A STUDY OF SOME THIOL ESTER HYDROLYSES AS MODELS FOR THE DEACYLATION STEP OF PAPAIN-CATALYSED HYDROLYSES.
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ABSTRACT:
SUBMITTER: LOWE G
PROVIDER: S-EPMC1206921 | biostudies-other | 1965 Jul
REPOSITORIES: biostudies-other
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Project description:The specificity of the proteolytic enzyme, papain, for the peptide bond of the substrate adjacent to that about to be cleaved and for the acyl residue of some N-acylglycine derivatives is manifest almost exclusively in the formation of the acyl-enzyme from the enzyme-substrate complex. Models for the enzyme-substrate complex and acyl-enzyme intermediate are suggested that account for these observations. In particular it is suggested that the peptide bond of the substrate adjacent to that about to be cleaved, is bound in the cleft of the enzyme between the NH group of glycine-66 and the backbone C=O group of aspartic acid-158, and provides a sensitive amplification mechanism through which the specificity of the enzyme for hydrophobic amino acids such as l-phenylalanine is relayed. It is also suggested that the distortion in the enzyme-substrate complex and the binding of the peptide bond adjacent to that about to be cleaved are also linked and behave co-operatively, the distortion of the protein facilitating binding and the stronger binding facilitating distortion. The results imply that between the enzyme-substrate complex and the acyl-enzyme a relaxation of the protein conformation must occur.
| S-EPMC1177119 | biostudies-other
Project description:1. Methyl thionohippurate was prepared and shown to be a specific substrate for both papain and ficin. 2. The ultraviolet-absorption properties of the acyl-enzyme intermediate for both papain and ficin with methyl thionohippurate was that expected of an acyl-thiol. The possibility that other functional groups present in papain or ficin might be the site of acylation has been excluded. 3. The change in extinction at the absorption maximum with time was as expected for the acyl-enzyme on the basis of the known Michaelis-Menten parameters for methyl thionohippurate. 4. The variation of extinction with initial substrate concentration for both papain and ficin was that expected from the Michaelis-Menten parameters. 5. The extinction of the absorption maximum of the thionohippuryl-enzyme intermediate was suppressed by the addition of methyl hippurate to the extent predicted from the Michaelis-Menten parameters. 6. The decay of the extinction for the acyl-enzyme was arrested by adjusting the pH of the solution to 2.5. 7. These experiments provide compelling evidence that the acylation by substrate of both papain and ficin takes place through a thiol residue.
| S-EPMC1206920 | biostudies-other
Project description:1. The hydrolyses of the p-nitrophenyl esters of N-benzyloxycarbonylglycine, alpha-N-benzyloxycarbonyl-L-lysine and N-methoxycarbonyl-L-phenylalanylglycine catalysed by papain (EC 3.4.22.2) have been studied in solvents having a variable composition of 2H2O and H2O. 2. kcat., which represents deacylation in the papain-catalysed hydrolysis of reactive esters, is some 2.3-fold less in 2H2O compared with H2O. The magnitude of kcat. has been determined as a function of the 2H atom fraction of the solvent. 3. Both linear and non-linear methods of least-square regression analysis have been applied to the data in order to obtain best-fit parameter values for several three-parameter models which express kcat. in terms of the 2H atom fraction of the solvent. These models represent some possible modes of restructuring of the active site protonic configuration consequent upon transition state formation. 4. The results of curve fitting reveal an essentially linear dependence of kcat. upon the 2H atom fraction, and it may therefore be concluded that the isotope effect originates from a single proton which is in the process of transfer in the transition state. 5. It is postulated on the basis of this and other evidence that the mobile proton is transferred from an attacking water molecule to the imidazole side chain of His-159 during tetrahedral intermediate formation. This has the effect of stabilizing the transition state and promoting catalysis. The role of His-159 in deacylation is therefore to provide general base catalysis. 6. Models that involve two or more protons, such as a two-proton relay system analogous to that proposed for the serine proteinases, or a multiproton 'medium' effect, are considered unlikely on the basis of the data reported in this paper. 7. A more detailed examination of possible transition state structures reveals that the only structure compatible with available experimental data and consistent with certain theoretical predictions is one in which the proton translocated in concern with reorganization of the heavy atom framework. In addition, the transition state vibrations of the mobile proton are strongly coupled to those of the heavy atoms. These properties of the transition state are also manifest in the transition state for the deacylation of serine proteinases.
