18 publications

18 publications

Addressable DNA–Myoglobin Photocatalysis

Niemeyer, C.M.

Chem. - Asian J. 2009, 4, 1064-1069, 10.1002/asia.200900082

A hybrid myoglobin, containing a single‐stranded DNA anchor and a redox‐active ruthenium moiety tethered to the heme center can be used as a photocatalyst. The catalyst can be selectively immobilized on a surface‐bound complementary DNA molecule and thus readily recycled from complex reaction mixtures. This principle may be applied to a range of heme‐dependent enzymes allowing the generation of novel light‐triggered photocatalysts. Photoactivatable myoglobin containing a DNA oligonucleotide as a structural anchor was designed by using the reconstitution of artificial heme moieties containing Ru3+ ions. This semisynthetic DNA–enzyme conjugate was successfully used for the oxidation of peroxidase substrates by using visible light instead of H2O2 for the activation. The DNA anchor was utilized for the immobilization of the enzyme on the surface of magnetic microbeads. Enzyme activity measurements not only indicated undisturbed biofunctionality of the tethered DNA but also enabled magnetic separation‐based enrichment and recycling of the photoactivatable biocatalyst.


Metal: Ru
Ligand type: Bipyridine
Host protein: Myoglobin (Mb)
Anchoring strategy: Supramolecular
Optimization: ---
Reaction: Photooxidation
Max TON: ---
ee: ---
PDB: ---
Notes: Horse heart myoglobin

An Artificial Di-Iron Oxo-Orotein with Phenol Oxidase Activity

DeGrado, W.F.; Lombardi, A.

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: Fe
Ligand type: Amino acid
Host protein: Due Ferri
Anchoring strategy: Dative
Optimization: Genetic
Reaction: Alcohol oxidation
Max TON: >50
ee: ---
PDB: 2KIK
Notes: kcat/KM ≈ 1380 M-1*min-1

Metal: Fe
Ligand type: Amino acid
Host protein: Due Ferri
Anchoring strategy: Dative
Optimization: Genetic
Reaction: Amine oxidation
Max TON: ---
ee: ---
PDB: 2KIK
Notes: kcat/KM ≈ 83 M-1*min-1

Artificial Metalloenzymes: Combining the Best Features of Homogeneous and Enzymatic Catalysis

Review

Ward, T.R.

Synlett 2009, 2009, 3225-3236, 10.1055/s-0029-1218305

By combining homogeneous with enzymatic catalysis, artificial metalloenzymes offer new perspectives for conferring unnatural activities to biomolecules. The article reassembles the important advances in the field of these hybrid catalysts and summarizes the contributions of our group to this continuously growing field of research.


Notes: ---

Artificial Metalloenzymes for Enantioselective Catalysis Based on the Biotin-Avidin Technology

Review

Ward, T.R.

Top. Organomet. Chem. 2009, 10.1007/3418_2008_3

Artificial metalloenzymes can be created by incorporating an active metal catalyst precursor in a macromolecular host. When considering such artificial metalloenzymes, the first point to address is how to localize the active metal moiety within the protein scaffold. Although a covalent anchoring strategy may seem most attractive at first, supramolecular anchoring strategy has proven most successful thus far. In this context and inspired by Whitesides’ seminal paper, we have exploited the biotin–avidin technology to anchor a biotinylated active metal catalyst precursor within either avidin or streptavidin. A combined chemical and genetic strategy allows a rapid (chemogenetic) optimization of both the activity and the selectivity of the resulting artificial metalloenzymes. The chiral environment, provided by second coordination sphere interactions between the metal and the host protein, can be varied by introduction of a spacer between the biotin anchor and the metal moiety or by variation of the ligand scaffold. Alternatively, mutagenesis of the host protein allows a fine tuning of the activity and the selectivity. With this protocol, we have been able to produce artificial metalloenzymes based on the biotin–avidin technology for the enantioselective hydrogenation of N-protected dehydroaminoacids, the transfer hydrogenation of prochiral ketones as well as the allylic alkylation of symmetric substrates. In all cases selectivities >90% were achieved. Most recently, guided by an X-ray structure of an artificial metalloenzyme, we have extended the chemogenetic optimization to a designed evolution scheme. Designed evolution combines rational design with combinatorial screening. In this chapter, we emphasize the similarities and the differences between artificial metalloenzymes and their homogeneous or enzymatic counterparts.


Notes: Book chapter

Artificial Metalloproteins Exploiting Vacant Space: Preparation, Structures, and Functions

Review

Watanabe, Y.

