Identification of a novel class in the alpha/beta hydrolase fold superfamily: the N-myc differentiation-related proteins

The alpha/beta hydrolases constitute a large protein superfamily that mainly consists of enzymes that catalyze a diverse range of reactions. These proteins exhibit the alpha/beta hydrolase fold, the essential features of which have recently been delineated: the presence of at least five parallel beta-strands, a catalytic triad in a specific order (nucleophile-acid-histidine), and a nucleophilic elbow. Because of the difficulties experimentally in identifying protein structures, we have used a Bayesian computational algorithm (PROBE) to identify the members of this superfamily based on distant sequence relationships. We found that the presence of five sequence motifs, which contain residues important for substrate binding and stabilization of the fold, are required for membership in this superfamily. The superfamily consists of at least 909 members, including the N-myc downstream regulated proteins, which are believed to be involved in cell differentiation. Unlike most of the other superfamily members, the N-myc downstream regulated proteins have never been proposed to possess the alpha/beta hydrolase fold and do not appear to be hydrolases.

Protease-containing silicates as active antifouling materials

Biocatalytic silicates, composite materials composed of alpha-chymotrypsin and a silicate prepolymer, were prepared via a two-step polymerization process following solubilization of the enzyme in the polymerization media. This new approach resulted in active and stable composites, and a calculated half-life of over 350 days in aqueous buffer at 30 degrees C. The high stability and activity of this biocatalytic silicate was likely due to the covalent attachment between alpha-chymotrypsin and the silicate matrix. The protease-containing silicate was resistant to fouling by nonselective protein binding, as demonstrated by the dramatically reduced binding of human serum albumin to the silicate material when compared to that of a silicate containing pre-inactivated alpha-chymotrypsin.

Nonaqueous biocatalytic synthesis of new cytotoxic doxorubicin derivatives: exploiting unexpected differences in the regioselectivity of salt-activated and solubilized subtilisin

Two enzymes, Mucor javanicus lipase and subtilisin Carlsberg (SC), catalyzed the nonaqueous acylation of doxorubicin (DOX). Compared to the untreated enzyme the rate of DOX acylation at the C-14 position with vinyl butyrate in toluene was 25-fold higher by lipase ion-paired with Aerosol OT (AOT) and 5-fold higher by lipase activated by 98% (w/w) KCl co-lyophilization (3.21 and 0.67 mumol/min g-lipase, respectively, vs 0.13 mumol/min g-lipase). Particulate subtilisin Carlsberg (SC) was nearly incapable of DOX acylation, but ion-paired SC (AOT-SC) catalyzed acylation at a rate of 2.85 mumol/min g-protease. The M. javanicus formulations, AOT-SC, and SC exclusively acylated the C14 primary hydroxyl group of DOX. Co-lyophilization of SC with 98% (w/w) KCl expanded the enzyme's regiospecificity such that KCl-SC additionally acylated the C4' hydroxyl and C3' amine groups. The total rate of DOX conversion with KCl-SC was 56.7 mumol/min g-protease. The altered specificity of KCl-SC is a new property of the enzyme imparted by the salt activation, and represents the first report of unnatural regioselectivity exhibited by a salt-activated enzyme. Using AOT-SC catalysis, four unique selectively acylated DOX analogues were generated, and KCl-SC was used to prepare DOX derivatives acylated at the alternative sites. Cytotoxicities of select derivatives were evaluated against the MCF7 breast cancer cell line (DOX IC50 = 27 nM) and its multidrug-resistant sub-line, MCF7-ADR (DOX IC50 = 27 muM). The novel derivative 14-(2-thiophene acetate) DOX was relatively potent against both cell lines (IC50 of 65 nM and 8 muM, respectively) and the 14-(benzyl carbonate) DOX analogue was as potent as DOX against the MCF7 line (25 nM). Activated biocatalysts and their novel regioselectivity differences thus enabled single-step reaction pathways to an effective collection of doxorubicin analogues.

Enzymatic synthesis of inulin-containing hydrogels

The Bacillus subtilis protease Proleather FG-F catalyzed the transesterification of inulin with vinyl acrylate (VA) in dimethylformamide (DMF). The reaction conversion for different VA concentrations was greater than 57% after 96 h at 50 degrees C. The degree of substitution (DS, defined as the amount of acrylate groups per 100 inulin fructofuranoside residues) with acrylate moieties can be controlled by varying the molar ratio of VA to inulin. Reasonable yields were obtained (44-51%, 2 days) using a two-step purification methodology. Inulin derivatized with VA (Inul-VA) was characterized by gel permeation chromatography, and its structure was established by (1)H, (13)C, and (1)H-(1)H correlation spectroscopy and (1)H-(13)C heteronuclear multiple quantum coherence NMR. The main positional isomer was at the 6 position of the fructofuranoside residue and two other minor isomers were observed at the 3 and 4 positions. Thus, the enzymatic reaction was largely regioselective. Furthermore, the inulin fructose residues were monosubstituted. Gels with swelling ratios at equilibrium of up to ca. 20 were prepared by free radical polymerization of aqueous solutions of Inul-VA with different DS and monomer concentrations. Gel pore sizes were calculated from swelling experiments and range from 19 to 57 A. To our knowledge, this work reports the first successful enzymatic modification of a polysaccharide solubilized in 100% DMF solution.

