxy-substituted Tetraarylporphyrin
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Eur. J. Biochem. 1998, 257, 121-130, 10.1046/j.1432-1327.1998.2570121.x
The topology of the binding site has been studied for two monoclonal antibodies 13G10 and 14H7, elicited against iron(III)‐α,α,α,β‐meso‐tetrakis(ortho‐carboxyphenyl)porphyrin {α,α,α,β‐Fe[(o‐COOHPh)4‐porphyrin]}, and which exhibit in the presence of this α,α,α,β‐Fe[(o‐COOHPh)4‐porphyrin] cofactor a peroxidase activity. A comparison of the dissociation constants of the complexes of 13G10 and 14H7 with various tetra‐aryl‐substituted porphyrin has shown that : (a) the central iron(III) atom of α,α,α,β‐Fe[(o‐COOHPh)4‐porphyrin] is not recognized by either of the two antibodies; and (b) the ortho‐carboxylate substituents of the meso‐phenyl rings of α,α,α,β‐Fe[(o‐COOHPh)4‐porphyrin] are essential for the recognition of the porphyrin by 13G10 and 14H7. Measurement of the dissociation constants for the complexes of 13G10 and 14H7 with the four atropoisomers of (o‐COOHPh)4‐porphyrinH2 as well as mono‐ and di‐ortho‐carboxyphenyl‐substituted porphyrins suggests that the three carboxylates in the α, α, β position are recognized by both 13G10 and 14H7 with the two in the α, β positions more strongly bound to the antibody protein. Accordingly, the topology of the active site of 13G10 and 14H7 has roughly two‐thirds of the α,α,α,β‐Fe[(o‐COOHPh)4‐porphyrin] cofactor inserted into the binding site of the antibodies, with one of the aryl ring remaining outside. Three of the carboxylates are bound to the protein but no amino acid residue acts as an axial ligand to the iron atom. Chemical modification of lysine, histidine, tryptophan and arginine residues has shown that only modification of arginine residues causes a decrease in both the binding of α,α,α,β‐Fe[(o‐COOHPh)4‐porphyrin] and the peroxidase activity of both antibodies. Consequently, at least one of the carboxylates of the hapten is bound to an arginine residue and no amino acids such as lysine, histidine or tryptophan participate in the catalysis of the heterolytic cleavage of the O‐O bond of H2O2. In addition, the amino acid sequence of both antibodies not only reveals the presence of arginine residues, which could be those involved in the binding of the carboxylates of the hapten, but also the presence of several amino acids in the complementary determining regions which could bind other carboxylates through a network of H bonds.
Metal: FeLigand type: ---Host protein: Antibody 13G10 / 14H7Anchoring strategy: AntibodyOptimization: Chemical & geneticNotes: ---
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A Designed Heme-[4Fe-4S] Metalloenzyme Catalyzes Sulfite Reduction like the Native Enzyme
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Science 2018, 361, 1098-1101, 10.1126/science.aat8474
Multielectron redox reactions often require multicofactor metalloenzymes to facilitate coupled electron and proton movement, but it is challenging to design artificial enzymes to catalyze these important reactions, owing to their structural and functional complexity. We report a designed heteronuclear heme-[4Fe-4S] cofactor in cytochrome c peroxidase as a structural and functional model of the enzyme sulfite reductase. The initial model exhibits spectroscopic and ligand-binding properties of the native enzyme, and sulfite reduction activity was improved—through rational tuning of the secondary sphere interactions around the [4Fe-4S] and the substrate-binding sites—to be close to that of the native enzyme. By offering insight into the requirements for a demanding six-electron, seven-proton reaction that has so far eluded synthetic catalysts, this study provides strategies for designing highly functional multicofactor artificial enzymes.
Metal: FeHost protein: Cytochrome c peroxidaseAnchoring strategy: DativeOptimization: Chemical & geneticNotes: Designed heteronuclear heme-[4Fe-4S] cofactor in cytochrome c peroxidase
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A Hydrogenase Model System Based on the Sequence of Cytochrome c: Photochemical Hydrogen Evolution in Aqueous Media
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Chem. Commun. 2011, 47, 8229, 10.1039/c1cc11157d
The diiron carbonyl cluster is held by a native CXXC motif, which includes Cys14 and Cys17, in the cytochrome c sequence. It is found that the diiron carbonyl complex works well as a catalyst for H2 evolution. It has a TON of ∼80 over 2 h at pH 4.7 in the presence of a Ru-photosensitizer and ascorbate as a sacrificial reagent in aqueous media.
