A study of some thiol ester hydrolyses as models for the deacylation step of papain-catalysed hydrolyses

1. The self-catalysed hydrolyses of the thiol esters, S-hippurylthioglycollic acid and S-ethyl monothiolsuccinate, have been shown to be slower than the deacylation step for the papain-catalysed hydrolysis of hippuric esters, by a factor approx. 10⁵. This difference in rate constants largely reflects a difference in activation energy, which together with other evidence drawn from the literature make it unlikely that a carboxylate ion could be the nucleophile responsible for the deacylation of acyl-papain. 2. The imidazole-catalysed hydrolysis of S-hippurylthioglycollic acid and ethyl thiolacetate have activation energies similar to that for the deacylation step in papain-catalysed hydrolyses. This, together with other evidence drawn from the literature, suggests that the imidazole of a histidine residue is the nucleophile responsible for the deacylation of acyl-papain.     

Revisiting the effect of water content on enzymatic peptide synthesis in non-aqueous medium

Enzymatic acyl-transfer reaction in organic medium competes with the hydrolytic side reaction depending on the water content. The effect of water content on aminolysis activity of -chymotrypsin for the synthesis of Bz-Tyr-Val-NH₂ in acetonitrile was examined under the conditions which were devoid of the hydrolytic deacylation. Excess H-Val-NH₂ (880 mM) was employed to keep the hydrolysis negligible. The aminolysis rate increased abruptly between 4 and 5% (v/v) water but a further increase in the water content did not affect the reaction rate. This suggests that water added more than 5% (v/v) does not enhance intrinsic enzyme activity but acts only as a nucleophile for the hydrolytic deacylation.     

Rate enhancement by catalytic groups in enzymes. Imidazole catalysis of the hydrolysis of N,O-diacetylserinamide as a model for general base catalysis in chymotrypsin

An attempt to estimate the importance of general acid-base catalysis in enzymic catalysis has been made, using the hydrolysis of the ester group of N,O-diacetylserinamide as a model for the deacylation of acyl-chymotrypsins. General base catalysis of this reaction by imidazole is estimated to reduce the activation energy by at least 31 kJ mol^?1. The rate of reaction, however, is not greatly enhanced because of an unfavourable change in the entropy of activation from ?132 to ?197 JK^?1 mol^?1. At about 300 K, a typical temperature for enzyme-catalysed reactions, the reduction in activation energy would cause a rate enhancement of about 3 × 10⁵-fold if the unfavourable entropy change did not occur. For specific acyl-chymotrypsins the entropy of activation for deacylation is about ?89 J K^?1 mol^?1, allowing the full effect of general base catalysis by imidazole to be realized. It is, therefore, postulated that in the active site of an enzyme, a properly oriented imidazole side chain may catalyse the rate of a reaction 10⁵-fold by general base catalysis.     

Papain-catalysed hydrolysis of some hippuric esters. A new mechanism for papain-catalysed hydrolyses

1. The Michaelis–Menten parameters for the papain-catalysed hydrolysis of a number of alkyl, aryl and alkyl-thiol esters of hippuric acid have been determined. 2. For all the aryl esters and most of the alkyl esters studied, the catalytic constant, k₀, is 2–3sec.⁻¹ and most probably represents deacylation of the common intermediate, hippuryl-papain. 3. Two alkyl esters and hippurylamide, however, have catalytic rate constants, k₀, less than 2–3sec.⁻¹. It is possible to interpret all the available kinetic data in terms of a three-step mechanism in which an enzyme–substrate complex is first formed, followed by acylation of the enzyme through an essential thiol group, followed by deacylation of the acyl-enzyme. 4. The logarithm of the ratio of the Michaelis–Menten parameters, which reflect the acylation rate constant, for four aryl esters of hippuric acid studied give a linear Hammett plot against the substituent constant, σ. Arguments are presented that indicate acid as well as nucleophilic catalysis in the acylation process and that the most likely proton donor is an imidazolium ion. 5. It is suggested that this imidazolium ion is part of the same histidine residue that has been tentatively implicated in the deacylation process (Lowe & Williams, 1965b). 6. A new mechanism is proposed for the papain-catalysed hydrolysis of N-acyl-α-amino acid derivatives.     