Top. Organomet. Chem. 2009, 10.1007/3418_2008_4

Molecular design of artificial metalloproteins is one of the most attractive subjects in bioinorganic chemistry. Protein vacant space has been utilized to prepare metalloproteins because it provides a unique chemical environment for application to catalysts and to biomaterials bearing electronic, magnetic, and medical properties. Recently, X-ray crystal structural analysis has increased in this research area because it is a powerful tool for understanding the interactions of metal complexes and protein scaffolds, and for providing rational design of these composites. This chapter reviews the recent studies on the preparation methods and X-ray crystal structural analyses of metal/protein composites, and their functions as catalysts, metal-drugs, etc.


Notes: ---

Design of Functional Metalloproteins

Review

Lu, Y.

Nature 2009, 460, 855-862, 10.1038/nature08304

Metalloproteins catalyse some of the most complex and important processes in nature, such as photosynthesis and water oxidation. An ultimate test of our knowledge of how metalloproteins work is to design new metalloproteins. Doing so not only can reveal hidden structural features that may be missing from studies of native metalloproteins and their variants, but also can result in new metalloenzymes for biotechnological and pharmaceutical applications. Although it is much more challenging to design metalloproteins than non-metalloproteins, much progress has been made in this area, particularly in functional design, owing to recent advances in areas such as computational and structural biology.


Notes: ---

Directed Evolution of Stereoselective Hybrid Catalysts

Review

Reetz, M.T.

Top. Organomet. Chem. 2009, 10.1007/3418_2008_12

Whereas the directed evolution of stereoselective enzymes provides a useful tool in asymmetric catalysis, generality cannot be claimed because enzymes as catalysts are restricted to a limited set of reaction types. Therefore, a new concept has been proposed, namely directed evolution of hybrid catalysts in which proteins serve as hosts for anchoring ligand/transition metal entities. Accordingly, appropriate genetic mutagenesis methods are applied to the gene of a given protein host, providing after expression a library of mutant proteins. These are purified and a ligand/transition metal anchored site-specifically. Following en masse ee-screening, the best hit is identified, and the corresponding mutant gene is used as a template for another round of mutagenesis, expression, purification, bioconjugation, and screening. This allows for a Darwinian optimization of transition metal catalysts.


Notes: ---

Incorporation of Biotinylated Manganese-Salen Complexes into Streptavidin: New Artificial Metalloenzymes for Enantioselective Sulfoxidation

Ward, T.R.

J. Organomet. Chem. 2009, 694, 930-936, 10.1016/j.jorganchem.2008.11.023

Incorporation of achiral biotinylated manganese-salen complexes into streptavidin yields artificial metalloenzymes for aqueous sulfoxidation using hydrogen peroxide. Four biotinylated salen ligands were synthesized and their manganese complexes were tested in combination with several streptavidin mutants, yielding moderate conversions (up to 56%) and low enantioselectivities (maximum of 13% ee) for the sulfoxidation of thioanisole.


Metal: Mn
Ligand type: Oxide; Salen
Host protein: Streptavidin (Sav)
Anchoring strategy: Supramolecular
Optimization: Chemical & genetic
Reaction: Sulfoxidation
Max TON: 28
ee: 13
PDB: ---
Notes: ---

Manganese-Substituted α-Carbonic Anhydrase as an Enantioselective Peroxidase

Review

Kazlauskas, R.J.

Top. Organomet. Chem. 2009, 10.1007/3418_2008_1

Carbonic anhydrase binds a zinc ion in a hydrophobic active site using the imidazole groups of three histidine residues. The natural role of carbonic anhydrase is to catalyze the reversible hydration of carbon dioxide to bicarbonate, but it also catalyzes hydrolysis of esters with moderate enantioselectivity. Replacing the active-site zinc with manganese yielded manganese-substituted carbonic anhydrase (CA[Mn]), which shows peroxidase activity with a bicarbonate-dependent mechanism. In the presence of bicarbonate and hydrogen peroxide, CA[Mn] catalyzed the efficient oxidation of o-dianisidine with k cat /K M = 1.4 × 106 M−1s−1, which is comparable to that for horseradish peroxidase, k cat /K M = 57 × 106 M−1s−1. CA[Mn] also catalyzed the moderately enantioselective epoxidation of olefins to epoxides (E = 5 for p-chlorostyrene). This enantioselectivity is similar to that for natural heme-based peroxidases, but has the advantage that CA[Mn] avoids formation of aldehyde side products. CA[Mn] degrades during the epoxidation, limiting the yield of the epoxidations to <12%. Replacement of active-site residues Asn62, His64, Asn67, Gln92, or Thr200 with alanine by site-directed mutagenesis decreased the enantioselectivity showing that the active site controls enantioselectivity of the epoxidation.