Metal: FeLigand type: CarbonylHost protein: Cytochrome cAnchoring strategy: DativeOptimization: ---Notes: Horse heart cytochrome C
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Allosteric Cooperation in a De Novo-Designed Two-Domain Protein
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Proc. Natl. Acad. Sci. U.S.A. 2020, 117, 33246-33253, 10.1073/pnas.2017062117
We describe the de novo design of an allosterically regulated protein, which comprises two tightly coupled domains. One domain is based on the DF (Due Ferri in Italian or two-iron in English) family of de novo proteins, which have a diiron cofactor that catalyzes a phenol oxidase reaction, while the second domain is based on PS1 (Porphyrin-binding Sequence), which binds a synthetic Zn-porphyrin (ZnP). The binding of ZnP to the original PS1 protein induces changes in structure and dynamics, which we expected to influence the catalytic rate of a fused DF domain when appropriately coupled. Both DF and PS1 are four-helix bundles, but they have distinct bundle architectures. To achieve tight coupling between the domains, they were connected by four helical linkers using a computational method to discover the most designable connections capable of spanning the two architectures. The resulting protein, DFP1 (Due Ferri Porphyrin), bound the two cofactors in the expected manner. The crystal structure of fully reconstituted DFP1 was also in excellent agreement with the design, and it showed the ZnP cofactor bound over 12 Å from the dimetal center. Next, a substrate-binding cleft leading to the diiron center was introduced into DFP1. The resulting protein acts as an allosterically modulated phenol oxidase. Its Michaelis–Menten parameters were strongly affected by the binding of ZnP, resulting in a fourfold tighter Km and a 7-fold decrease in kcat. These studies establish the feasibility of designing allosterically regulated catalytic proteins, entirely from scratch.
Notes: diFe-DFP3: Km 2.9 mM, kcat 0.7 min-1, 10 turnovers for 1 mM substrate, 20 uM protein. On binding ZnP, Km decreased 4x, and kcat decreased 7x, resulting in a lower kcat/Km overall.
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Alteration of the Oxygen-Dependent Reactivity of De Novo Due Ferri Proteins
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Nat. Chem. 2012, 4, 900-906, 10.1038/NCHEM.1454
De novo proteins provide a unique opportunity to investigate the structure–function relationships of metalloproteins in a minimal, well-defined and controlled scaffold. Here, we describe the rational programming of function in a de novo designed di-iron carboxylate protein from the Due Ferri family. Originally created to catalyse the O2-dependent, two-electron oxidation of hydroquinones, the protein was reprogrammed to catalyse the selective N-hydroxylation of arylamines by remodelling the substrate access cavity and introducing a critical third His ligand to the metal-binding cavity. Additional second- and third-shell modifications were required to stabilize the His ligand in the core of the protein. These structural changes resulted in at least a 106-fold increase in the relative rate between the arylamine N-hydroxylation and hydroquinone oxidation reactions. This result highlights the potential for using de novo proteins as scaffolds for future investigations of the geometric and electronic factors that influence the catalytic tuning of di-iron active sites.
Metal: FeLigand type: Amino acidHost protein: Due FerriAnchoring strategy: DativeOptimization: GeneticNotes: ---
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A Metal Ion Regulated Artificial Metalloenzyme
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Dalton Trans. 2017, 46, 4325-4330, 10.1039/C7DT00533D
An artificial metalloenzyme containing both a regulatory and a catalytic domain is selectively activated in presence of Fe2+ ions.
Metal: FeLigand type: BypyridineHost protein: Lactoccal multidrug resistant regulator (LmrR)Anchoring strategy: CovalentOptimization: GeneticNotes: ---
Metal: ZnLigand type: BypyridineHost protein: Lactoccal multidrug resistant regulator (LmrR)Anchoring strategy: CovalentOptimization: GeneticNotes: ---
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An Artificial Di-Iron Oxo-Orotein with Phenol Oxidase Activity
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Nat. Chem. Biol. 2009, 5, 882-884, 10.1038/nchembio.257
Here we report the de novo design and NMR structure of a four-helical bundle di-iron protein with phenol oxidase activity. The introduction of the cofactor-binding and phenol-binding sites required the incorporation of residues that were detrimental to the free energy of folding of the protein. Sufficient stability was, however, obtained by optimizing the sequence of a loop distant from the active site.
