catELISA: a facile general route to catalytic antibodies

Biomacromolecule-Assisted Screening for Reaction Discovery and Catalyst Optimization

Reaction discovery and catalyst screening lie at the heart of synthetic organic chemistry. While there are efforts at de novo catalyst design using computation/artificial intelligence, at its core, synthetic chemistry is an experimental science. This review overviews biomacromolecule-assisted screening methods and the follow-on elaboration of chemistry so discovered. All three types of biomacromolecules discussed─enzymes, antibodies, and nucleic acids─have been used as "sensors" to provide a readout on product chirality exploiting their native chirality. Enzymatic sensing methods yield both UV-spectrophotometric and visible, colorimetric readouts. Antibody sensors provide direct fluorescent readout upon analyte binding in some cases or provide for cat-ELISA (Enzyme-Linked ImmunoSorbent Assay)-type readouts. DNA biomacromolecule-assisted screening allows for templation to facilitate reaction discovery, driving bimolecular reactions into a pseudo-unimolecular format. In addition, the ability to use DNA-encoded libraries permits the barcoding of reactants. All three types of biomacromolecule-based screens afford high sensitivity and selectivity. Among the chemical transformations discovered by enzymatic screening methods are the first Ni(0)-mediated asymmetric allylic amination and a new thiocyanopalladation/carbocyclization transformation in which both C-SCN and C-C bonds are fashioned sequentially. Cat-ELISA screening has identified new classes of sydnone-alkyne cycloadditions, and DNA-encoded screening has been exploited to uncover interesting oxidative Pd-mediated amido-alkyne/alkene coupling reactions.

Structural basis of the broad substrate tolerance of the antibody 7B9-catalyzed hydrolysis of p-nitrobenzyl esters

Catalytic antibody 7B9, which was elicited against p-nitrobenzyl phosphonate transition-state analogue (TSA) 1, hydrolyzes a wide range of p-nitrobenzyl monoesters and thus shows broad substrate tolerance. To reveal the molecular basis of this substrate tolerance, the 7B9 Fab fragment complexed with p-nitrobenzyl ethylphosphonate 2 was crystallized and the three-dimensional structure was determined. The crystal structure showed that the strongly antigenic p-nitrobenzyl moiety occupied a relatively shallow antigen-combining site and therefore the alkyl moiety was located outside the pocket. These results support the observed broad substrate tolerance of 7B9 and help rationalize how 7B9 can catalyze various p-nitrobenzyl ester derivatives. The crystal structure also showed that three amino acid residues (Asn^H33, Ser^H95, and Arg^L96) were placed in key positions to form hydrogen bonds with the phosphonate oxygens of the transitions-state analogue. In addition, the role of these amino acid residues was examined by site-directed mutagenesis to alanine: all mutants (Asn^H33Ala, Ser^H95Ala, and Arg^L96Ala) showed no detectable catalytic activity. Coupling the findings from our structural studies with these mutagenesis results clarified the structural basis of the observed broad substrate tolerance of antibody 7B9-catalyzed hydrolyses. Our findings provide new strategies for the generation of catalytic antibodies that accept a broad range of substrates, aiding their practical application in synthetic organic chemistry.

ReactELISA: Monitoring a Carbon Nucleophilic Metabolite by ELISA-a Study of Lipid Metabolism

We here present a conceptually novel reaction-based ELISA principle (ReactELISA) for quantitation of the carbon nucleophilic lipid metabolite acetoacetate. Key to the assay is the utilization of a highly chemoselective Friedländer reaction that captures and simultaneously stabilizes the nucleophilic metabolite directly in the biological matrix. By developing a bifunctional biotinylated capture probe, the Friedländer-acetoacetate adduct can be trapped and purified directly in streptavidin coated wells. Finally, we outline the selection and refinement of a highly selective recombinant antibody for specific adduct quantitation. The setup is very robust and, as we demonstrate via miniaturization for microplate format, amenable for screening of compounds or interventions that alter lipid metabolism in liver cell cultures. The assay-principle should be extendable to quantitation of other nucleophilic or electrophilic and perhaps even more reactive metabolites provided suitable capture probes and antibodies.

