Kinetic studies on the mechanism and the specificity of peptide semisynthesis catalyzed by the serine proteases alpha-chymotrypsin and beta-trypsin

The 3D model of the lipase/acyltransferase from Candida parapsilosis, a tool for the elucidation of structural determinants in CAL-A lipase superfamily

Because lipids are hydrophobic, the development of efficient bioconversions in aqueous media free of organic solvents is particularly challenging for green oleochemistry. Within this aim, enzymes exhibiting various abilities to catalyze acyltransfer reaction in water/lipid systems have been identified. Among these, CpLIP2 from Candida parapsilosis has been characterized as a lipase/acyltransferase, able to catalyze acyltransfer reactions preferentially to hydrolysis in the presence of particularly low acyl acceptor concentration and high thermodynamic activity of water (aw>0.9). Lipase/acyltransferases are thus of great interest, being able to produce new esters at concentrations above the thermodynamic equilibrium of hydrolysis/esterification with limited to no release of free fatty acids. Here, we present a 3D model of CpLIP2 based on homologies with crystallographic structures of Pseudozyma antarctica lipase A. Indeed, the two enzymes have 31% of identity in their primary sequence, yielding a same general structure, but different catalytic properties. The quality of the calculated CpLIP2 model was confirmed by several methods. Limited proteolysis confirmed the location of some loops at the surface of the protein 3D model. Directed mutagenesis also supported the structural model constructed on CAL-A template: the functional properties of various mutants were consistent with their structure-based putative involvement in the oxyanion hole, substrate specificity, acyltransfer or hydrolysis catalysis and structural stability. The CpLIP2 3D model, in comparison with CAL-A 3D structure, brings insights for the elucidation and improvement of the structural determinants involved in the exceptional acyltransferase properties of this promising biocatalyst and of homologous enzymes of the same family.

Homologous yeast lipases/acyltransferases exhibit remarkable cold-active properties

Lipases/acyltransferases catalyse acyltransfer to various nucleophiles preferentially to hydrolysis even in aqueous media with high thermodynamic activity of water (a w >0.9). Characterization of hydrolysis and acyltransfer activities in a large range of temperature (5 to 80 °C) of secreted recombinant homologous lipases of the Pseudozyma antarctica lipase A superfamily (CaLA) expressed in Pichia pastoris, enlighten the exceptional cold-activity of two remarkable lipases/acyltransferases: CpLIP2 from Candida parapsilosis and CtroL4 from Candida tropicalis. The activation energy of the reactions catalysed by CpLIP2 and CtroL4 was 18-23 kJ mol(-1) for hydrolysis and less than 15 kJ mol(-1) for transesterification between 5 and 35 °C, while it was respectively 43 and 47 kJ mol(-1) with the thermostable CaLA. A remarkable consequence is the high rate of the reactions catalysed by CpLIP2 and CtroL4 at very low temperatures, with CpLIP2 displaying at 5 °C 65 % of its alcoholysis activity and 45 % of its hydrolysis activity at 30 °C. These results suggest that, within the CaLA superfamily and its homologous subgroups, common structural determinants might allow both acyltransfer and cold-active properties. Such biocatalysts are of great interest for the efficient synthesis or functionalization of temperature-sensitive lipid derivatives, or more generally to lessen the environmental impact of biocatalytic processes.

gamma-Glutamyltranspeptidase-catalysed acyl-transfer to the added acceptor does not proceed via the ping-pong mechanism

Acyl-transfer catalysed by gamma-glutamyltranspeptidase from bovine kidney was studied using gamma-L- and gamma-D-Glu-p-nitroanilide as the donor and GlyGly as the acceptor. The transfer of the gamma-Glu group to GlyGly was shown to be accompanied by transfer of the gamma-Glu group to water (hydrolysis). The results were compared with acyl-transfer catalysed by the representative serine protease, alpha-chymotrypsin. The main difference between the kinetic mechanism of the acyl-transfer reactions catalysed by these enzymes, which contain an active-site serine and form an acyl-enzyme intermediate but belong to different enzyme classes, was found to consist in the role of the enzyme-donor-acceptor complex. This complex is not formed at any acceptor concentrations in the acyl-transfer reactions catalysed by the serine proteases. In contrast, in the gamma-glutamyltranspeptidase-catalysed acyl-transfer the pathway going through the ternary enzyme-donor-acceptor complex formed from the enzyme-acceptor complex becomes the main pathway of the transfer reaction even at moderate acceptor concentrations. As a result, gamma-glutamyltranspeptidase catalysis follows a sequential mechanism with random equilibrium addition of the substrates and ordered release of the products. The second distinction concerns the inhibitory effect of the acceptor. In the case of alpha-chymotrypsin this was the result of true inhibition, i.e. a dead-end formation of the enzyme-acceptor complex. A salt effect caused by the acceptor was the rationale of a similar effect observed in acyl-transfer catalysed by gamma-glutamyltranspeptidase.