Metal: FeLigand type: Amino acidHost protein: Due FerriAnchoring strategy: DativeOptimization: GeneticNotes: kcat/KM ≈ 1380 M-1*min-1
Metal: FeLigand type: Amino acidHost protein: Due FerriAnchoring strategy: DativeOptimization: GeneticNotes: kcat/KM ≈ 83 M-1*min-1
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An Artificial Enzyme Made by Covalent Grafting of an FeII Complex into β-Lactoglobulin: Molecular Chemistry, Oxidation Catalysis, and Reaction-Intermediate Monitoring in a Protein
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Chem. - Eur. J. 2015, 21, 12188-12193, 10.1002/chem.201501755
An artificial metalloenzyme based on the covalent grafting of a nonheme FeII polyazadentate complex into bovine β‐lactoglobulin has been prepared and characterized by using various spectroscopic techniques. Attachment of the FeII catalyst to the protein scaffold is shown to occur specifically at Cys121. In addition, spectrophotometric titration with cyanide ions based on the spin‐state conversion of the initial high spin (S=2) FeII complex into a low spin (S=0) one allows qualitative and quantitative characterization of the metal center’s first coordination sphere. This biohybrid catalyst activates hydrogen peroxide to oxidize thioanisole into phenylmethylsulfoxide as the sole product with an enantiomeric excess of up to 20 %. Investigation of the reaction between the biohybrid system and H2O2 reveals the generation of a high spin (S=5/2) FeIII(η2‐O2) intermediate, which is proposed to be responsible for the catalytic sulfoxidation of the substrate.
Metal: FeLigand type: Poly-pyridineHost protein: ß-lactoglobulinAnchoring strategy: CovalentOptimization: ---Notes: ---
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An Artificial Heme Enzyme for Cyclopropanation Reactions
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Angew. Chem. Int. Ed. 2018, 57, 7785-7789, 10.1002/anie.201802946
An artificial heme enzyme was created through self‐assembly from hemin and the lactococcal multidrug resistance regulator (LmrR). The crystal structure shows the heme bound inside the hydrophobic pore of the protein, where it appears inaccessible for substrates. However, good catalytic activity and moderate enantioselectivity was observed in an abiological cyclopropanation reaction. We propose that the dynamic nature of the structure of the LmrR protein is key to the observed activity. This was supported by molecular dynamics simulations, which showed transient formation of opened conformations that allow the binding of substrates and the formation of pre‐catalytic structures.
Metal: FeLigand type: Protoporphyrin IXHost protein: Lactoccal multidrug resistant regulator (LmrR)Anchoring strategy: SupramolecularOptimization: Chemical & geneticNotes: ---
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An Artificial Oxygenase Built from Scratch: Substrate Binding Site Identified Using a Docking Approach
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Angew. Chem. Int. Ed. 2013, 52, 3922-3925, 10.1002/anie.201209021
The substrate for an artificial iron monooxygenase was selected by using docking calculations. The high catalytic efficiency of the reported enzyme for sulfide oxidation was directly correlated to the predicted substrate binding mode in the protein cavity, thus illustrating the synergetic effect of the substrate binding site, protein scaffold, and catalytic site.
Notes: ---
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An Evolutionary Path to Altered Cofactor Specificity in a Metalloenzyme
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Nat. Commun. 2020, 11, 10.1038/s41467-020-16478-0
AbstractAlmost half of all enzymes utilize a metal cofactor. However, the features that dictate the metal utilized by metalloenzymes are poorly understood, limiting our ability to manipulate these enzymes for industrial and health-associated applications. The ubiquitous iron/manganese superoxide dismutase (SOD) family exemplifies this deficit, as the specific metal used by any family member cannot be predicted. Biochemical, structural and paramagnetic analysis of two evolutionarily related SODs with different metal specificity produced by the pathogenic bacterium Staphylococcus aureus identifies two positions that control metal specificity. These residues make no direct contacts with the metal-coordinating ligands but control the metal’s redox properties, demonstrating that subtle architectural changes can dramatically alter metal utilization. Introducing these mutations into S. aureus alters the ability of the bacterium to resist superoxide stress when metal starved by the host, revealing that small changes in metal-dependent activity can drive the evolution of metalloenzymes with new cofactor specificity.