Binding of Euplotes octocarinatus centrin to peptide from xeroderma pigmentosum group C protein (XPC)

Trp is buried in the hydrophobic cavity, the peptide folds into an α-helix, and the interaction is enthalpically driven from ITC.

High-throughput platform assay technology for the discovery of pre-microrna-selective small molecule probes

MicroRNAs (miRNA) play critical roles in human development and disease. As such, the targeting of miRNAs is considered attractive as a novel therapeutic strategy. A major bottleneck toward this goal, however, has been the identification of small molecule probes that are specific for select RNAs and methods that will facilitate such discovery efforts. Using pre-microRNAs as proof-of-concept, herein we report a conceptually new and innovative approach for assaying RNA-small molecule interactions. Through this platform assay technology, which we term catalytic enzyme-linked click chemistry assay or cat-ELCCA, we have designed a method that can be implemented in high throughput, is virtually free of false readouts, and is general for all nucleic acids. Through cat-ELCCA, we envision the discovery of selective small molecule ligands for disease-relevant miRNAs to promote the field of RNA-targeted drug discovery and further our understanding of the role of miRNAs in cellular biology.

Enzyme immunoassays as screening tools for catalysts and reaction discovery

This feature article summarizes the development and use of immunoassay techniques (ELISA) as screening tools for fast identification of efficient catalysts in libraries and for the discovery of new chemical reactions.

Mining electron density for functionally relevant protein polysterism in crystal structures

This review focuses on conceptual and methodological advances in our understanding and characterization of the conformational heterogeneity of proteins. Focusing on X-ray crystallography, we describe how polysterism, the interconversion of pre-existing conformational substates, has traditionally been analyzed by comparing independent crystal structures or multiple chains within a single crystal asymmetric unit. In contrast, recent studies have focused on mining electron density maps to reveal previously ‘hidden’ minor conformational substates. Functional tests of the importance of minor states suggest that evolutionary selection shapes the entire conformational landscape, including uniquely configured conformational substates, the relative distribution of these substates, and the speed at which the protein can interconvert between them. An increased focus on polysterism may shape the way protein structure and function is studied in the coming years.

cat-ELCCA: a robust method to monitor the fatty acid acyltransferase activity of ghrelin O-acyltransferase (GOAT)

Assays armed with catalytic signal amplification have arisen as superior systems for ultrasensitive detection of analytes. Here we describe a conceptually new enzyme assay based on cat-ELISA, catalytic assay using enzyme-linked click chemistry assay (cat-ELCCA), where an enzyme-linked azide is utilized to arm the assay with catalytic fluorescence signal amplification. Using this assay technology, we have developed the first potentially high-throughput screen for the recently disclosed acyltransferase, ghrelin O -acyltransferase (GOAT).

Enzyme assays

Enzyme assays are analytical tools to visualize enzyme activities. In recent years a large variety of enzyme assays have been developed to assist the discovery and optimization of industrial enzymes, in particular for "white biotechnology" where selective enzymes are used with great success for economically viable, mild and environmentally benign production processes. The present article highlights the aspects of fluorogenic and chromogenic substrates, sensors, and enzyme fingerprinting, which are our particular areas of interest.

Label-free continuous enzyme assays with macrocycle-fluorescent dye complexes

We introduce a new economic, convenient and general assay principle based on the reversible interaction of water-soluble macrocycles and fluorescent dyes. We show that amino acid decarboxylase activity can be continuously monitored by measuring changes in fluorescence, which result from the competition of the enzymatic product and the dye for forming a complex with a cucurbituril or calixarene macrocycle. The new assay provides a complementary method to the use of antibodies, radioactive markers and labeled substrates.

Screening systems

Enzyme screening technology has undergone massive developments in recent years, particularly in the area of high-throughput screening and microarray methods. Screening consists of testing each sample of a sample library individually for the targeted reaction. This requires enzyme assays that accurately test relevant parameters of the reaction, such as catalytic turnover with a given substrate and selectivity parameters such as enantio- and regioselectivity. Enzyme assays also play an important role outside of enzyme screening, in particular for drug screening, medical diagnostics, and in the area of cellular and tissue imaging. In the 1990s, methods for high-throughput screening of enzyme activities were perceived as a critical bottleneck. As illustrated partly in this chapter, a large repertoire of efficient screening strategies are available today that allow testing of almost any reaction with high-throughput.

