scholarly journals Evidence that the mechanism of antibody-catalysed hydrolysis of arylcarbamates can be determined by the structure of the immunogen used to elicit the catalytic antibody

2007 ◽  
Vol 401 (3) ◽  
pp. 721-726 ◽  
Author(s):  
Guillaume Boucher ◽  
Bilal Said ◽  
Elizabeth L. Ostler ◽  
Marina Resmini ◽  
Keith Brocklehurst ◽  
...  
Keyword(s):  
Phenyl Group ◽  
Catalytic Antibody ◽  
Antibody Preparation ◽  
Tetrahedral Intermediate ◽  
Rate Determining Step ◽  
Catalysed Reaction ◽  
Leaving Group ◽  
Antibody Catalysis ◽  
Elicitation Process ◽  
Hydrolysis Of

A kinetically homogeneous anti-phosphate catalytic antibody preparation was shown to catalyse the hydrolysis of a series of O-aryl N-methyl carbamates containing various substituents in the 4-position of the O-phenyl group. The specific nature of the antibody catalysis was demonstrated by the adherence of these reactions to the Michaelis–Menten equation, the complete inhibition by a hapten analogue, and the failure of the antibody to catalyse the hydrolysis of the 2-nitrophenyl analogue of the 4-nitrophenylcarbamate substrate. Hammett σ–ρ analysis suggests that both the non-catalysed and antibody-catalysed reactions proceed by mechanisms in which development of the aryloxyanion of the leaving group is well advanced in the transition state of the rate-determining step. This is probably the ElcB (elimination–addition) mechanism for the non-catalysed reaction, but for the antibody-catalysed reaction might be either ElcB or BAc2 (addition–elimination), in which the elimination of the aryloxy group from the tetrahedral intermediate has become rate-determining. This result provides evidence of the dominance of recognition of phenolate ion character in the phosphate hapten in the elicitation process, and is discussed in connection with data from the literature that suggest a BAc2 mechanism, with rate-determining formation of the tetrahedral intermediate for the hydrolysis of carbamate substrates catalysed by an antibody elicited by a phosphonamidate hapten in which phenolate anion character is minimized. The present paper contributes to the growing awareness that small differences in the structure of haptens can produce large differences in catalytic characteristics.

Effect of Medium on Reactivity for Alkaline Hydrolysis of p-Nitrophenyl Acetate and S-p-Nitrophenyl Thioacetate in DMSO-H2O Mixtures of Varying Compositions: Ground State and Transition State Contributions

2021 ◽  
Author(s):  
Ik-Hwan Um ◽  
Seungjae Kim
Keyword(s):  
Transition State ◽  
Alkaline Hydrolysis ◽  
Ground State ◽  
Rate Constants ◽  
Kinetic Data ◽  
Reaction Medium ◽  
Stepwise Mechanism ◽  
Rate Determining Step ◽  
Leaving Group ◽  
Hydrolysis Of

Second-order rate constants (kN) for reactions of p-nitrophenyl acetate (1) and S-p-nitrophenyl thioacetate (2) with OH‒ have been measured spectrophotometrically in DMSO-H2O mixtures of varying compositions at 25.0 ± 0.1 oC. The kN value increases from 11.6 to 32,800 M‒1s‒1 for the reactions of 1 and from 5.90 to 190,000 M‒1s‒1 for those of 2 as the reaction medium changes from H2O to 80 mol % DMSO, indicating that the effect of medium on reactivity is more remarkable for the reactions of 2 than for those of 1. Although 2 possesses a better leaving group than 1, the former is less reactive than the latter by a factor of 2 in H2O. This implies that expulsion of the leaving group is not advanced in the rate-determining transition state (TS), i.e., the reactions of 1 and 2 with OH‒ proceed through a stepwise mechanism, in which expulsion of the leaving group from the addition intermediate occurs after the rate-determining step (RDS). Addition of DMSO to H2O would destabilize OH‒ through electronic repulsion between the anion and the negative-dipole end in DMSO. However, destabilization of OH‒ in the ground state (GS) is not solely responsible for the remarkably enhanced reactivity upon addition of DMSO to the medium. The effect of medium on reactivity has been dissected into the GS and TS contributions through combination of the kinetic data with the transfer enthalpies (ΔΔHtr) from H2O to DMSO-H2O mixtures for OH‒ ion.

scholarly journals The mechanism of the hydrolysis of acylimidazoles in aqueous mineral acids. The excess acidity method for reactions that are not acid catalyzed

1997 ◽  
Vol 75 (8) ◽  
pp. 1093-1098 ◽  
Author(s):  
Robin A. Cox
Keyword(s):  
Imidazole Ring ◽  
Carbonyl Oxygen ◽  
Pseudo First Order Reaction ◽  
Acid Media ◽  
Tetrahedral Intermediate ◽  
Reaction Rate Constants ◽  
Rate Determining Step ◽  
Reversible Addition ◽  
Acid Catalyzed ◽  
Hydrolysis Of

The mechanism of the hydrolysis of acetylimidazole in aqueous perchloric, sulfuric, and hydrochloric acid mixtures has been determined. Benzoylimidazole was also studied in the latter two acids. The method of analyzing the available data, pseudo-first-order reaction rate constants as a function of acid concentration and, in one case, temperature, is the excess acidity method, here applied to the same reaction in the three different acid media, allowing their comparison. The reaction is not acid catalyzed; the rates decrease with increasing acidity. The substrate reacts in the form that is monoprotonated on the imidazole ring; it is 100% protonated at acidities much lower than those used here. Acetylimidazole is shown to become diprotonated at high acidity [Formula: see text], protonating on the carbonyl oxygen, but the diprotonated form is not reactive. The hydrolysis involves the reversible addition of one water molecule to the substrate to give a tetrahedral intermediate; at low acidities the decomposition of this hydrate is the rate-determining step, but as the acidity increases and the water activity decreases its formation becomes rate limiting. Hydroxide catalysis was also observed in dilute perchloric acid, but this is swamped by nucleophilic catalysis by the acid anion in HCl and H2SO4. Keywords: acylimidazoles, excess acidity, hydrolysis, protonation, tetrahedral intermediate.