Notes: ---

Meso-Unsubstituted Iron Corrole in Hemoproteins: Remarkable Differences in Effects on Peroxidase Activities between Myoglobin and Horseradish Peroxidase

Hayashi, T

J. Am. Chem. Soc. 2009, 131, 15124-15125, 10.1021/ja907428e

Myoglobin (Mb) and horseradish peroxidase (HRP) were both reconstituted with a meso-unsubstituted iron corrole and their electronic configurations and peroxidase activities were investigated. The appearance of the 540 nm band upon incorporation of the iron corrole into apoMb indicates axial coordination by the proximal histidine imidazole in the Mb heme pocket. Based on 1H NMR measurements using the Evans method, the total magnetic susceptibility of the iron corrole reconstituted Mb was evaluated to be S = 3/2. In contrast, although a band does not appear in the vicinity of 540 nm during reconstitution of the iron corrole into the matrix of HRP, a spectrum similar to that of the iron corrole reconstituted Mb is observed upon the addition of dithionite. This observation suggests that the oxidation state of the corrole iron in the reconstituted HRP can be assigned as +4. The catalytic activities of both proteins toward guaiacol oxidation are quite different; the iron corrole reconstituted HRP decelerates H2O2-dependent oxidation of guaiacol, while the same reaction catalyzed by iron corrole reconstituted Mb has the opposite effect and accelerates the reaction. This finding can be attributed to the difference in the oxidation states of the corrole iron when these proteins are in the resting state.


Metal: Fe
Ligand type: Corrole
Host protein: Myoglobin (Mb)
Anchoring strategy: Reconstitution
Optimization: ---
Max TON: ---
ee: ---
PDB: ---
Notes: ---

Metal: Fe
Ligand type: Corrole
Anchoring strategy: Reconstitution
Optimization: ---
Max TON: ---
ee: ---
PDB: ---
Notes: ---

Noncovalent Modulation of pH-Dependent Reactivity of a Mn–Salen Cofactor in Myoglobin with Hydrogen Peroxide

Lu, Y.

Chem. - Eur. J. 2009, 15, 7481-7489, 10.1002/chem.200802449

To demonstrate protein modulation of metal‐cofactor reactivity through noncovalent interactions, pH‐dependent sulfoxidation and 2,2′‐azino‐bis(3‐ethylbenzthiazoline‐6‐sulphonic acid) (ABTS) oxidation reactivity of a designed myoglobin (Mb) containing non‐native Mn–salen complex (1) was investigated using H2O2 as the oxidant. Incorporation of 1 inside the Mb resulted in an increase in the turnover numbers through exclusion of water from the metal complex and prevention of Mn–salen dimer formation. Interestingly, the presence of protein in itself is not enough to confer the increase activity as mutation of the distal His64 in Mb to Phe to remove hydrogen‐bonding interactions resulted in no increase in the turnover numbers, while mutation His64 to Arg, another residue with ability to hydrogen‐bond interactions, resulted in an increase in reactivity. These results strongly suggest that the distal ligand His64, through its hydrogen‐bonding interaction, plays important roles in enhancing and fine‐tuning reactivity of the Mn–salen complex. Nonlinear least‐squares fitting of rate versus pH plots demonstrates that 1⋅Mb(H64X) (X=H, R and F) and the control Mn–salen 1 exhibit pKa values varying from pH 6.4 to 8.3, and that the lower pKa of the distal ligand in 1⋅Mb(H64X), the higher the reactivity it achieves. Moreover, in addition to the pKa at high pH, 1⋅Mb displays another pKa at low pH, with pKa of 5.0±0.08. A comparison of the effect of different pH on sulfoxidation and ABTS oxidation indicates that, while the intermediate produced at low pH conditions could only perform sulfoxidation, the intermediate at high pH could oxidize both sulfoxides and ABTS. Such a fine‐control of reactivity through hydrogen‐bonding interactions by the distal ligand to bind, orient and activate H2O2 is very important for designing artificial enzymes with dramatic different and tunable reactivity from catalysts without protein scaffolds.