Characterization of the Prostate-Specific Antigen (PSA) Catalytic Mechanism: A Pre-Steady-State and Steady-State Study

Prostate-specific antigen (PSA), an enzyme of 30 kDa grouped in the kallikrein family is synthesized to high levels by normal and malignant prostate epithelial cells. Therefore, it is the main biomarker currently used for early diagnosis of prostate cancer. Here, presteady-state and steady-state kinetics of the PSA-catalyzed hydrolysis of the fluorogenic substrate Mu-His-Ser-Ser-Lys-Leu-Gln-AMC (spanning from pH 6.5 to pH 9.0, at 37.0°C) are reported. Steady-state kinetics display at every pH value a peculiar feature, represented by an initial “burst” phase of the fluorescence signal before steady-state conditions are taking place. This behavior, which has been already observed in other members of the kallikrein family, suggests the occurrence of a proteolytic mechanism wherefore the acylation step is faster than the deacylation process. This feature allows to detect the acyl intermediate, where the newly formed C-terminal carboxylic acid of the cleaved substrate forms an ester bond with the -OH group of the Ser195 catalytic residue, whereas the AMC product has been already released. Therefore, the pH-dependence of the two enzymatic steps (i.e., acylation and deacylation) has been separately characterized, allowing the determination of pK_a values. On this basis, possible residues are tentatively identified in PSA, which might regulate these two steps by interacting with the two portions of the substrate.     

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.     

The deacylation of acyl-cycloamyloses : The catalytic effects of benzimidazole derivatives on the rate

Cycloheptaamylose cinnamate, an intermediate in the hydrolysis of m-nitrophenyl cinnamate by cycloheptaamylose, was isolated in pure form. The deacylation of acyl-cycloamyloses (cinnamate and acetate) catalyzed by noncovalently complexed 6-nitrobenzimidazole (1) was studied. The reaction was enzyme-like. Saturation of acyl-cycloamylose by 1 was observed; the rate and dissociation constants were determined from Lineweaver-Burk plots. The catalyzed reaction rates at neutral pH were two to three times larger than those of the spontaneous reactions for cycloheptaamylose or cyclohexaamylose cinnamate, respectively. The catalytic effect of 1 on the deacylation rate of cyclohexaamylose cinnamate became smaller as the pH of the solution was raised. The deacylation of cyclohexaamylose acetate was followed by nmr spectroscopy, whereas the deacylation of cycloamylose cinnamates was followed by uv spectroscopy and extraction of trans-cinnamic acid with ether. Thermodynamic parameters for the rates of deacylation of cycloamylose cinnamates and dissociation constants of cycloamylose cinnamate-1 complexes were obtained and discussed.     

Kinetic Origin of Substrate Specificity in Post-Transfer Editing by Leucyl-tRNA Synthetase

The intrinsic editing capacities of aminoacyl-tRNA synthetases ensure a high-fidelity translation of the amino acids that possess effective non-cognate aminoacylation surrogates. The dominant error-correction pathway comprises deacylation of misaminoacylated tRNA within the aminoacyl-tRNA synthetase editing site. To assess the origin of specificity of Escherichia coli leucyl-tRNA synthetase (LeuRS) against the cognate aminoacylation product in editing, we followed binding and catalysis independently using cognate leucyl- and non-cognate norvalyl-tRNA^Leu and their non-hydrolyzable analogues. We found that the amino acid part (leucine versus norvaline) of (mis)aminoacyl-tRNAs can contribute approximately 10-fold to ground-state discrimination at the editing site. In sharp contrast, the rate of deacylation of leucyl- and norvalyl-tRNA^Leu differed by about 10⁴-fold. We further established the critical role for the A76 3′-OH group of the tRNA^Leu in post-transfer editing, which supports the substrate-assisted deacylation mechanism. Interestingly, the abrogation of the LeuRS specificity determinant threonine 252 did not improve the affinity of the editing site for the cognate leucine as expected, but instead substantially enhanced the rate of leucyl-tRNA^Leu hydrolysis. In line with that, molecular dynamics simulations revealed that the wild-type enzyme, but not the T252A mutant, enforced leucine to adopt the side-chain conformation that promotes the steric exclusion of a putative catalytic water. Our data demonstrated that the LeuRS editing site exhibits amino acid specificity of kinetic origin, arguing against the anticipated prominent role of steric exclusion in the rejection of leucine. This feature distinguishes editing from the synthetic site, which relies on ground-state discrimination in amino acid selection.     