The second nucleophile molecule binds to the acyl-enzyme-nucleophile complex in alpha-chymotrypsin catalysis. Kinetic evidence for the interaction

alpha-Chymotrypsin-catalyzed acyl transfer was studied using three acyl-group donors (Mal-L-Ala-L-Ala-L-PheOMe, Bz-L-TyrOEt and Ac-L-TrpOEt; Mal, maleyl; Bz, benzoyl; OMe, methyl ester; OEt, ethyl ester) and a series of amino-acid amides. Most of the reactions studied can be described by the simplest kinetic model without the nucleophile binding to the acyl-enzyme. The alpha-chymotrypsin-catalyzed transfer of the Mal-L-Ala-L-Ala-L-Phe group to the amides of L-Phe and L-Tyr showed a linear dependence of the partition constant, p, on the nucleophile concentration which can be interpreted by the hydrolysis of the acyl-enzyme-nucleophile complex. The alpha-chymotrypsin-catalyzed transfer of the Bz-L-Tyr and Ac-L-Trp groups to several amino-acid amides showed unusual behavior which can be interpreted by the kinetic model involving formation of a complex of the acyl-enzyme with two nucleophile molecules. These observations can explain the conflicting conclusions concerning the kinetics of alpha-chymotrypsin-catalyzed acyl transfer evident in previous studies.

Nucleophile specificity in alpha-chymotrypsin- and subtilisin-(Bacillus subtilis strain 72) catalyzed reactions

Nucleophilic properties of amino-acid amides were studied systematically in acyl-transfer reactions catalyzed by alpha-chymotrypsin and subtilisin from Bacillus subtilis strain 72 (subtilisin 72) using Mal-L-Ala-L-Ala-L-PheOMe as the acyl-group donor. In alpha-chymotrypsin-catalyzed reactions, the nucleophile reactivities increase in the following order: D-AlaNH2 < GlyNH2 < L-AlaNH2 < L-SerNH2 < L-ThrNH2 < L-HisNH2 < L-ValNH2 < L-LeuNH2 < L-TrpNH2 < L-MetNH2 < L-NvaNH2 < L-PheNH2 < L-IleNH2 < L-TyrNH2 < L-ArgNH2. In reactions catalyzed by subtilisin 72, the reactivities increase as follows: L-LeuNH2 < L-IleNH2 < L-ThrNH2 < L-ArgNH2 < L-TrpNH2 < L-NvaNH2 < L-ValNH2 < L-MetNH2 < L-AlaNH2 < L-SerNH2 < D-AlaNH2 < GlyNH2. In alpha-chymotrypsin-catalyzed reactions, hydrophobic interactions are entirely responsible for the differences between the reactivity of the nucleophiles for amides of all the amino-acids tested with the exception of D-AlaNH2, L-ArgNH2 and L-TyrNH2. In reactions catalyzed by subtilisin 72, amino-acid side-chain characteristics and the nucleophile reactivities are not related. The data obtained show the low selectivity of the S1' subsite of subtilisin 72 and high specificity of this subsite in alpha-chymotrypsin.

Peptide synthesis by proteases in organic solvents: Medium effect on substrate specificity

The substrate specificities of alpha-chymotrypsin and subtilisins for peptide synthesis in hydrophilic organic solvents were investigated. Chymotrypsin exhibited high specificity to aromatic amino acids as acyl donors, while subtilisin Carlsberg and subtilisin BPN' were specific to aromatic and neutral aliphatic amino acids, in accordance with the S1 specificities of the enzymes for peptide hydrolysis in aqueous solutions. On the contrary, chymotrypsin exhibited higher specificities to hydrophilic amino acid amides as acyl acceptors (nucleophiles) for peptide synthesis with N-acetyl-L-tyrosine ethyl ester, in contrast to the S1' specificity for peptide hydrolysis and peptide synthesis in aqueous solutions. Furthermore, nucleophile specificity changed with the change in water-organic solvent composition; the increase in water content led to increase in relative reactivity of leucinamide to that of alaninamide. It was also found that protection of the carboxyl group of alanine by amidation is much preferable to protection by esterification in terms of reactivity as nucleophiles.

Electrostatic effects in the alpha-chymotrypsin-catalyzed acyl transfer. I. Influence of different inorganic salts

We investigated the deacylation of two acyl-alpha-chymotrypsins by added nucleophiles. The nucleophile binding site of the enzyme shows a strong preference for positively charged compounds. Most of our data can be explained by direct electrostatic interaction between the ionic nucleophiles and two negatively charged residues which are located close to the active site of the enzyme molecule. The influence of inorganic salts on the acyl transfer includes the following effects: (1) reduction of electrostatic interactions between the acyl-enzyme and the nucleophile by addition of salts; (2) binding of divalent cations to the nucleophile binding site of the acyl-enzyme leading to a significantly changed specificity; and (3) linear dependence of the activity coefficients of the added nucleophiles on salt concentration.