Ligand type: Amino acidHost protein: Superoxide dismutase (SOD)Anchoring strategy: DativeOptimization: GeneticNotes: PDB: 6EX3, 6EX4, 6EX5, 6QV8, 6QV9
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A Noncanonical Proximal Heme Ligand Affords an Efficient Peroxidase in a Globin Fold
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J. Am. Chem. Soc. 2018, 140, 1535-1543, 10.1021/jacs.7b12621
Expanding the range of genetically encoded metal coordination environments accessible within tunable protein scaffolds presents excellent opportunities for the creation of metalloenzymes with augmented properties and novel activities. Here, we demonstrate that installation of a noncanonical Nδ-methyl histidine (NMH) as the proximal heme ligand in the oxygen binding protein myoglobin (Mb) leads to substantial increases in heme redox potential and promiscuous peroxidase activity. Structural characterization of this catalytically modified myoglobin variant (Mb NMH) revealed significant changes in the proximal pocket, including alterations to hydrogen-bonding interactions involving the prosthetic porphyrin cofactor. Further optimization of Mb NMH via a combination of rational modification and several rounds of laboratory evolution afforded efficient peroxidase biocatalysts within a globin fold, with activities comparable to those displayed by nature’s peroxidases.
Metal: FeHost protein: Myoglobin (Mb)Anchoring strategy: SupramolecularOptimization: Chemical & geneticNotes: Oxidation of amplex red
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Artificial Heme Enzymes for the Construction of Gold-Based Biomaterials
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Int. J. Mol. Sci. 2018, 19, 2896, 10.3390/ijms19102896
Many efforts are continuously devoted to the construction of hybrid biomaterials for specific applications, by immobilizing enzymes on different types of surfaces and/or nanomaterials. In addition, advances in computational, molecular and structural biology have led to a variety of strategies for designing and engineering artificial enzymes with defined catalytic properties. Here, we report the conjugation of an artificial heme enzyme (MIMO) with lipoic acid (LA) as a building block for the development of gold-based biomaterials. We show that the artificial MIMO@LA can be successfully conjugated to gold nanoparticles or immobilized onto gold electrode surfaces, displaying quasi-reversible redox properties and peroxidase activity. The results of this work open interesting perspectives toward the development of new totally-synthetic catalytic biomaterials for application in biotechnology and biomedicine, expanding the range of the biomolecular component aside from traditional native enzymes.
Metal: FeHost protein: Mimochrome Fe(III)-S6G(D)-MC6 (De novo designed peptide)Anchoring strategy: CovalentOptimization: Chemical & geneticNotes: Immobilization of the ArM on gold surfaces via a lipoic acid anchor.
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Artificial Iron Hydrogenase Made by Covalent Grafting of Knölker's Complex into Xylanase: Application in Asymmetric Hydrogenation of an Aryl Ketone in Water
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Biotechnol. Appl. Biochem. 2020, 67, 563-573, 10.1002/bab.1906
We report a new artificial hydrogenase made by covalent anchoring of the iron Knölker's complex to a xylanase S212C variant. This artificial metalloenzyme was found to be able to catalyze efficiently the transfer hydrogenation of the benchmark substrate trifluoroacetophenone by sodium formate in water, yielding the corresponding secondary alcohol as a racemic. The reaction proceeded more than threefold faster with the XlnS212CK biohybrid than with the Knölker's complex alone. In addition, efficient conversion of trifluoroacetophenone to its corresponding alcohol was reached within 60 H with XlnS212CK, whereas a ≈2.5-fold lower conversion was observed with Knölker's complex alone as catalyst. Moreover, the data were rationalized with a computational strategy suggesting the key factors of the selectivity. These results suggested that the Knölker's complex was most likely flexible and could experience free rotational reorientation within the active-site pocket of Xln A, allowing it to access the subsite pocket populated by trifluoroacetophenone.
Metal: FeLigand type: CyclopentadienylHost protein: Xylanase A (XynA)Anchoring strategy: CovalentOptimization: ---Notes: ---
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Artificial Metalloenzymes as Catalysts for Oxidative Lignin Degradation
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ACS Sustainable Chem. Eng. 2018, 6, 15100-15107, 10.1021/acssuschemeng.8b03568
We report novel artificial metalloenzymes (ArMs), containing tris(pyridylmethyl)amine (TPA), for the atom economic oxidation of lignin β-O-4 model compounds, using hydrogen peroxide. The protein scaffold alters the selectivity of the reaction from a low yielding cleavage reaction when using the parent Fe-tpa complex to a high yielding benzylic alcohol oxidation when using the complex incorporated into a protein scaffold, SCP-2L A100C. Engineering the protein scaffold to incorporate glutamic acid was found to improve the ArM activity, showing that rational design of the protein environment using metal binding amino acids can be a first step toward improving the overall activity of an artificial metalloenzyme.
