Watanabe, Y.

Coord. Chem. Rev. 2007, 251, 2717-2731, 10.1016/j.ccr.2007.04.007

Design of artificial metalloproteins is one of the most important subjects in the field of bioinorganic chemistry. In order to prepare them, vacant space of proteins has been utilized because it gives us unique chemical environment to construct catalysts and materials. This article reviews on preparation methods and properties of metal/protein composites. The discussion includes our recent results and development in the screening of composites, crystal structures, molecular design of bio-inspired systems concerning catalysts, electrochemistry, and materials.

Novič, M.

Mol. Divers. 2007, 11, 141-152, 10.1007/s11030-008-9068-x

The counter propagation artificial neural networks (CP-ANNs) were used to develop a quantitative structure-selectivity relationship (QSSR) for a set of artificial metalloenzymes. The artificial metalloenzymes consist of biotinylated rhodium-diphosphine complexes incorporated in streptavidin mutants acting as host protein. Such hybrid catalysts have been shown to be good enantioselective hydrogenation catalysts for acetamidoacrylic acid. The descriptor-based models were constructed to predict enantiomeric excess (%ee) on the basis of the catalyst structures originating from docking simulations. 3D molecular descriptors for the docked ligands structures were computed. The relative arrangement of guest and host molecules was coded using distance descriptors (Rh-Cα interatomic distances); the diversity of the mutant proteins at the position S112 was coded with molecular descriptors for the sequence of three neighboring amino acids (T111-S112X-G113). The selection of testing samples for the external model validation was based on the Kohonen mapping. The final model trained by two thirds of the entire dataset was characterized by satisfactory statistical parameters for the external test set (R = 0.953 and RMS = 16.8 %ee). The proposed procedure of docking-based descriptor generation thus appears as a promising alternative to the full characterization of the complex structure by experimental or computational methods.

Ward, T.R.

Org. Biomol. Chem. 2007, 5, 1835, 10.1039/b702068f

Artificial metalloenzymes based on biotin–streptavidin technology, a “fusion” of chemistry and biology, illustrate how asymmetric catalysts can be improved and evolved using chemogenetic approaches.

DeGrado, W.F.; Lombardi, A.

C. R. Chim. 2007, 10, 703-720, 10.1016/j.crci.2007.03.010

A major objective in protein science is the design of enzymes with novel catalytic activities that are tailored to specific applications. Such enzymes may have great potential in biocatalysis and biosensor technology, such as in degradation of pollutants and biomass, and in drug and food processing. To reach this objective, investigations into the basic biochemical functioning of metalloproteins are still required. In this perspective, metalloprotein design provides a powerful approach first to contribute to a more comprehensive understanding of the way metalloproteins function in biology, with the ultimate goal of developing novel biocatalysts and sensing devices. Metalloprotein mimetics have been developed through the introduction of novel metal-binding sites into naturally occurring proteins as well as through de novo protein design. We have approached the challenge of reproducing metalloprotein active sites by using a miniaturization process. We centered our attention on iron-containing proteins, and we developed models for heme proteins and diiron–oxo proteins. In this paper we summarize the results we obtained on the design, structural, and functional properties of DFs, a family of artificial diiron proteins.

Mahy, J.-P.

C. R. Chim. 2007, 10, 684-702, 10.1016/j.crci.2006.12.014

Catalytic antibodies with a metalloporphyrin cofactor or “hemoabzymes”, used as models for hemoproteins like peroxidases and cytochrome P450s, represent a promising route to catalysts tailored for selective oxidation reactions. The first strategy has been to produce anti-porphyrin antibodies, raised against various N-substituted- and meso-carboxyaryl-porphyrins, which led to monoclonal antibodies exhibiting, in the presence of the corresponding iron-porphyrin cofactor, a significant peroxidase activity. We ourselves obtained an artificial hemoprotein by associating a monoclonal antibody, 13G10, and its iron(III)-α,α,α,β-meso-tetrakis(ortho-carboxyphenyl)porphyrin (Fe(ToCPP)) hapten, which exhibited a significant peroxidase activity. Biological studies suggested that in this antibody, a carboxylic acid side chain of the protein participated in the catalysis, but no amino acid residue acting as an axial ligand of the iron was detected. Therefore, to provide the iron atom with an axial ligand, we raised antibodies against microperoxidase 8, a heme octapeptide containing a histidine bound to the iron atom. This strategy was successful, as an antibody–microperoxidase 8 complex (3A3–MP8) led to the best kcat/Km ever reported for antibody–porphyrin complexes. The ability of the 3A3–MP8 complex to catalyze the selective oxidation of substrates was studied and it was found able to catalyze the regioselective nitration of aromatics by NO2−/H2O2 as well as the stereoselective oxidation of sulfides like thioanisole by H2O2. Other strategies based on antibodies have to be developed to obtain more efficient biomimetic systems for cytochrome P450s. A first one could involve the modification of anti-substrate antibodies by covalent linkage of an iron(III)-porphyrin close to the binding site of the substrate, to obtain an artificial hemoprotein able to catalyze its regioselective oxidation.