Metal: Mn
Ligand type: Salen
Host protein: Myoglobin (Mb)
Anchoring strategy: Covalent
Optimization: Chemical & genetic
Reaction: Sulfoxidation
Max TON: 4.1
ee: 50
PDB: ---
Notes: Sperm whale myoglobin

Polymerization of Phenylacetylene by Rhodium Complexes within a Discrete Space of apo-Ferritin

Ueno, T.; Watanabe, Y.

J. Am. Chem. Soc. 2009, 131, 6958-6960, 10.1021/ja901234j

Polymerization reactions of phenylacetylene derivatives are promoted by rhodium complexes within the discrete space of apo-ferritin in aqueous media. The catalytic reaction provides polymers with restricted molecular weight and a narrow molecular weight distribution. These results suggest that protein nanocages have potential for use as various reaction spaces through immobilization of metal catalysts on the interior surfaces of the protein cages.


Metal: Rh
Ligand type: Norbornadiene
Host protein: Ferritin
Anchoring strategy: Dative
Optimization: ---
Max TON: ---
ee: ---
PDB: 2ZUR
Notes: ---

Rational Design of a Structural and Functional Nitric Oxide Reductase

Lu, Y.

Nature 2009, 462, 1079-1082, 10.1038/nature08620

Protein design provides a rigorous test of our knowledge about proteins and allows the creation of novel enzymes for biotechnological applications. Whereas progress has been made in designing proteins that mimic native proteins structurally1,2,3, it is more difficult to design functional proteins4,5,6,7,8. In comparison to recent successes in designing non-metalloproteins4,6,7,9,10, it is even more challenging to rationally design metalloproteins that reproduce both the structure and function of native metalloenzymes5,8,11,12,13,14,15,16,17,18,19,20. This is because protein metal-binding sites are much more varied than non-metal-containing sites, in terms of different metal ion oxidation states, preferred geometry and metal ion ligand donor sets. Because of their variability, it has been difficult to predict metal-binding site properties in silico, as many of the parameters, such as force fields, are ill-defined. Therefore, the successful design of a structural and functional metalloprotein would greatly advance the field of protein design and our understanding of enzymes. Here we report a successful, rational design of a structural and functional model of a metalloprotein, nitric oxide reductase (NOR), by introducing three histidines and one glutamate, predicted as ligands in the active site of NOR, into the distal pocket of myoglobin. A crystal structure of the designed protein confirms that the minimized computer model contains a haem/non-haem FeB centre that is remarkably similar to that in the crystal structure. This designed protein also exhibits NO reduction activity, and so models both the structure and function of NOR, offering insight that the active site glutamate is required for both iron binding and activity. These results show that structural and functional metalloproteins can be rationally designed in silico.


Metal: Fe
Ligand type: Amino acid
Host protein: Myoglobin (Mb)
Anchoring strategy: Dative
Optimization: Genetic
Reaction: NO reduction
Max TON: ~5
ee: ---
PDB: 3K9Z
Notes: Design of a catalytically active non-haem iron-binding site (FeB) in sperm whale myoglobin.

Selective Oxidation of Aromatic Sulfide Catalyzed by an Artificial Metalloenzyme: New Activity of Hemozymes

Mahy, J.-P.

Org. Biomol. Chem. 2009, 7, 3208, 10.1039/b907534h

Two new artificial hemoproteins or “hemozymes”, obtained by non covalent insertion of Fe(III)-meso-tetra-p-carboxy- and -p-sulfonato-phenylporphyrin into xylanase A from Streptomyces lividans, were characterized by UV-visible spectroscopy and molecular modeling studies, and were found to catalyze the chemo- and stereoselective oxidation of thioanisole into the S sulfoxide, the best yield (85 ± 4%) and enantiomeric excess (40% ± 3%) being obtained with Fe(III)-meso-tetra-p-carboxyphenylporphyrin-Xln10A as catalyst in the presence of imidazole as co-catalyst.


Metal: Fe
Ligand type: Porphyrin
Host protein: Xylanase A (XynA)
Anchoring strategy: Supramolecular
Optimization: ---
Reaction: Sulfoxidation
Max TON: 145
ee: 40
PDB: ---
Notes: ---

Stereoselective Hydrogenation of Olefins Using Rhodium-Substituted Carbonic Anhydrase—A New Reductase

Kazlauskas, R.J.