A red-fluorescent substrate microarray for lipase fingerprinting

A lipase substrate microarray was obtained by printing aliphatic C2-C12 monoesters of (5R)- and (5S)-3-(5,6-dihydroxyhexyloxy)benzaldehyde by reductive alkylation on amine-functionalized glass slides coated with bovine serum albumin and a short PEG linker. The microarray features 12 substrates and their 66 possible binary mixtures spotted in a 9 x 36 spot array. Lipase reactions are detected by chemoselective NaIO(4)-oxidation of the 1,2-diol hydrolysis product to form an aldehyde, which is then tagged with the red-fluorescent dye rhodamine B sulfohydrazide . Specific fingerprints are produced by active enzymes. These experiments provide the first example of lipase fingerprinting using microarrays.

A theoretical approach to some analytical properties of heterogeneous enzymatic assays

Heterogeneous enzymatic assays (HEA), where an enzyme in solution acts upon an immobilized substrate, are been increasingly used. Given their high throughput and versatility they hold great potential for developing massive enzyme inhibitor screening. However, current HEA lack, in general, rigorous quantitative use. This is in part due to technical problems as a multiplicity of suboptimal substrate populations achieved with traditional immobilization techniques but, more importantly, is due to a poor understanding of the particular kinetic behavior of these systems. This paper addresses the kinetic features of HEA that arise from the very low amount of solid-phase substrate and the resulting inalterability of the free enzyme concentration during the assay, which classify HEA as enzyme quasi-saturable systems (EQSS). We assessed the optimal enzyme concentration working range and time of reaction. We also considered certain attributes of HEA for evaluating isosteric inhibitors. These studies were done on the basis of a simplified model for the kinetics of EQSS and a formal splitting of the functional factor of the analytical sensitivity of an enzymatic assay into [E(o)]/K(m)-dependent and temporal components.

Enzymes in the synthesis of bioactive compounds: the prodigious decades

The growing demand for enantiomerically pure pharmaceuticals has impelled research on enzymes as catalysts for asymmetric synthetic transformations. However, the use of enzymes for this purpose was rather limited until the discovery that enzymes can work in organic solvents. Since the advent of the PCR the number of available enzymes has been growing rapidly and the tailor-made biocatalysts are becoming a reality. Thus, it has been possible the use of enzymes for the synthesis of new innovative medicines such as carbohydrates and their incorporation to modern methods for drug development, such as combinatorial chemistry. Finally, the genomic research is allowing the manipulation of whole genomes opening the door to the combinatorial biosynthesis of compounds. In this review, our intention is to highlight the main landmarks that have led to transfer the chemical efficiency shown by the enzymes in the cell to the synthesis of bioactive molecules in the lab during the last 20 years.

Catalytic antibodies: hapten design strategies and screening methods

Catalytic antibodies have emerged as powerful tools for the efficient and specific catalysis of a wide range of chemical transformations. Generating antibody catalysts that achieve enzymatic efficiency remains a challenging task, which has long been the source of great interest both in the design of more effective haptens for immunization and in the development of more direct and efficient screening methods for the selection of antibodies with desired catalytic capacities. In this review, we describe the development of different hapten design strategies, including a transition state analog (TSA) approach, 'bait-and-switch' catalysis, and reactive immunization. We also comment on recent developments in the screening process that allow for a more efficient identification of antibody catalysts.

Isolation of antigens and antibodies by affinity chromatography

Antibody-antigen binding constants are commonly strong enough for an effective affinity purification of antibodies (by immobilized antigens) or antigens (by immobilized antibodies) to work out a straightforward purification method. A drawback is that antibodies are large protein molecules and subject to denaturation under conditions required for the elution from the complex. Structures of antigens can vary but usually antigens are also equally subject to similar problems. The lability of the components can sometimes make the procedure sophisticated, but usually in all cases it is possible to find a satisfactory approach. In certain cases, specific interactions of the Fc part of antibodies are more facile to exploit for their purification.