Highly enantioselective oxidation of cis-cyclopropylmethanols to corresponding aldehydes catalyzed by chloroperoxidase

Chloroperoxidase (CPO) catalyzes the enantioselective oxidation of cyclopropylmethanols, such as 2-methylcyclopropylmethanol, to cyclopropyl aldehydes using tert-butyl hydroperoxide as the terminal oxidant. In all cases, CPO oxidation of cis-cyclopropanes shows much higher enantioselectivity than with the trans isomers, although CPO gives similar catalytic activity on both isomers. This presents the first example for a heme enzyme that catalyzes the enantioselective oxidation of cyclopropylmethanols. This finding enables a novel route to the synthesis of optically active cyclopropane derivatives, which occur widely in natural products and compounds of pharmaceutical interest. In addition, chiral cyclopropane molecules may be useful model substrates to investigate reaction mechanisms of CPO and the related cytochromes P450.

Protein-containing hydrophobic coatings and films

The incorporation of enzymes and other proteins into hydrophobic polymeric coatings and films has been investigated in this study with the goal of generating biologically active materials for biocatalysis, antifouling surfaces, and biorecognition. The protein-polymer composites are created using standard solution coating techniques with poly(methyl methacrylate), polystyrene, and poly(vinyl acetate) as polymers and alpha-chymotrypsin and trypsin as biocatalysts. The specific enzyme is first extracted into a nonpolar organic solvent using hydrophobic ion-pairing. The ion-paired enzyme is dried and redissolved into a solvent also miscible with the polymer. This solution is then poured over a surface and the solvent is allowed to evaporate to form the enzyme-containing coating, which can then be delaminated to form a film. Leaching of enzyme from and activity of the biocatalytic coatings and films were evaluated. The biocatalytic coatings showed no loss of activity over ca. one week. For the biocatalytic films, the leaching rate was initially high followed by a slow rate of enzyme loss. Activity was measurable for at least one month, with only ca. one-third of the initial activity lost in that time, while, being continuously incubated in a buffer solution. Activity was also exhibited on macromolecular (protein) substrates. The biocatalytic coatings could be reused over 100 times with only a modest loss of activity. Finally, coatings and films containing a lectin (Concanavalin A) were capable of selectively binding to glycoproteins, thereby extending the application of such films for use in bioseparations and biorecognition.

Combinatorial array-based enzymatic polyester synthesis

A combinatorial strategy for biocatalytic polymer synthesis is demonstrated. A library of polymers was synthesized in 96 deep-well plates using AA-BB polycondensations of acyl donors and acceptors. The library was based on four straight-chain diesters as acyl donors (C(3)-C(10)) with aliphatic/aromatic diols as well as more diverse structures including carbohydrates, nucleic acids, and a natural steroid diol used as acyl acceptors. The lipase from Candida antarctica was active in acetonitrile and was capable of catalyzing the polycondensation of the aforementioned monomers to polymers with M(w)'s reaching as high as 20,000 Da, including the preparation of novel sugar-containing polyesters. The combinatorial approach to biocatalytic polymer synthesis described herein serves as a foundation for polymeric materials discovery by demonstrating that polymer arrays can be produced from structurally complex monomers.

Generation of a broad esterolytic subtilisin using combined molecular evolution and periplasmic expression

Concomitant activity improvement of an evolved enzyme toward two very different ester substrates was achieved when a unique combination of functional periplasmic enzyme expression in Escherichia coli, random mutagenesis, DNA shuffling and cell-based kinetic screenings was applied. Specifically, we focused on the conversion of subtilisin E into an enzyme with broader esterase activity as opposed to its native amidase activity. Cell-based microtiter assays were performed on N-acetyl-D,L-phenylalanine p-nitrophenyl ester (Phe-NPE) and sucrose 1'-adipate (S1'A), as well as on the tetrapeptide amide substrate N-succinyl-L-Ala-L-Ala-L-Pro-L-Phe-p-nitroanilide. After a single modified cycle of directed molecular evolution, we isolated a number of clones exhibiting increased activity toward Phe-NPE. In the following rounds of screenings, mutants with improved activity on Phe-NPE were also tested on S1'A. Three mutants were identified with increased esterolytic activity on Phe-NPE and S1'A, while having similar amidase activity to that of the parental enzymes. Because the two ester substrates are structurally distinct, we have evolved a more general esterolytic subtilisin and this may have important applications in synthesis.