| S-EPMC1163425 | biostudies-other
Project description:1. The maximum rate of production of p-nitrophenol (V(max.)) for both papain- and ficin-catalysed hydrolyses of p-nitrophenyl hippurate is independent of methanol concentration up to 2m for papain and 1.5m for ficin. 2. The observed catalytic constant (k(0)) for the production of hippuric acid for both papain- and ficin-catalysed hydrolyses of methyl hippurate decreases with increasing methanol concentration, 1/k(0) being linearly dependent on the methanol concentration. The k(MeOH)/k(H2O) ratio is determined. 3. These results provide strong evidence against general base catalysis for the rate-determining step in the deacylation of hippuryl-papain and hippuryl-ficin and probably for other specific acyl-papains and acyl-ficins. 4. The rate-determining step for the deacylation of the non-specific trans-cinnamoyl-papain appears to be different from that for the specific hippuryl-papain, and is probably subject to general base catalysis. It is possible, however, to accommodate all these observations in a single four-step reaction pathway. 5. Propan-2-ol did not influence the rate of production of hippuric acid for the papain-catalysed hydrolysis of methyl hippurate. A similar result has previously been reported for the ficin-catalysed hydrolysis of methyl hippurate. Ethanol and of course methanol (see 2) decrease the rate of production of hippuric acid for both papain- and ficin-catalysed hydrolyses of methyl hippurate. It is suggested that the secondary alcohol is incapable for structural reasons of approaching the bond to be hydrolysed.
| S-EPMC1270121 | biostudies-other
Project description:1. N-Benzoyl-l-serine methyl ester was synthesized and evaluated as a substrate for bromelain (EC 3.4.22.4) and for papain (EC 3.4.22.2). 2. For the bromelain-catalysed hydrolysis at pH7.0, plots of [S(0)]/v(i) (initial substrate concn./initial velocity) versus [S(0)] are markedly curved, concave downwards. 3. Analysis by lattice nomography of a modifier kinetic mechanism in which the modifier is substrate reveals that concave-down [S(0)]/v(i) versus [S(0)] plots can arise when the ratio of the rate constants that characterize the breakdown of the binary (ES) and ternary (SES) complexes is either less than or greater than 1. In the latter case, there are severe restrictions on the values that may be taken by the ratio of the dissociation constants of the productive and non-productive binary complexes. 4. Concave-down [S(0)]/v(i) versus [S(0)] plots cannot arise from compulsory substrate activation. 5. Computational methods, based on function minimization, for determination of the apparent parameters that characterize a non-compulsory substrate-activated catalysis are described. 6. In an attempt to interpret the catalysis by bromelain of the hydrolysis of N-benzoyl-l-serine methyl ester in terms of substrate activation, the general substrate-activation model was simplified to one in which only one binary ES complex (that which gives rise directly to products) can form. 7. In terms of this model, the bromelain-catalysed hydrolysis of N-benzoyl-l-serine methyl ester at pH7.0, I=0.1 and 25 degrees C is characterized by K(m) (1) (the dissociation constant of ES)=1.22+/-0.73mm, k (the rate constant for the breakdown of ES to E+products, P)=1.57x10(-2)+/-0.32x10(-2)s(-1), K(a) (2) (the dissociation constant that characterizes the breakdown of SES to ES and S)=0.38+/-0.06m, and k' (the rate constant for the breakdown of SES to E+P+S)=0.45+/-0.04s(-1). 8. These parameters are compared with those in the literature that characterize the bromelain-catalysed hydrolysis of alpha-N-benzoyl-l-arginine ethyl ester and of alpha-N-benzoyl-l-arginine amide; K(m) (1) and k for the serine ester hydrolysis are somewhat similar to K(m) and k(cat.) for the arginine amide hydrolysis and K(as) and k' for the serine ester hydrolysis are somewhat similar to K(m) and k(cat.) for the arginine ester hydrolysis. 9. A previous interpretation of the inter-relationships of the values of k(cat.) and K(m) for the bromelain-catalysed hydrolysis of the arginine ester and amide substrates is discussed critically and an alternative interpretation involving substantial non-productive binding of the arginine amide substrate to bromelain is suggested. 10. The parameters for the bromelain-catalysed hydrolysis of the serine ester substrate are tentatively interpreted in terms of non-productive binding in the binary complex and a decrease of this type of binding by ternary complex-formation. 11. The Michaelis parameters for the papain-catalysed hydrolysis of the serine ester substrate (K(m)=52+/-4mm, k(cat.)=2.80+/-0.1s(-1) at pH7.0, I=0.1, 25.0 degrees C) are similar to those for the papain-catalysed hydrolysis of methyl hippurate. 12. Urea and guanidine hydrochloride at concentrations of 1m have only small effects on the kinetic parameters for the hydrolysis of the serine ester substrate catalysed by bromelain and by papain.
| S-EPMC1168089 | biostudies-other
Project description: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, k(0), 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, k(0), 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, sigma. 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-alpha-amino acid derivatives.
| S-EPMC1206922 | biostudies-other
Project description:Precatalysts active for the dehydropolymerisation of primary amine-boranes are generally based on mid or late transition metal. We have found that the activity of the precatalyst system formed from CpR2TiCl2 and 2nBuLi towards the dehydrogenation of the secondary amine-borane Me2NH·BH3, to yield the cyclic diborazane [Me2N-BH2]2, increases dramatically with increasing electron-donating character of the cyclopentadienyl rings (CpR). Application of the most active precatalyst system (CpR = η-C5Me5) to the primary amine-borane MeNH2·BH3 enabled the first synthesis of high molar mass poly(N-methylaminoborane), [MeNH-BH2] n , the BN analogue of polypropylene, by an early transition metal such as catalyst. Significantly, unlike other dehydropolymerization precatalysts for MeNH2·BH3 such as [Ir(POCOP)H2], skeletal nickel, and [Rh(COD)Cl]2, the Ti precatalyst system was also active towards a range of substrates including BzNH2·BH3 (Bz = benzyl) yielding high molar mass polymer. Moreover, in contrast to the late transition metal catalysed dehydropolymerisation of MeNH2·BH3 and also the Ziegler-Natta polymerisation of olefins, studies indicate that the Ti-catalyzed dehydropolymerization reactions proceed by a step-growth rather than a chain-growth mechanism.