Directed evolution of an extremely fast phosphotriesterase by in vitro compartmentalization

We describe the selection of a phosphotriesterase with a very fast k(cat) (over 10(5) s(-1)), 63 times higher than the already very efficient wild-type enzyme. The enzyme was selected from a library of 3.4 x 10(7) mutated phosphotriesterase genes using a novel strategy based on linking genotype and phenotype by in vitro compartmentalization (IVC) using water-in-oil emulsions. First, microbeads, each displaying a single gene and multiple copies of the encoded protein, are formed by compartmentalized in vitro translation. These microbeads can then be selected for catalysis or binding. To select for catalysis the microbeads are re-emulsified in a reaction buffer of choice with a soluble substrate. The product and any unreacted substrate are coupled to the beads when the reaction is finished. Product-coated beads, displaying active enzymes and the genes that encode them, are detected with anti-product antibodies and selected using flow cytometry. This completely in vitro process selects for all enzymatic features simultaneously (substrate recognition, product formation, rate acceleration and turnover) and single enzyme molecules can be detected.

The use of enzyme immunoassays for the detection of abzymatic activities. Application to an enantioselective thioacetal hydrolysis activity

Relying on the particularly high specificity displayed by antibodies, enzyme immunoassays have proved to be one of the most efficient tools for early detection of the catalytic activities displayed by antibodies. We took advantage of such an assay, namely the Cat-enzyme-linked immunoassay (EIA) approach developed in our laboratories, both to exhibit and characterise an antibody-catalysed thioacetal hydrolysis. Monoclonal antibody (mAb) H3-32 was thus identified to accelerate the hydrolysis reaction of thioacetal substrate (NC9) to vanillylmandelic acid (VMA), with a k(cat) of 0.148 h(-1) (k(uncat) = 6.85 x 10(-5) h(-1)), and a K(M) of 720 microM. Taking advantage of the enantiomeric discrimination between (R)- and (S)-VMA displayed by some of the anti-H3 monoclonal antibodies, we were also able to determine that (S)-VMA was preferentially formed during this abzymatic hydrolysis with a 47% enantiomeric excess. All these EIA measurements were confirmed through HPLC analyses.

A method for the detection and screening of catalytic anti-DNA antibodies

We have developed a microtiter plate assay for the detection and screening of anti-DNA hydrolytic antibodies. The affinity-linked oligonucleotide nuclease assay (ALONA) makes use of substrates with a digoxigenin on the 5'-end of the 3'-biotinylated DNA strands. The substrate binds specifically to the wells of streptavidin-coated microtiter plates where the reaction takes place. Uncleaved substrate retains the digoxigenin label, which is then detected with an enzyme-labeled anti-digoxigenin antibody. We first assessed the efficiency of this assay by measuring S1 nuclease and DNase I activities and the inhibitory effect of EDTA on the reaction. The ALONA procedure was then successfully applied to the screening of a high number of hybridoma clones derived from nonimmunized (NZB x NZW)F1 mice with spontaneous lupus erythematosus. We detected three potential catalytic antibodies and investigated their substrate specificity. Overall, our findings demonstrate the value of the ALONA method for high throughput screening of potential nucleases and catalytic antibodies. Although this assay was designed for the selection of catalysts active in DNA hydrolysis, it can be adapted to detect most types of substrate cleavage reaction.