Towards more active biocatalysts in organic media: increasing the activity of salt-activated enzymes

The activation of freeze-dried subtilisin Carlsberg (SC) in hexane has been systematically studied and partially optimized with respect to the freezing method, the addition of inorganic salts and lyoprotectants, the initial concentration and final weight percent of additives, and the amount of water added to the organic solvent. Activity and water content were found to correlate directly with the kosmotropicity of the activating salt (kosmotropic salts bind water molecules strongly relative to the strength of water-water interactions in bulk solution). Combinations of kosmotropic salts with known lyoprotectants such as poly(ethylene glycol) (PEG) and sugars did not yield an appreciably more active catalyst. However, the combination of the kosmotropic sodium acetate with the strongly buffering sodium carbonate activated the enzyme more than the individual additives alone. Enzyme activity was enhanced further by the addition of small amounts of water to the organic solvent. Under optimal conditions, enzyme activity in hexane was improved over 27,000-fold relative to the salt-free enzyme, reaching a catalytic efficiency that was within one order of magnitude of k(cat)/K(m) for hydrolysis of the same substrate in aqueous buffer. Further activation to attain even higher catalytic efficiencies may be possible with additional optimization.

Chemoenzymatic synthesis of sucrose-containing aromatic polymers

A chemoenzymatic approach was developed to prepare sucrose-containing aromatic polymers. The protease from Bacillus licheniformis catalyzed the transesterification of sucrose with a diester of terephthalic acid in pyridine to give the mono- and diester products. At 45 degrees C, >70% of sucrose was consumed after 1 day and sucrose diester began to form after 6 days when >95% of sucrose had been converted to sucrose monoester. The final yield of sucrose diester after 20 days was 13.8%. The sucrose monoester was identified as sucrose 1'-terephthalate and the diester products consisted of sucrose 6,1'-diterephthalate and sucrose 6',1'-diterephthalate in a ratio of 2:1. The sucrose diester products were polymerized with ethylene-glycol and ethylene-diamine to give poly(ethylene-terephthalate) and poly(ethylene-terephthalamide), with sucrose contained in the polymer backbone. The polycondensation reactions were carried out in dimethylsulfoxide (DMSO) at 70 degrees C using zinc acetate as a catalyst. The sucrose-containing polyester and polyamide were obtained at 65% yield for 24 h and at 73% yield for 12 h, respectively. End-group analysis of the polymers by (13)C-NMR or (1)H-NMR in DMSO provided a number average molecular weight of 3200 and 4300 Da, respectively. Structural analyses of the polymers were performed with (1)H-NMR, (13)C-NMR, and FTIR. On the basis of (13)C-NMR, acylation of the C1', C6, and C6' hydroxyls were maintained in the polymer backbones.

Aromatic hydroxylation catalyzed by toluene 4-monooxygenase in organic solvent/aqueous buffer mixtures

Toluene 4-monooxygenase is a four-protein component diiron enzyme complex. The enzyme catalyzes the hydroxylation of toluene to give p-cresol with approximately 96% regioselectivity. The performance of the enzyme in two-phase reaction systems consisting of toluene, hexane, or perfluorohexane and an aqueous buffer was tested. In each of the cosolvent systems, containing up to 93% (v/v) of solvent, the enzyme was active and exhibited regioselectivity indistinguishable from the aqueous reaction. Using the perfluorohexane/buffer system, a number of polycyclic aromatic hydrocarbons were oxidized that were not readily oxidized in aqueous buffer. An instability of the hydroxylase component and a substantial uncoupling of NADH utilization and product formation were observed in reactions that were continued for longer than approximately 3 min. More stable enzyme complexes will be needed for broad applicability of this hydroxylating system in nonaqueous media.

Industrial biocatalysis today and tomorrow

The use of biocatalysis for industrial synthetic chemistry is on the verge of significant growth. Biocatalytic processes can now be carried out in organic solvents as well as aqueous environments, so that apolar organic compounds as well as water-soluble compounds can be modified selectively and efficiently with enzymes and biocatalytically active cells. As the use of biocatalysis for industrial chemical synthesis becomes easier, several chemical companies have begun to increase significantly the number and sophistication of the biocatalytic processes used in their synthesis operations.