Metal: FeLigand type: Tris(pyridylmethyl)amine (TPA)Host protein: Steroid Carrier Protein 2L (SCP-2L)Anchoring strategy: Cystein-maleimideOptimization: Chemical & geneticNotes: Reaction performed with a lignin model compound and hydrogen peroxide as oxidizing agent
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Artificial Metalloproteins with Dinuclear Iron–Hydroxido Centers
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J. Am. Chem. Soc. 2021, 143, 2384-2393, 10.1021/jacs.0c12564
Dinuclear iron centers with a bridging hydroxido or oxido ligand form active sites within a variety of metalloproteins. A key feature of these sites is the ability of the protein to control the structures around the Fe centers, which leads to entatic states that are essential for function. To simulate this controlled environment, artificial proteins have been engineered using biotin–streptavidin (Sav) technology in which Fe complexes from adjacent subunits can assemble to form [FeIII–(μ-OH)–FeIII] cores. The assembly process is promoted by the site-specific localization of the Fe complexes within a subunit through the designed mutation of a tyrosinate side chain to coordinate the Fe centers. An important outcome is that the Sav host can regulate the Fe···Fe separation, which is known to be important for function in natural metalloproteins. Spectroscopic and structural studies from X-ray diffraction methods revealed uncommonly long Fe···Fe separations that change by less than 0.3 Å upon the binding of additional bridging ligands. The structural constraints imposed by the protein host on the di-Fe cores are unique and create examples of active sites having entatic states within engineered artificial metalloproteins.
Reaction: ---Max TON: ---ee: ---PDB: ---Notes: PDB: 6VOZ, 6VO9
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Artificial Peroxidase-Like Hemoproteins Based on Antibodies Constructed from a Specifically Designed Ortho-Carboxy Substituted Tetraarylporphyrin Hapten and Exhibiting a High Affinity for Iron-Porphyrins
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FEBS Lett. 1996, 395, 73-76, 10.1016/0014-5793(96)01006-X
In order to get catalytic antibodies modelling peroxidases BALB/c mice have been immunized with iron(III)α,α,α,β‐mesotetrakis‐orthocarboxyphenyl‐porphyrin (Fe(ToCPP))‐KLH conjugates. Monoclonal antibodies have been produced by the hybridoma technology. Three antibodies, 2 IgG, and 1 IgG2a, were found to bind both Fe(ToCPP) and the free base ToCPPH2 with similar binding constants. None of those antibodies was found to bind tetraphenylporphyrin. Those results suggest that the recognition of Fe(ToCPP) by the antibodies was mainly due to the binding of the carboxylate groups to some amino acid residues of the protein. True K d values of 2.9 × 10−9 M and 5.5 × 10−9 M have been determined for the two IgG1‐Fe(ToCPP) complexes. Those values are the best ones ever reported for iron‐porphyrin‐antibody complexes. UV‐vis. studies have shown that the two IgG1‐Fe(ToCPP) complexes were highspin hexacoordinate iron(III) complexes, with no amino acid residue binding the iron, whereas the IgG2α‐Fe(ToCPP) complex was a low‐spin hexacoordinate iron(III) complex with two strong ligands binding the iron atom. Both IgG1 ‐Fe(ToCPP) complexes were found to catalyze the oxidation of 2,2′‐azinobis (3ethylbenzothiazoline‐6‐sulfonic acid (ABTS) 5‐fold more efficiently than Fe(ToCPP) alone whereas the binding of IgG2a to this iron‐porphyrin had no effect on its catalytic activity. k cat values of 100 min−1 and 63 min−1 and k cat/K m. values of 105 M−1 s−1 and 119 M−1 s−1 have been found respectively for the two IgG1‐Fe(ToCPP) complexes.
Metal: FeLigand type: PorphyrinHost protein: Antibody 13G10Anchoring strategy: SupramolecularOptimization: ---Notes: kcat/KM = 105 M-1 * s-1
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A Structural View of Synthetic Cofactor Integration into [FeFe]-Hydrogenases
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Chem. Sci. 2016, 7, 959-968, 10.1039/C5SC03397G
Crystal structures of semisynthetic [FeFe]-hydrogenases with variations in the [2Fe] cluster show little structural differences despite strong effects on activity.
Metal: FeHost protein: [FeFe]-hydrogenase from C. pasteurianum (CpI)Anchoring strategy: DativeOptimization: ChemicalNotes: H2 evolution activity of the ArM: 2874 (mmol H2)*min-1*(mg protein)-1.