Evolution of catalytic antibody repertoire in autoimmune mice

We have attempted to efficiently obtain catalytic antibodies (catAbs) with amidase/esterase activity in the expanded sequence space of the antibody repertoire. In doing so, we used an autoimmune mouse strain, MRL/lpr, that is known to produce enhanced levels of autoantibodies. We applied different types of haptens, such as, and, that are supposed to mimic the transition state of the substrate in the ester/amide hydrolysis. Among them, hapten (2) could not be used, as it was readily broken down after synthesis. Upon immunization with hapten (1), catAbs preferentially evolved in MRL/lpr mice, but this did not happen upon immunization with haptens (3) and (4). Independently, immunization to MRL/lpr mice with successfully elicited the catAbs with the ability to activate vitamin B(6) prodrugs. The common observation seen in these two cases is that most of the catAbs derived from MRL/lpr mice by hapten (1) and half of them by hapten (5) had a Lys at H95, which is at the junctional N region between the V(H) and J(H) gene segments. Despite the conservation of Lys (H95), analyses of the N-region and utilization of the D gene segment in the heavy chain gene showed that these catAbs were from several independent clones of the same family. Studies of site-directed mutagenesis suggest that, in the catAbs elicited from hapten (1), a Lys (H95) and a His (L91) are involved in the catalytic function. Both residues are known to interact with the phosphonate moiety of hapten (1). Such studies also suggest that, in the catAbs elicited from hapten (5), a Lys (H95) and a His (H35) are involved in the catalytic function. These basic amino acids seem to be important for binding to the phosphonate hapten, as they were not changed even after extensive evolution following multiple mutations. By contrast, in normal BALB/c mice, immunization of hapten (1) resulted in eliciting catAbs in lower yield and the majority were the non-catAbs, whose sequences were quite different from those of the catAbs from MRL/lpr mice. They were clonally related to one another and most of them originated from a single clone. The positions of the interacting key residues in the CDRs that interact with the phosphorus moiety strongly differ between our catAbs and other reported catAbs with esterase/amidase activity, which were elicited by the phosphonate/phosphonamidate haptens from normal mice. Further comparison of antibodies elicited by the phosphorus haptens, such as DNA, RNA, phosphocholine, and phosphotyrosine, indicated that none of them had sequence similarity in the basic amino acids and their positions in the CDRs, except for one example, which is anti-DNA antibody elicited from C3H-lpr mice. Analysis based on the classification of canonical structures of the antibodies again suggested that our catAbs derived from MRL/lpr mice belong to an unusual class that is not listed in the literature. Taken together, the above evidence suggests that the unique catalytic subsets that existed in the initial repertoire in the MRL/lpr mice could effectively be captured by the phosphonate haptens through the interaction with the Lys at H95. In the BALB/c mice, however, another noncatalytic subset with an ability to bind only to a moiety other than the phosphonate moiety alternatively evolved, because of the lowest abundance or elimination of the catalytic subsets.

Structural diversity of antibody catalysts

The structural diversity of the immune response may be considerably restricted by the structure of the hapten used to elicit catalytic antibodies. The ligand-binding mode and the shapes of the binding pockets of hydrolytic antibodies induced to different transition-state analogs that contain an unsubstituted arylphosphonate group are very similar. Moreover, antibodies elicited against a single transition state analog evolve from a single germline gene or different precursors, depending on the nature of the hapten. Germline antibodies seem to adopt multiple conformations with antigen binding, together with somatic mutation stabilizing the conformation with optimum complementarity to antigen.

Esterolytic antibodies as mechanistic and structural models of hydrolases-a quantitative analysis

Understanding enzymes quantitatively and mimicking their remarkable catalytic efficiency is a paramount challenge. Here, we applied esterolytic antibodies (the D-Abs) to dissect and quantify individual elements of enzymatic catalysis such as transition state (TS) stabilization, nucleophilic reactivity and conformational changes. Kinetic and mutagenic analysis of the D-Abs were combined with existing structural evidence to show that catalysis by the D-Abs is driven primarily by stabilization of the tetrahedral oxyanionic intermediate of ester hydrolysis formed by the nucleophilic attack of an exogenous (solution) hydroxide anion. The side-chain of TyrH100d is shown to be the main H-bond donor of the D-Abs oxyanion hole. The pH-rate and pH-binding profiles indicate that the strength of this H-bond increases dramatically as the neutral substrate develops into the oxyanionic TS, resulting in TS stabilization of 5-7 kcal/mol, which is comparable to oxyanionic TS stabilization in serine hydrolases. We show that the rate of the exogenous (intermolecular) nucleophilic attack can be enhanced by 2000-fold by replacing the hydroxide nucleophile with peroxide, an alpha-nucleophile that is much more reactive than hydroxide. In the presence of peroxide, the rate saturates (k(cat)(max)) at 6 s(-1). This rate-ceiling appears to be dictated by the rate of the induced-fit conformational rearrangement leading to the active antibody-TS complex. The selective usage of negatively charged exogenous nucleophiles by the D-Abs led to the identification of a positively charged channel. Imprinted by the negatively-charged TS-analogue against which these antibodies were elicited, this channel presumably directs the nucleophile to the antibody-bound substrate. Our findings are discussed in comparison with serine esterases and, in particular, with cocaine esterase (cocE), which possesses a tyrosine based oxyanion hole.