Protease-catalyzed synthetic reactions and immobilization-activation of the enzymes in hydrophilic organic solvents

The catalytic feature of serine proteases for synthetic reactions in hydrophilic organic solvents and effects of immobilization by complexation with polysaccharides are described. Free alpha-chymotrypsin and subtilisin Carlsberg catalyze esterification, transesterification, and peptide synthesis in hydro-organic cosolvents with less than 10% water. Subtilisin BPN' is catalytically less active. The medium effects on the reaction kinetics and product yield were investigated in terms of the nature of solvent and water content in the reaction systems. The substrate- and stereo-specificities of the enzymes suggest that the enzymes maintain their native conformations in these low-water organic solvents. The catalytic activities of the proteases markedly increase by immobilization or complexation with polysaccharides, such as chitin or chitosan. The results of the rate measurements suggest that the primary role of the support materials is the activation of the enzymes and the increase in substrate concentration at reaction sites.

Kinetic study of nucleophile specificity in dipeptide synthesis catalyzed by clostridiopeptidase B

The kinetic parameters of Clostridiopeptidase B-catalyzed aminolysis of carbobenzoxyarginyl methyl ester leading to the formation of various dipeptides are investigated. The deacylation rates of the acylenzyme were evaluated by direct product analysis using high-performance liquid chromatography on a reversed-phase column. On the basis of the partitioning ratio and the first-order and second-order rate constants for the deacylation step, large differences in the nucleophile reactivities, which appear to be related to a S'1-P'1 interaction, were observed. The order of specificity was established as Leu much greater than Ser greater than Phe greater than Val greater than Ala = Gly much greater than Pro with second-order rate constants ranging from 578,614 M-1 s-1 for leucinamide to 5132 M-1 s-1 in the case of prolinamide. All of the amino acid amides had a nucleophilic strength at least 10 times higher than that of water during the deacylation step. The data reported here represent the first experimental evidence for the existence of a S'1 site engaged in the recognition of the amino acid side chain residue for this enzyme. The recognition site showed an increase in the affinity along with an increase in the hydrophobicity of the amino acid amide side chains.

Acyl group transfer by proteases forming an acylenzyme intermediate: kinetic model analysis (including hydrolysis of acylenzyme- nucleophile complex)

The quantitative analysis of peptide synthesis via transfer of the acyl moiety from the activated donor (S) to the nucleophile (N), catalysed by proteases forming an acylenzyme intermediate, has been continued. The new kinetic model takes into account the hydrolysis of an acylenzyme-nucleophile complex (EAN). The intensity of the hydrolysis is characterized by parameter gamma equal to the ratio of the rate constant of EAN hydrolysis and the rate constant of peptide formation. The ability of the EAN complex to hydrolyse leads to a decrease in the apparent nucleophile reactivity (beta) of the aminocomponent. As a result, the maximal fractional conversions of S and N to the peptide decrease, and the apparent nucleophile reactivity becomes dependent on the nucleophile concentration. The pattern of parameter gamma influence on maximal fractional conversions depends on which component is in an excess. It is with the donor excess that hydrolysis of the EAN complex affects the peptide yield dramatically. Analytical expressions for the estimation of maximal product concentration were obtained and their accuracy evaluated.

Beta-lactamase-catalyzed aminolysis of depsipeptides: amine specificity and steady-state kinetics

beta-Lactamases catalyze not only the hydrolysis but also the aminolysis of certain depsipeptides [Pratt, R. F., & Govardhan, C. P. (1984) Proc. Natl. Acad. Sci. U.S.A. 81, 1302-1306]. This paper explores further the specificity of the aminolysis reaction with respect to the structure of the amine and also the steady-state kinetics of the reaction. The amines preferred by the class C beta-lactamase of Enterobacter cloacae P99 appear to be aromatic D-alpha-amino acids. The general order of substrate effectiveness at pH 7.5 appears to be aromatic D-alpha-amino acids greater than large aliphatic D-alpha-amino acids greater than small aliphatic D-alpha-amino acids approximately small aliphatic L-alpha-amino acids greater than large L-alpha-amino acids. Charges on the aliphatic side chains seem unimportant. Ineffective as acyl acceptors were beta-amino acids, alpha-amino phosphonic acids, and, in general, amines, including amino acid carboxyl derivatives and peptides. There is thus strong evidence for specific interaction between the amine and the enzyme. A detailed kinetics study was made of the P99 beta-lactamase-catalyzed aminolysis of m-[[(phenylacetyl)glycyl]oxy]benzoic acid by D-phenylalanine. The steady-state kinetics were complex because of the presence of parallel enzyme-catalyzed hydrolysis and aminolysis reactions. An empirical rate equation was obtained for the total reaction. This has important elements in common with that previously found for the aminolysis of specific peptides by the DD-peptidases of various Streptomyces strains [e.g., Frere, J.-M., Ghuysen, J.-M., Perkins, H.R., & Nieto, M. (1973) Biochem. J. 135, 483-492].(ABSTRACT TRUNCATED AT 250 WORDS)