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Biosynthesis of a Site-Specific DNA Cleaving Protein
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J. Am. Chem. Soc. 2008, 130, 13194-13195, 10.1021/ja804653f
An E. coli catabolite activator protein (CAP) has been converted into a sequence-specific DNA cleaving protein by genetically introducing (2,2′-bipyridin-5-yl)alanine (Bpy-Ala) into the protein. The mutant CAP (CAP-K26Bpy-Ala) showed comparable binding affinity to CAP-WT for the consensus operator sequence. In the presence of Cu(II) and 3-mercaptopropionic acid, CAP-K26Bpy-Ala cleaves double-stranded DNA with high sequence specificity. This method should provide a useful tool for mapping the molecular details of protein−nucleic acid interactions.
Metal: CuLigand type: BipyridineHost protein: Catabolite activator protein (CAP)Anchoring strategy: ---Optimization: Chemical & geneticNotes: Catabolite activator protein from E. coli
Metal: FeLigand type: BipyridineHost protein: Catabolite activator protein (CAP)Anchoring strategy: ---Optimization: Chemical & geneticNotes: Catabolite activator protein from E. coli
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Capture and Characterization of a Reactive Haem– Carbenoid Complex in an Artificial Metalloenzyme
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Nat. Catal. 2018, 1, 578-584, 10.1038/s41929-018-0105-6
Non-canonical amino acid ligands are useful for fine-tuning the catalytic properties of metalloenzymes. Here, we show that recombinant replacement of the histidine ligand proximal to haem in myoglobin with Nδ-methylhistidine enhances the protein’s promiscuous carbene-transfer chemistry, enabling efficient styrene cyclopropanation in the absence of reductant, even under aerobic conditions. The increased electrophilicity of the modified Fe(iii) centre, combined with subtle structural adjustments at the active site, allows direct attack of ethyl diazoacetate to produce a reactive carbenoid adduct, which has an unusual bridging Fe(iii)–C–N(pyrrole) configuration as shown by X-ray crystallography. Quantum chemical calculations suggest that the bridged complex equilibrates with the more reactive end-on isomer, ensuring efficient cyclopropanation. These findings underscore the potential of non-canonical ligands for extending the capabilities of metalloenzymes by opening up new reaction pathways and facilitating the characterization of reactive species that would not otherwise accumulate.
Notes: Structure of the Mb*(NMH) haem-iron complex
Notes: Structure of the Mb*(NMH) haem-iron–carbenoid complex
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Catalysis Without a Headache: Modification of Ibuprofen for the Design of Artificial Metalloenzyme for Sulfide Oxidation
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J. Mol. Catal. A: Chem. 2016, 416, 20-28, 10.1016/j.molcata.2016.02.015
A new artificial oxidase has been developed for selective transformation of thioanisole. The catalytic activity of an iron inorganic complex, FeLibu, embedded in a transport protein NikA has been investigated in aqueous media. High efficiency (up to 1367 t), frequency 459 TON min−1 and selectivity (up to 69%) make this easy to use catalytic system an asset for a sustainable chemistry.
Metal: FeLigand type: BPHMENHost protein: Human serum albumin (HSA)Anchoring strategy: SupramolecularOptimization: ---Notes: ---
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Catalytic Cyclopropanation by Myoglobin Reconstituted with Iron Porphycene: Acceleration of Catalysis due to Rapid Formation of the Carbene Species
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J. Am. Chem. Soc. 2017, 139, 17265-17268, 10.1021/jacs.7b10154
Myoglobin reconstituted with iron porphycene catalyzes the cyclopropanation of styrene with ethyl diazoacetate. Compared to native myoglobin, the reconstituted protein significantly accelerates the catalytic reaction and the kcat/Km value is 26-fold enhanced. Mechanistic studies indicate that the reaction of the reconstituted protein with ethyl diazoacetate is 615-fold faster than that of native myoglobin. The metallocarbene species reacts with styrene with the apparent second-order kinetic constant of 28 mM–1 s–1 at 25 °C. Complementary theoretical studies support efficient carbene formation by the reconstituted protein that results from the strong ligand field of the porphycene and fewer intersystem crossing steps relative to the native protein. From these findings, the substitution of the cofactor with an appropriate metal complex serves as an effective way to generate a new biocatalyst.
Notes: Cyclopropanation of styrene with ethyl diazoacetate: kcat/KM = 1.3 mM-1 * s-1, trans/cis = 99:1
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Chalcogenide Substitution in the [2Fe] Cluster of [FeFe]-Hydrogenases Conserves High Enzymatic Activity
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Dalton Trans. 2017, 46, 16947-16958, 10.1039/C7DT03785F
Combination of biological and chemical methods allow for creation of [FeFe]-hydrogenases with an artificial synthetic cofactor.