Hayashi, T

J. Am. Chem. Soc. 2007, 129, 12906-12907, 10.1021/ja074685f

The iron porphycene with two propionates at the peripheral positions of the framework was incorporated into the heme pocket of horseradish peroxidase. In the presence of hydrogen peroxide, the ferric iron porphycene was smoothly converted into the iron(IV)-oxo porphycene π-cation radical species, which was confirmed by the appearance of a band around 800 nm in the UV−vis spectrum. The protein with the iron porphycene showed a 10-fold higher reactivity for the thioanisole oxidation when compared to the native protein. In contrast, the guaiacol oxidation proceeded with similar reaction rates in both proteins. The kinetic analyses indicated that the ferric porphycene in the protein more slowly reacts with hydrogen peroxide than the native heme, whereas the high oxidation states show higher reactivities during oxidations of an organic substrate. The formation of the iron(IV)-oxo species of porphycene and its reactivities in the hemoprotein matrix are demonstrated.

Ward, T.R.

Adv. Synth. Catal. 2007, 349, 1923-1930, 10.1002/adsc.200700022

We report on our efforts to create efficient artificial metalloenzymes for the enantioselective hydrogenation of N‐protected dehydroamino acids using either avidin or streptavidin as host proteins. Introduction of chiral amino acid spacers – phenylalanine or proline – between the biotin anchor and the flexible aminodiphosphine moiety 1, combined with saturation mutagenesis at position S112X of streptavidin, affords second generation artificial hydrogenases displaying improved organic solvent tolerance, reaction rates (3‐fold) and (S)‐selectivities (up to 95 % ee for N‐acetamidoalanine and N‐acetamidophenylalanine). It is shown that these artificial metalloenzymes follow Michaelis–Menten kinetics with an increased affinity for the substrate and a higher kcat than the protein‐free catalyst (compare kcat 3.06 min−1 and KM 7.38 mM for [Rh(COD)Biot‐1]+ with kcat 12.30 min−1 and KM 4.36 mM for [Rh(COD)Biot‐(R)‐Pro‐1]+ ⊂ WT Sav). Finally, we present a straightforward protocol using Biotin‐Sepharose to immobilize artificial metalloenzymes (>92 % ee for N‐acetamidoalanine and N‐acetamidophenylalanine using [Rh(COD)Biot‐(R)‐Pro‐1]+ ⊂ Sav S112W).

Ward, T.R.

C. R. Chim. 2007, 10, 678-683, 10.1016/j.crci.2007.02.020

We report on our efforts to create efficient artificial metalloenzymes for the enantioselective hydrogenation of N-protected dehydroamino acids using streptavidin as host protein. Introduction of an (R)-proline spacer between the biotin anchor and the diphosphine moiety affords a versatile ligand Biot-(R)-Pro-1 which displays good (S)-selectivities in the presence of streptavidin (91% ee). The resulting artificial metalloenzyme [Rh(Biot-(R)-Pro-1)(COD)]+ ⊂ WT-Sav displays increased stability against organic solvents.

Seelig, B.; Szostak, J.W.

Nature 2007, 448, 828-831, 10.1038/nature06032

Enzymes are exceptional catalysts that facilitate a wide variety of reactions under mild conditions, achieving high rate-enhancements with excellent chemo-, regio- and stereoselectivities. There is considerable interest in developing new enzymes for the synthesis of chemicals and pharmaceuticals1,2,3 and as tools for molecular biology. Methods have been developed for modifying and improving existing enzymes through screening, selection and directed evolution4,5. However, the design and evolution of truly novel enzymes has relied on extensive knowledge of the mechanism of the reaction6,7,8,9,10. Here we show that genuinely new enzymatic activities can be created de novo without the need for prior mechanistic information by selection from a naive protein library of very high diversity, with product formation as the sole selection criterion. We used messenger RNA display, in which proteins are covalently linked to their encoding mRNA11, to select for functional proteins from an in vitro translated protein library of >1012independent sequences without the constraints imposed by any in vivo step. This technique has been used to evolve new peptides and proteins that can bind a specific ligand12,13,14,15,16,17,18, from both random-sequence libraries12,14,15,16 and libraries based on a known protein fold17,18. We now describe the isolation of novel RNA ligases from a library that is based on a zinc finger scaffold18,19, followed by in vitro directed evolution to further optimize these enzymes. The resulting ligases exhibit multiple turnover with rate enhancements of more than two-million-fold.