Kinetic evaluation of conversion of phosphatidylcholine to phosphatidylethanolamine by phospholipase D from different sources

Transphosphatidylation from phosphatidylcholine (PC) to phosphatidylethanolamine (PE) was conducted by seven phospholipase D preparations from different sources, one of which was of cabbage origin and other six of Streptomyces origin. The reactions were carried out at 30 degrees C using mixture of ethyl acetate containing PC and buffer containing ethanolamine and phospholipase D. To obtain the activity ratio of transphosphatidylation and hydrolysis at various ratios of ethanolamine and water concentrations, the apparent rate constant ratios of transphosphatidylation and hydrolysis, (k'3/k3)app, were calculated, keeping the concentration of PC constant (17.8 mM). Among the seven enzymes examined, five showed good transphosphatidylation, in which 100% of PC could be converted to PE at ethanolamine concentrations ranging from 0.3 to 1.0 M, while two showed poor transphosphatidylation activity. At higher ethanolamine concentrations, the reaction rate was decreased due to substrate inhibition. Hydrolytic reactions were conducted at 30 degrees C with respective enzymes by using mixture of ethyl acetate containing PC or PE and buffer containing phospholipase D. The ratio of (kcat/Km)PE/(kcat/Km)PC was calculated to determine the substrate specificity of various phospholipase D enzymes. The values of (k'3/k3)app varied with the origin of the enzymes, whereas the values of (kcat/Km)PE/(kcat/Km)PC were not so different. The results obtained show that (k'3/k3)app is a good parameter to select an enzyme and that the timing of stopping the reaction is also important to avoid the hydrolysis of the product.

Reaction mechanism, specificity and pH-dependence of peptide synthesis catalyzed by the metalloproteinase thermolysin

The initial rates of peptide bond formation catalyzed by the metalloproteinase thermolysin were determined. The dependence of the formation rates on the concentration of the carboxyl donor and the acceptor can be explained by a rapid-equilibrium random bireactant mechanism, in which the binding of one substrate has a positive influence on the binding of the other (synergism). The specificity of the enzyme for the donor and acceptor in the condensation reaction was further investigated by determining the apparent kinetic parameters kcat and Km for various substrates. The pH-dependence of the initial rates of synthesis was found to be identical to the pH-dependence of the hydrolytic action of the enzyme. The rates are also shown to be independent of the pKa of the amino group of the acceptor, indicating that deprotonation of the attacking nucleophile in the synthetic reaction is not rate-limiting.

A spectrophotometric assay for the characterization of the S' subsite specificity of alpha-chymotrypsin

The partitioning of maleylphenylalanine-alpha-chymotrypsin formed using maleylphenylalanine methyl ester as acyl donor between amino acid-derived nucleophiles and water was determined spectrophotometrically. The interpretation of the results obtained from graphical analysis gave evidence of a high conformational specificity of alpha-chymotrypsin towards basic amino acid derivatives in the P'1 position including significant differences between the amide and methyl ester of arginine. Amides of neutral amino acids with large side-chains show higher nucleophile reactivity in comparison with glycine amide.

Peptide synthesis catalyzed by the serine proteinases chymotrypsin and trypsin

The ratio of the initial rates of aminolysis and hydrolysis in peptide semisynthesis catalyzed by chymotrypsin (EC 3.4.21.1) and trypsin (EC 3.4.21.4) was found to depend non-linearly on the concentration of the added nucleophile. This is in agreement with a mechanism for the peptide semisynthesis where nucleophile binding to the acyl-enzyme precedes the aminolysis reaction. The acyl-enzyme-nucleophile complex can still be deacylated by water. A temperature optimum was observed for peptide synthesis for valinamide as nucleophile. This and the similarity of the P'1 specificity in peptide hydrolysis and nucleophile specificity in peptide semisynthesis also support the mechanism including the nucleophile binding. The influence of added nucleophiles on the acylation step during peptide synthesis was studied by determining kcat and Km for the appearance of the leaving group from the acyl donor. Acceptor (= nucleophile) specificity was shown to be more important for high ratios of aminolysis: hydrolysis than donor specificity. The maximum product concentration during kinetically controlled peptide semisynthesis was found to be independent of the enzyme content.