Remarkable remote chiral recognition in a reaction mediated by a catalytic antibody

The crystal structures of catalytic antibody D2.3 Fab with the two enantiomers, 7D and 7L, which represent transition state analogues for the hydrolysis of the corresponding esters, 6D and 6L, were determined to better understand remarkable reactivity differences: the L-ester displayed significantly tighter binding (K(M)) and increased catalytic activity (k(cat)) with D2.3, even though the chiral center is 7 bonds distant from the reaction center. Surprisingly, the electron densities of the liganded phosphonates, 7D and 7L, within the D2.3 binding/reaction site were essentially identical, highlighting the subtle influences of protein interactions on chemical behavior.

Two general methods for the isolation of enzyme activities by colony filter screening

We describe two general methodologies, based on filter-sandwich assays, for isolating enzymatic activities from a large repertoire of protein variants expressed in the cytoplasm of E. coli cells. The enzymes are released by the freezing and thawing of bacterial colonies grown on a porous master filter and diffuse to a second "reaction" filter that closely contacts the master filter. Reaction substrates can be immobilized either on the filter or on the enzyme itself (which is then, in turn, captured on the reaction filter). The resulting products are detected with suitable affinity reagents. We used biotin ligase as a model enzyme to assess the performance of the two methodologies. Active enzymes were released by the bacteria, locally biotinylated the immobilized target substrate peptide, and allowed the sensitive and specific detection of individual catalytically active colonies.

Catalytic antibodies induced by a zwitterionic hapten

A zwitterionic hapten 4 featuring both positively and negatively charged functional groups was designed and synthesized with the goal of generating catalytic antibodies for the hydrolysis of ester 6 and amide 7. Of the 36 monoclonal antibodies specific to BSA-4 (bovine serum albumin) that were isolated, six accelerated the hydrolysis of 6. Two catalytic antibodies with distinctively different and representative kinetic behaviors were selected for detailed kinetic studies. Whereas H8-2-6F11 showed burst kinetic behavior, which can be attributed to the formation of an acyl intermediate, H8-1-2D5 did not, but it did exhibit high multiple turnover activity. The rate of hydrolysis of 6 catalyzed by H8-1-2D5 followed Michaelis-Menten kinetics; the apparent values of the Michaelis-Menten constant Km and the catalytic constant kcat were 488 microM and 3.5 min(-1), respectively. The catalytic rate enhancement (kcat/kun) observed for H8-1-2D5 was 1.3 x 10(5), which is approximately two orders of magnitude greater than those for monofunctional haptens. Thus H8-1-2D5 compares well in catalytic activity with antibodies isolated by a related approach called heterologous immunization.

Kinetic and titration methods for determination of active site contents of enzyme and catalytic antibody preparations

Kinetic characterization of enzymes and analogous catalysts such as catalytic antibodies requires knowledge of the molarity of functional sites. Various stoichiometric titration methods are available for the determination of active-site concentrations of some enzymes and these are exemplified in the second part of this article. Most of these are not general in that they require the existence of certain types of either intermediate or active-site residues that are susceptible to specific covalent modification. Thus they are not readily applicable to many enzymes and they are rarely available currently for titration of catalytic antibody active sites. In the first part of the article we discuss a general kinetic method for the investigation of active-site availability in preparations of macromolecular catalysts. The method involves steady-state kinetics to provide Vmax and Km and single-turnover first-order kinetics using excess of catalyst over substrate to provide the analogous parameters k(obs)lim and K(m)app. The active-site contents of preparations that contain only active catalyst (Ea) and inert material (Ei) may be calculated as [Ea](T) = Vmax)/k(obs)lim. This is true even if nonproductive binding to E(a) occurs. For polyclonal catalytic antibody preparations, which may contain binding but noncatalytic material (Eb) in addition to Ea and Ei, the significance of Vmax/k(obs)lim is more complex but provides an upper limit to E(a). This can be refined by consideration of the relative values of Km and the equilibrium dissociation constant of EbS. Analysis of the Ea, Eb, Ei system requires the separate determination of Ei. For catalytic antibodies this may be achieved by analytical affinity chromatography using an immobilized hapten or hapten analog and an ELISA procedure to ensure the clean separation of Ei from the Ea + Eb mixture.