Hydrogen-deuterium exchange of the tryptophan residues in bovine α-lactalbumin

Effects of deuteration on the Raman spectrum of a tryptophan residue have been examined. The 1386 cm^?1 line of deuterated tryptophan residue has been found to be useful for tracing the hydrogen-deuterium exchange reaction of this residue in a protein. An examination on bovine α-lactalbumin at pH 6.4 and at 20°C indicates that two of the four tryptophan residues exchange with a rate constant much greater than 9 × 10^?4 sec^?1, while the other two exchange with a rate constant of 4 × 10^?5 sec^?1. The latter two have been assigned to Trp 28 and Trp 108 of this protein. The kinetics of hydrogen-deuterium exchange reaction of completely “free” tryptophan residue have been examined by a proton magnetic resonance study on tryptophan itself. By taking the result of this examination into account, the chance of exposure to the solvent for Trp 28 or Trp 108 has been estimated to be 3 × 10^?6 at pH 6.4 and at 20°C.     

Kinetics of Avibactam Inhibition against Class A,C, and D β-Lactamases

Avibactam is a non-β-lactam β-lactamase inhibitor with a spectrum of activity that includes β-lactamase enzymes of classes A, C, and selected D examples. In this work acylation and deacylation rates were measured against the clinically important enzymes CTX-M-15, KPC-2, Enterobacter cloacae AmpC, Pseudomonas aeruginosa AmpC, OXA-10, and OXA-48. The efficiency of acylation (k₂/K_i) varied across the enzyme spectrum, from 1.1 × 10¹ m⁻¹s⁻¹ for OXA-10 to 1.0 × 10⁵ for CTX-M-15. Inhibition of OXA-10 was shown to follow the covalent reversible mechanism, and the acylated OXA-10 displayed the longest residence time for deacylation, with a half-life of greater than 5 days. Across multiple enzymes, acyl enzyme stability was assessed by mass spectrometry. These inhibited enzyme forms were stable to rearrangement or hydrolysis, with the exception of KPC-2. KPC-2 displayed a slow hydrolytic route that involved fragmentation of the acyl-avibactam complex. The identity of released degradation products was investigated, and a possible mechanism for the slow deacylation from KPC-2 is proposed.     

Specific interaction of initiation factor IF2 of E. coli with formylmethionyl-tRNA f Met.

The interaction of E.coli initiation factor IF2 with formylmethionyl-tRNA_f^Met has been studied by measuring the inhibition by IF2 of the spontaneous deaminoacylation of the charged tRNA. We find that IF2 protects fMet-tRNA_f^Met against spontaneous deacylation. The formylation is an absolute requirement for this protection and no effect of GTP was found. The association constant for IF2 binding to fMet-tRNA_f^Met at 37°C and physiological ionic conditions was estimated at about 10⁶ M^?1.     

PHOSPHOLIPASE ACTIVITY IN SQUID AND FROG AXONS

Evidence for the presence of phosphatide acylhydrolase activity (EC 3.1.1) in centrifuged homogenate supernatants and extracts of squid giant axons and centrifuged homogenate supernatants of frog sciatic nerve bundles is reported. The enzyme was assayed by measurement of the rate of deacylation of [U-¹⁴C]phosphatidyl choline. The deacylation activity in the nerve homogenate supernatants exhibits: a pH maximum at 7.2–7.4 (25°C); a calcium ion maximum at 12–13 mM-CaCl₂(aq); a K_m value of 3.4 × 10^?4 M (25°C); and a temperature maximum at 37°C. The activation energy over the range 8–37°C is 5.7 ± 0.2kcal-mol^?1.     

Viscosity-molecular weight relationships,intrinsic chain flexibility,and dynamic solution properties of guar galactomannan

Molecular theories of the viscosity of dilute and more concentrated solutions of random-coil polymers have been applied to five molecular-weight fractions of guar galactomannan. The variation in intrinsic viscosity ([η]; dL.g^?1) with molecular weight (M_r) followed the relationship [η] = 3.8 × 10^?4) M_r^0.723, consistent with random-coil behaviour. The intrinsic stiffness of the galactomannan backbone was estimated by evaluating the “characteristic ratio” C_∝, which is ～ 12.6 and agrees well with results for carboxymethylcellulose, which has a closely similar, β-(1→4)-linked polymer backbone. At intermediate concentrations (c), up to specific viscosities of ～ 10, η_sp was proportional to c^1.3, while at higher concentrations, η_sp was ～c^5.1. This exponent is higher than is usually observed for polymers interacting purely by physical entanglement, and is evidence for more specific polymer-polymer interactions (“hyperentanglements”). The concentration dependence and the time-scale of entanglement coupling have been monitored by both steady-shear and oscillatory measurements, and a generality of response has been demonstrated.     