Metal: FeHost protein: [FeFe]-hydrogenase from C. pasteurianum (CpI)Anchoring strategy: DativeOptimization: ChemicalNotes: ---
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Constructing Protein Polyhedra via Orthogonal Chemical Interactions
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Nature 2020, 578, 172-176, 10.1038/s41586-019-1928-2
Many proteins exist naturally as symmetrical homooligomers or homopolymers1. The emergent structural and functional properties of such protein assemblies have inspired extensive efforts in biomolecular design2,3,4,5. As synthesized by ribosomes, proteins are inherently asymmetric. Thus, they must acquire multiple surface patches that selectively associate to generate the different symmetry elements needed to form higher-order architectures1,6—a daunting task for protein design. Here we address this problem using an inorganic chemical approach, whereby multiple modes of protein–protein interactions and symmetry are simultaneously achieved by selective, ‘one-pot’ coordination of soft and hard metal ions. We show that a monomeric protein (protomer) appropriately modified with biologically inspired hydroxamate groups and zinc-binding motifs assembles through concurrent Fe3+ and Zn2+ coordination into discrete dodecameric and hexameric cages. Our cages closely resemble natural polyhedral protein architectures7,8 and are, to our knowledge, unique among designed systems9,10,11,12,13 in that they possess tightly packed shells devoid of large apertures. At the same time, they can assemble and disassemble in response to diverse stimuli, owing to their heterobimetallic construction on minimal interprotein-bonding footprints. With stoichiometries ranging from [2 Fe:9 Zn:6 protomers] to [8 Fe:21 Zn:12 protomers], these protein cages represent some of the compositionally most complex protein assemblies—or inorganic coordination complexes—obtained by design.
Ligand type: HydroxaamateHost protein: Cytochrome cb562Anchoring strategy: CovalentOptimization: Chemical & geneticNotes: ---
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Construction and In Vivo Assembly of a Catalytically Proficient and Hyperthermostable De Novo Enzyme
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Nat. Commun. 2017, 8, 10.1038/s41467-017-00541-4
Although catalytic mechanisms in natural enzymes are well understood, achieving the diverse palette of reaction chemistries in re-engineered native proteins has proved challenging. Wholesale modification of natural enzymes is potentially compromised by their intrinsic complexity, which often obscures the underlying principles governing biocatalytic efficiency. The maquette approach can circumvent this complexity by combining a robust de novo designed chassis with a design process that avoids atomistic mimicry of natural proteins. Here, we apply this method to the construction of a highly efficient, promiscuous, and thermostable artificial enzyme that catalyzes a diverse array of substrate oxidations coupled to the reduction of H2O2. The maquette exhibits kinetics that match and even surpass those of certain natural peroxidases, retains its activity at elevated temperature and in the presence of organic solvents, and provides a simple platform for interrogating catalytic intermediates common to natural heme-containing enzymes.
Metal: FeLigand type: PorphyrinHost protein: C45 (c-type cytochrome maquette)Anchoring strategy: SupramolecularOptimization: GeneticNotes: Oxidation of 2,2′-azino-bis(3-ethylbenzothiazo-line-6-sulfonic acid (ABTS)
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Coordination Chemistry of Iron(III)-Porphyrin-Antibody Complexes Influence on the Peroxidase Activity of the Axial Coordination of an Imidazole on the Iron Atom
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Eur. J. Biochem. 2002, 269, 470-480, 10.1046/j.0014-2956.2001.02670.x
An artificial peroxidase‐like hemoprotein has been obtained by associating a monoclonal antibody, 13G10, and its iron(III)–α,α,α,β‐meso‐tetrakis(ortho‐carboxyphenyl)porphyrin [Fe(ToCPP)] hapten. In this antibody, about two‐thirds of the porphyrin moiety is inserted in the binding site, its ortho‐COOH substituents being recognized by amino‐acids of the protein, and a carboxylic acid side chain of the protein acts as a general acid base catalyst in the heterolytic cleavage of the O–O bond of H2O2, but no amino‐acid residue is acting as an axial ligand of the iron. We here show that the iron of 13G10–Fe(ToCPP) is able to bind, like that of free Fe(ToCPP), two small ligands such as CN–, but only one imidazole ligand, in contrast to to the iron(III) of␣Fe(ToCPP) that binds two. This phenomenon is general for a series of monosubstituted imidazoles, the 2‐ and 4‐alkyl‐substituted imidazoles being the best ligands, in agreement with the hydrophobic character of the antibody binding site. Complexes of antibody 13G10 with less hindered iron(III)–tetraarylporphyrins bearing only one [Fe(MoCPP)] or two meso‐[ortho‐carboxyphenyl] substituents [Fe(DoCPP)] also bind only one imidazole. Finally, peroxidase activity studies show that imidazole inhibits the peroxidase activity of 13G10–Fe(ToCPP) whereas it increases that of 13G10–Fe(DoCPP). This could be interpreted by the binding of the imidazole ligand on the iron atom which probably occurs in the case of 13G10–Fe(ToCPP) on the less hindered face of the porphyrin, close to the catalytic COOH residue, whereas in the case of 13G10–Fe(DoCPP) it can occur on the other face of the porphyrin. The 13G10–Fe(DoCPP)–imidazole complex thus constitutes a nice artificial peroxidase‐like hemoprotein, with the axial imidazole ligand of the iron mimicking the proximal histidine of peroxidases and a COOH side chain of the antibody acting as a general acid‐base catalyst like the distal histidine of peroxidases does.