| S-EPMC5933219 | biostudies-literature
Project description:To detail the development of ester-free thiol-ene dental resins with enhanced mechanical performance, limited potential for water uptake/leachables/degradation and low polymerization shrinkage stress.Thiol-terminated oligomers were prepared via a thiol-Michael reaction and a bulky tetra-allyl monomer containing urethane linkages was synthesized. The experimental oligomers and/or monomers were photopolymerized using visible light activation. Several thiol-ene formulations were investigated and their performance ranked by comparisons of the thermo-mechanical properties, polymerization shrinkage stress, water sorption/solubility, and reactivity with respect to a control comprising a conventional BisGMA/TEGDMA dental resin.The ester-free thiol-ene formulations had significantly lower viscosities, water sorption and solubility than the BisGMA/TEGDMA control. Depending on the resin, the limiting functional conversions were equivalent to or greater than that of BisGMA/TEGDMA. At comparable conversions, lower shrinkage stress values were achieved by the thiol-ene systems. The polymerization shrinkage stress was dramatically reduced when the tetra-allyl monomer was used as the ene in ester-free thiol-ene mixtures. Although exhibiting lower Young's modulus, flexural strength, and glass transition temperatures, the toughness values associated with thiol-ene resins were greater than that of the BisGMA/TEGDMA control. In addition, the thiol-ene polymerization resulted in highly uniform polymer networks as indicated by the narrow tan delta peak widths.Employing the developed thiol-ene resins in dental composites will reduce shrinkage stress and moisture absorption and form tougher materials. Furthermore, their low viscosities are expected to enable higher loadings of functionalized micro/nano-scale filler particles relevant for practical dental systems.
| S-EPMC5033514 | biostudies-literature
Project description:ObjectivesTo assess the performance of thiol-ene dental composites based on selected ester-free thiol-ene formulations. Further, to point out the benefits/drawback of having a hydrolytically stable thiol-ene matrix within a glass filled composite.MethodsComposite samples containing 50-65wt% of functionalized glass microparticles were prepared and photopolymerized in the presence of a suitable visible light photoinitiator. Shrinkage stress measurements were conducted as a function of the irradiation time. Degrees of conversion were measured by FT-IR analysis by comparing the double bond signals before and after photopolymerization. Mechanical tests were carried out on specimens after curing as well as after extended aging in water. Dynamic mechanical analysis was employed to track the changes in storage modulus near body temperature. The properties of the thiol-ene composites were compared with those of the BisGMA/TEGDMA control.ResultsDepending on the resin type, similar or higher conversions were achieved in thiol-ene composites when compared to the dimethacrylate controls. At comparable conversions, lower shrinkage stress values were achieved. Although exhibiting lower initial elastic moduli, the thiol-ene composites' flexural strengths were found to be comparable with the controls. Contrary to the control, the mechanical properties of the ester-free thiol-ene composites were shown to be unaffected by extensive aging in water and at least equaled that of the control after aging in water for just five weeks.SignificanceEmploying non-degradable step-growth networks as organic matrices in dental composites will provide structurally uniform, tough materials with extended service time.
| S-EPMC4617615 | biostudies-literature
Project description:The chemical step of natural protein synthesis, peptide bond formation, is catalysed by the large subunit of the ribosome. Crystal structures have shown that the active site for peptide bond formation is composed entirely of RNA. Recent work has focused on how an RNA active site is able to catalyse this fundamental biological reaction at a suitable rate for protein synthesis. On the basis of the absence of important ribosomal functional groups, lack of a dependence on pH, and the dominant contribution of entropy to catalysis, it has been suggested that the role of the ribosome is limited to bringing the substrates into close proximity. Alternatively, the importance of the 2'-hydroxyl of the peptidyl-transfer RNA and a Brønsted coefficient near zero have been taken as evidence that the ribosome coordinates a proton-transfer network. Here we report the transition state of peptide bond formation, based on analysis of the kinetic isotope effect at five positions within the reaction centre of a peptidyl-transfer RNA mimic. Our results indicate that in contrast to the uncatalysed reaction, formation of the tetrahedral intermediate and proton transfer from the nucleophilic nitrogen both occur in the rate-limiting step. Unlike in previous proposals, the reaction is not fully concerted; instead, breakdown of the tetrahedral intermediate occurs in a separate fast step. This suggests that in addition to substrate positioning, the ribosome is contributing to chemical catalysis by changing the rate-limiting transition state.
| S-EPMC3154986 | biostudies-literature