31P Magnetic relaxation studies of yeast transfer RNAPhe.

The molecular mechanism of thermal unfolding of yeast tRNA^Phe in 20 mM NaCl, 1 mM EDTA, and 10 mM MgSO₄, pH 7.1 ± 0.1, has been examined by ³¹P magnetic relaxation and the nuclear Overhauser effect methods at 40.48 MHz in the temperature range of 22.5–80°C. Two partially resolved ³¹P resonance peaks of yeast tRNA^Phe have been found to behave distinctively different in their longitudinal relaxation times. Individual intensities of the two partially resolved peaks have been quantitatively estimated by the use of relaxation data and the nuclear Overhauser effect as a function of temperature. The results of these observations largely support the earlier suggestion by Guéron and Shulman that the high- and low-field parts of the main ³¹P resonance cluster originate from phosphorus nuclei belonging to the double-helical and nonhelical regions of the tRNA, respectively. The spin-lattice relaxation of the phosphorus nucleus has been found to be determined dominantly by the dipolar interaction with the surrounding ribose protons at this observing frequency. Rotational correlation times for the two portions of the ribose-phosphate backbone of the tRNA have been separately deduced from the quantitative treatment of the ³¹P nuclear spin-lattice relaxation times (T₁) and the nuclear Overhauser effect. The result indicates that the two portions undergo internal motions at distinctively different rates of 10⁸–10¹⁰ sec^?1 order in the temperature range of 22.5–80°C, and that the thermal activation of these motions occurs at least in three distinctive steps, i.e., 22.5–31, 31–40, and 40–80°C. The rates of the internal motions and the associated activation energies in respective steps give some insight into the thermo-induced change of the yeast tRNA^Phe structure.     

A rate-limiting step of enteropeptidase hydrolysis

It has been shown for the first time that deacylation is the rate-limiting step in the enteropeptidase-catalyzed hydrolysis of highly effective oligopeptide substrates containing four Asp residues in positions P2–P5. On the other hand, the rate-limiting step in the hydrolysis of low-efficiency peptide substrates containing less than four Asp or Glu residues in positions P2–P5 is acylation, as it has previously been suggested for all amide and peptide substrates of serine proteases on the basis of classical works of Bender et al. The method of introduction of an additional nucleophile or another effector that selectively affects the deacylation step was used to determine the rate-limiting step in the enteropeptidase hydrolysis of N ^α-benzyloxycarbonyl-L-lysine thiobenzyl ester, the highly efficient amide substrate GlyAsp₄-Lys β-naphthyl amide, and the low-efficiency peptide substrate VLSAADK-GNVKAAWG (where a hyphen denotes the hydrolysis site).     

Effects of phorbol-12,13-diesters on prostaglandin production and phospholipase activity in canine kidney (MDCK) cells

Two tumor promoting phorbol-12,13-diesters, 12-0-tetradecanoyl-phorbol-13-acetate and phorbol-12,13-didecanoate, at concentrations of 10^?9 to 10^?10 M, stimulated prostaglandin production by dog kidney (MDCK) cells cultured in serum-supplemented medium. The non-tumor producing phorbol diester, 4α-phorbol-12,13-didecanoate, at a concentration of 10^?7 M, had no effect. The two biologically active phorbol diesters, but not the non-tumor promoting analog, stimulated deacylation of the cellular phospholipids of MDCK cells radioactively labelled with [³H]arachidonic acid. Most of the arachidonic acid was converted into prostaglandins.     

Thermocycling steps and optimization of multiplex PCR

Multiplex PCR (M-PCR), a method that detects more than two target loci in a single reaction, relies on the variables which influence single template specific PCR. We describe here the role of temperature cycles in ensuring the efficiency of detection. We have designed a multi-step protocol, which uses gradients between the temperature steps. This has facilitated the target specific annealing in the developed M-PCR. We have examined various thermocycling steps and optimized the M-PCR protocol using 10⁵ to 10¹ cells of Escherichia coli, Salmonella typhi, and Vibrio cholera as template in a single reaction. The sensitivity of the detection observed was 10² cells of each pathogen used in the study.     