Metal: FeLigand type: PorphyrinHost protein: Antibody 13G10Anchoring strategy: SupramolecularOptimization: ---Notes: kcat/KM = 15200 M-1 * s-1
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Coordination Chemistry Studies and Peroxidase Activity of a New Artificial Metalloenzyme Built by the “Trojan Horse” Strategy
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J. Mol. Catal. A: Chem. 2010, 317, 19-26, 10.1016/j.molcata.2009.10.016
In the general context of green chemistry, a considerable research effort is devoted to the elaboration of new artificial metalloproteins that catalyze, under mild conditions, the oxidation of a wide range of organic compounds, using cheap and environmentally friendly oxidants. A new artificial hemoprotein was obtained by the so-called “Trojan horse” strategy involving the non-covalent insertion of a cationic iron–porphyrin–estradiol cofactor into an anti-estradiol antibody. UV–vis titrations showed the formation of a 1/2 antibody/cofactor complex with a dissociation constant KD = 4.10−7 M. UV–vis determination of the Fe-imidazole binding constants showed that the protein provided a weak steric hindrance around the iron–porphyrin cofactor. The antibody–estradiol–iron–porphyrin complex displayed a peroxidase activity and catalyzed the oxidation of ABTS by H2O2 with about double the efficiency of the iron–porphyrin–estradiol alone. Kinetic studies revealed that this was due to a faster formation of the intermediate high valent iron–oxo species in the presence of the antibody protein. Consequently, the association of an anti-estradiol antibody with an iron–porphyrin–estradiol cofactor leads to a new artificial hemoprotein with an interesting peroxidase activity and the “Trojan horse” strategy appears as a valuable method to generate artificial metalloenzymes that could act as biocatalysts for selective oxidations.
Metal: FeLigand type: PorphyrinHost protein: Antibody 7A3Anchoring strategy: SupramolecularOptimization: ---Notes: k1 = 574 M-1 * min-1
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Cross-Linked Artificial Enzyme Crystals as Heterogeneous Catalysts for Oxidation Reactions
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J. Am. Chem. Soc. 2017, 139, 17994-18002, 10.1021/jacs.7b09343
Designing systems that merge the advantages of heterogeneous catalysis, enzymology, and molecular catalysis represents the next major goal for sustainable chemistry. Cross-linked enzyme crystals display most of these essential assets (well-designed mesoporous support, protein selectivity, and molecular recognition of substrates). Nevertheless, a lack of reaction diversity, particularly in the field of oxidation, remains a constraint for their increased use in the field. Here, thanks to the design of cross-linked artificial nonheme iron oxygenase crystals, we filled this gap by developing biobased heterogeneous catalysts capable of oxidizing carbon–carbon double bonds. First, reductive O2 activation induces selective oxidative cleavage, revealing the indestructible character of the solid catalyst (at least 30 000 turnover numbers without any loss of activity). Second, the use of 2-electron oxidants allows selective and high-efficiency hydroxychlorination with thousands of turnover numbers. This new technology by far outperforms catalysis using the inorganic complexes alone, or even the artificial enzymes in solution. The combination of easy catalyst synthesis, the improvement of “omic” technologies, and automation of protein crystallization makes this strategy a real opportunity for the future of (bio)catalysis.
Metal: FeLigand type: ---Host protein: NikAAnchoring strategy: SupramolecularOptimization: ChemicalNotes: Cross-Linked Enzyme Crystals (CLEC) as catalysts.
Metal: FeLigand type: ---Host protein: NikAAnchoring strategy: SupramolecularOptimization: ChemicalNotes: Cross-Linked Enzyme Crystals (CLEC) as catalysts.