Chem. - Eur. J. 2009, 15, 1370-1376, 10.1002/chem.200801673

One useful synthetic reaction missing from nature's toolbox is the direct hydrogenation of substrates using hydrogen. Instead nature uses cofactors like NADH to reduce organic substrates, which adds complexity and cost to these reductions. To create an enzyme that can directly reduce organic substrates with hydrogen, researchers have combined metal hydrogenation catalysts with proteins. One approach is an indirect link where a ligand is linked to a protein and the metal binds to the ligand. Another approach is direct linking of the metal to protein, but nonspecific binding of the metal limits this approach. Herein, we report a direct hydrogenation of olefins catalyzed by rhodium(I) bound to carbonic anhydrase (CA‐[Rh]). We minimized nonspecific binding of rhodium by replacing histidine residues on the protein surface using site‐directed mutagenesis or by chemically modifying the histidine residues. Hydrogenation catalyzed by CA‐[Rh] is slightly slower than for uncomplexed rhodium(I), but the protein environment induces stereoselectivity favoring cis‐ over trans‐stilbene by about 20:1. This enzyme is the first cofactor‐independent reductase that reduces organic molecules using hydrogen. This catalyst is a good starting point to create variants with tailored reactivity and selectivity. This strategy to insert transition metals in the active site of metalloenzymes opens opportunities to a wider range of enzyme‐catalyzed reactions.


Metal: Rh
Ligand type: COD
Anchoring strategy: Metal substitution
Optimization: Genetic
Reaction: Hydrogenation
Max TON: 15.8
ee: ---
PDB: ---
Notes: ---

Metal: Rh
Ligand type: COD
Anchoring strategy: Metal substitution
Optimization: Genetic
Reaction: Hydrogenation
Max TON: 80.5
ee: ---
PDB: 4CAC
Notes: PDB ID 4CAC = Structure of Zn containing hCAII

Supramolecular Interactions Between Functional Metal Complexes and Proteins

Review

Duhme-Klair, A.K.

Dalton Trans. 2009, 10141, 10.1039/b915776j

This perspective illustrates the principles and applications of molecular recognition directed binding of transition metal complexes to proteins. After a brief introduction into non-covalent interactions and the importance of complementarity, the focus of the first part is on biological systems that rely on non-covalent forces for metal complex binding, such as proteins involved in bacterial iron uptake and the oxygen-storage protein myoglobin. The second part of the perspective will illustrate how the replacement of native with non-native metal-centres can give rise to artificial metalloenzymes with novel catalytic properties. Subsequently, examples of spectroscopic probes that exploit the characteristic photophysical properties of metal-complexes for the non-covalent labelling, visualisation and investigation of proteins will be described. Finally, the use of kinetically inert metal complexes as scaffolds in drug design will be discussed and it will be highlighted how the binding of metal ions or organometallic fragments to existing drugs or drug candidates can improve their activity or even alter their mode of action.


Notes: ---

The Protein Environment Drives Selectivity for Sulfide Oxidation by an Artificial Metalloenzyme

Cavazza, C.; Ménage, S.

ChemBioChem 2009, 10, 545-552, 10.1002/cbic.200800595

Magic Mn–salen metallozyme: The design of an original, artificial, inorganic, complex‐protein adduct, has led to a better understanding of the synergistic effects of both partners. The exclusive formation of sulfoxides by the hybrid biocatalyst, as opposed to sulfone in the case of the free inorganic complex, highlights the modulating role of the inorganic‐complex‐binding site in the protein.


Metal: Mn
Ligand type: Salen
Anchoring strategy: Supramolecular
Optimization: Chemical
Reaction: Sulfoxidation
Max TON: 97
ee: ---
PDB: ---
Notes: ---

Various Strategies for Obtaining Artificial Hemoproteins: From "Hemoabzymes" to "Hemozymes"

Mahy, J.-P.

Biochimie 2009, 91, 1321-1323, 10.1016/j.biochi.2009.03.002

The design of artificial hemoproteins that could lead to new biocatalysts for selective oxidation reactions of organic compounds presents a huge interest especially in pharmacology, both for a better understanding of the metabolic profile of drugs and for the synthesis of enantiomerically pure molecules that could be involved in the design of drugs. The present results show that the so-called “host-guest strategy” that involves the non-covalent incorporation of anionic water-soluble iron-porphyrins into xylanase A from Streptomyces lividans, a low cost protein, leads to such an artificial hemoprotein that is able to perform the stereoselective oxidation of sulfides.


Metal: Fe
Ligand type: Porphyrin
Host protein: Xylanase A (XynA)
Anchoring strategy: Supramolecular
Optimization: Chemical
Reaction: Sulfoxidation
Max TON: ---
ee: 36
PDB: ---
Notes: ---