N-(phenylacetyl)glycyl-D-aziridine-2-carboxylate, an acyclic amide substrate of beta-lactamases: importance of the shape of the substrate in beta-lactamase evolution

Certain acyclic depsipeptides, but not peptides, are substrates of typical beta-lactamases [Pratt, R.F., & Govardhan, C.P. (1984) Proc. Natl. Acad. Sci. U.S.A. 81, 1302]. This may reflect either the greater chemical reactivity of depsipeptides (and of beta-lactams, the natural substrates) than peptides or the greater ease of distortion of the depsipeptide (ester) than the peptide (amide) group into a penicillin-like conformation. The latter explanation has been shown to be more likely by employment of a novel beta-lactamase substrate. N-(phenylacetyl)glycyl-D-aziridine-2-carboxylate, which combines a high chemical reactivity with a close to tetrahedral amide nitrogen atom. Although this substrate was better (higher kcat/KM) than a comparable depsipeptide for beta-lactamases, it was poorer than the depsipeptide for the Streptomyces R61 D-alanyl-D-alanine peptidase (which catalyzes specific peptide hydrolysis). It therefore seems likely that one vital feature of the putative evolution of a DD-peptidase into a beta-lactamase would have been modification of the active site to, on one hand, accommodate bicyclic beta-lactams and, on the other, exclude productive binding of planar acyclic amides. Certain serine beta-lactamases and the R61 DD-peptidase also catalyze methanolysis and aminolysis by D-phenylalanine of the N-acylaziridine. The latter reaction, the first amide aminolysis shown to be catalyzed by a beta-lactamase, is a very close analogue of the transpeptidase reaction of DD-peptidases. The methanolysis reaction appeared to proceed by way of the same acyl-enzyme intermediate as formed from depsipeptides possessing the same acyl moiety as the aziridine. The kinetics of methanolysis were employed to determine whether acylation or deacylation was rate limiting to the hydrolysis reaction under saturating substrate concentrations. The kinetics of the aminolysis reaction, catalyzed by the Enterobacter cloacae P99 beta-lactamase, showed the characteristics of, and were interpreted in terms of, a sequential mechanism previously deduced for depsipeptides and this enzyme [Pazhanisamy, S., & Pratt, R. F. (1989) Biochemistry 28, 6875-6882]. This mechanism features two separate binding sites, only one of which is productive. Strikingly, the binding of the N-acylaziridine to the nonproductive site was very tight, such that essentially all hydrolysis at substrate concentrations above 0.1Km proceeded via the ternary complex; this could also be true of penicillins.     

Regulation of arachidonic acid metabolism in madin-darby canine kidney cells Comparison of A23187 and 12-O-tetradecanoyl-phorbol-13-acetate

Challenge of Madin-Darby canine kidney (MDCK) cells with the divalent cation ionophore A23187 caused a marked increase in the deacylation of [³H]arachidonic acid but not of [¹⁴C]palmitic acid. When the cells were treated with 12-O-tetradecanoyl-phorbol-13-acetate (TPA) and A23187, there was an additional increase in the deacylation of [³H]arachidonic acid compared to that observed with either agent alone. In contrast to deacylation, the stimulation of prostaglandin production by A23187 was small compared to the stimulation by TPA. Cycloheximide inhibited synthesis of prostaglandins in TPA-treated cells, but did not block the stimulated deacylation caused by either TPA or A23187. These data indicate that, while both TPA and A23187 stimulated the deacylation of [³H]arachidonic acid, TPA had an additional, cycloheximide-sensitive effect that was required for efficient conversion of the released fatty acids to prostaglandins. Thus, although required, deacylation appeared to be independent of and insufficient to stimulate maximum prostaglandin synthesis in these cells.     

15N-NMR spectroscopy. IV. Comparison of poly(L-lysine) and isopoly(L-lysine)

The natural abundance ¹⁵N-nmr spectroscopy has been used to characterize the isomeric polymers (L -Lys)_n and iso (L -Lys)_n in aqueous solution. Although the peptide nitrogens of the two polymers have nearly equivalent shifts at pH < 10, the amino nitrogens differ by 5–6 ppm at pH < 7 and provide an easy means of identification. Furthermore, the polymers are distinguishable by the pK_a of the amino group and the basicity of the peptide nitrogen. At pH 10.3 and 25°C, (Lys)_n exhibits line broadening and an upfield chemical shift of the peptide nitrogen, indicative of the coil → helix transition. The formation of 100% helix may produce a shift as large as 5 ppm, which probably makes ¹⁵N-nmr spectroscopy more suitable for studies of this transition.