Novel methods for biocatalyst screening

There have been a number of recent advances in catalysis assays applicable for screening biocatalyst libraries in high-throughput format. These include instrumental assays such as high-performance liquid chromatography, mass spectrometry, capillary electrophoresis and IR-thermography, reagent-based assays producing spectroscopic signals (UV/VIS or fluorescence) in response to reaction progress, and assays based on fluorogenic or chromogenic substrates. These fluorogenic substrates enable the assaying of a variety of enzymes in enantioselective and stereoselective manner, including alcohol dehydrogenases, aldolases, lipases, amidases, epoxide hydrolases and phosphatases.

Critical analysis of antibody catalysis

Antibody molecules elicited with rationally designed transition-state analogs catalyze numerous reactions, including many that cannot be achieved by standard chemical methods. Although relatively primitive when compared with natural enzymes, these catalysts are valuable tools for probing the origins and evolution of biological catalysis. Mechanistic and structural analyses of representative antibody catalysts, generated with a variety of strategies for several different reaction types, suggest that their modest efficiency is a consequence of imperfect hapten design and indirect selection. Development of improved transition-state analogs, refinements in immunization and screening protocols, and elaboration of general strategies for augmenting the efficiency of first-generation catalytic antibodies are identified as evident, but difficult, challenges for this field. Rising to these challenges and more successfully integrating programmable design with the selective forces of biology will enhance our understanding of enzymatic catalysis. Further, it should yield useful protein catalysts for an enhanced range of practical applications in chemistry and biology.

Highly sensitive and rapid detection of antibody catalysis by luminescent bacteria

A highly sensitive, inexpensive, and facile bioluminescent assay for the detection of catalytic antibodies has been developed. This assay may be used for the early detection of antibody catalysis. The efficiency of this technique was exemplified by the use of the luminescent bacterium VhM42 for monitoring an antibody-catalyzed retroaldol fragmentation reaction with aldolase antibodies 38C2 and 24H6.

Man-made enzymes--from design to in vitro compartmentalisation

In the past few years, a variety of methods have been developed to allow the in vitro evolution of a range of biomolecules including novel and improved biocatalysts (enzymes). These methods for directed evolution differ in the size and characteristics of the gene repertoire, in the way of linking genotype and phenotype, and in the selection approach. Selections for enzymes can be performed indirectly (for binding of a transition-state analogue or mechanism-based inhibitor), and directly using either intramolecular single-turnover selections (e.g. with SELEX) or the normal (intermolecular, multiple turnover) mode of enzymatic reactions. Each of these methods has distinct strengths and weaknesses. The best system (or combinations of systems) to use depends on the specific target for evolution and the evolutionary distance that needs to be crossed.

The kinetic basis of a general method for the investigation of active site content of enzymes and catalytic antibodies: first-order behaviour under single-turnover and cycling conditions

The theoretical foundation has been laid for the investigation of catalytic systems using first-order kinetics and for a general kinetic method of investigation of the active site content, E(a), of enzymes, catalytic antibodies, and other enzyme-like catalysts. The method involves a combination of steady-state and single-turnover kinetics to provide Vmax and Km and k(lim)(obs) and K(app)(m), respectively. The validity of the method is shown to remain valid for two extensions of the simple two-step enzyme catalysis model (a) when the catalyst preparation contains molecules (Eb) that bind substrate but fail to catalyse product formation and (b) when the catalyst itself binds substrate non-productively as well as productively. The former is a particularly serious complication for polyclonal catalytic antibodies and the latter a potential complication for all catalysts. For the simple model and for (b) Vmax/k(lim)(obs) provides the value of [Ea]T and for (a) its upper limit. This can be refined by consideration of the relative values of Km and the equilibrium dissociation constant of EbS. For the polyclonal catalytic antibody preparation investigated, the fact that K(app/m) > Km demonstrates for the first time the presence of a substrate-binding but non-catalytic component in a polyclonal preparation. First-order behaviour in catalytic systems occurs not only with a large excess of catalyst over substrate but also with lower catalyst/substrate ratios, including the equimolar condition, when K(app)(m) >> [S]0, a phenomenon that is not widely appreciated.