The tetrahedral intermediate from the hydration of N-methylformanilide

1993 ◽  
Vol 71 (12) ◽  
pp. 2109-2122 ◽  
Author(s):  
J. Peter Guthrie ◽  
Jonathan Barker ◽  
Patricia A. Cullimore ◽  
Jinqiao Lu ◽  
David C. Pike
Keyword(s):  
Aqueous Solution ◽  
Free Energy ◽  
Dimethyl Acetal ◽  
Heat Of Formation ◽  
Basic Solution ◽  
Tetrahedral Intermediate ◽  
Rate Determining Step ◽  
Free Energy Of Formation ◽  
Hydrolysis Of ◽  
Energy Of Formation

Heats of hydrolysis of N-methylformanilide dimethyl acetal have been measured in basic solution. The heat of formation of N-methylformanilide was obtained by determining the equilibrium constant in aqueous solution for its formation from formic acid and N-methylaniline as a function of temperature:[Formula: see text]. These data permit the calculation of the heat of formation of N-methylformanilide dimethyl acetal, [Formula: see text]. The free energy of formation of the tetrahedral intermediate in the hydrolysis of N-methylformanilide was calculated by methods we have previously reported. Consideration of the energetics of the intermediates and the known rates of reaction leads to the conclusion that the rate-determining step for alkaline hydrolysis is cleavage of the C—N bond.

scholarly journals Polyclonal antibody-catalysed amide hydrolysis

1992 ◽  
Vol 284 (3) ◽  
pp. 675-680 ◽  
Author(s):  
G Gallacher ◽  
M Searcey ◽  
C S Jackson ◽  
K Brocklehurst
Keyword(s):  
Polyclonal Antibody ◽  
Carboxy Group ◽  
Catalytic Antibody ◽  
Amino Group ◽  
Immunization Schedule ◽  
Keyhole Limpet Haemocyanin ◽  
Antibody Preparation ◽  
Amide Hydrolysis ◽  
Hydrolysis Of ◽  
Ester Substrate

1. The activated amide (4-nitroanilide), N-(4-nitrophenyl) N'-butyl-1,4-phenylenediacetamide (III) was synthesized. 2. A polyclonal antibody preparation (PCA 270-29) was elicited in a multigeneration cross-bred sheep (no. 270) and isolated 29 weeks into the immunization schedule by procedures described previously for PCA 270-22 [Gallacher, Jackson, Searcey, Badman, Goel, Topham, Mellor & Brocklehurst (1991) Biochem J. 271, 871-881]. These involved the use of an amide conjugate bonded through the carboxy group of 4-nitrophenyl 4′-carboxymethylphenyl phosphate and an amino group of keyhole-limpet haemocyanin as the immunogen. 3. PCA 270-29 was shown to catalyse the hydrolysis of both the carbonate ester substrate 4-nitrophenyl 4′-(3-aza-2-oxoheptyl)phenyl carbonate (I) and the amide substrate (III). Both catalyses obeyed the Michaelis-Menten equation with the following values of the parameters at 25 degrees C: for the hydrolysis of (I) at pH 8.0, Km = 3.96 +/- 0.28 microM and k(cat.) = 0.135 +/- 0.004 s-1 (k(non-cat.) = 1.99 x 10(-4) s-1); for the hydrolysis of (III) at pH 9.0, Km = 5.4 +/- 1.4 microM and k(cat.) = (5.95 +/- 0.75) x 10(-5) s-1 (k(non-cat.) = approx. 2 x 10(-7) s-1). 4. The finding that PCA 270-29 is almost equally effective as a catalyst for the hydrolysis of the amide (III) as for that of the carbonate ester (I) when allowance is made for the different intrinsic reactivities of the two types of substrate is discussed. The catalytic characteristics of PCA 270-29, the first example of a polyclonal catalytic antibody preparation shown to catalyse the hydrolysis of an amide and the first example of an antibody preparation (monoclonal or polyclonal) with such catalytic character to be produced by use of a phosphate immunogen, are compared with those of the small number of other antibody-mediated hydrolyses of amides in the literature.

scholarly journals Evidence for ‘lock and key’ character in an anti-phosphonate hydrolytic antibody catalytic site augmented by non-reaction centre recognition: variation in substrate selectivity between an anti-phosphonate antibody, an anti-phosphate antibody and two hydrolytic enzymes

2004 ◽  
Vol 381 (1) ◽  
pp. 125-130 ◽  
Author(s):  
Sanjiv SONKARIA ◽  
Guillaume BOUCHER ◽  
José FLÓREZ-ÁLVAREZ ◽  
Bilal SAID ◽  
Syeed HUSSAIN ◽  
...  
Keyword(s):  
Hydrolytic Enzymes ◽  
Catalytic Site ◽  
Catalytic Antibody ◽  
Substrate Selectivity ◽  
Reaction Centre ◽  
Antibody Preparation ◽  
Leaving Group ◽  
Catalytically Active ◽  
Group Part ◽  
Kinetic Selectivity

The substrate selectivities of an anti-phosphonate and an anti-phosphate kinetically homogeneous polyclonal catalytic antibody preparation and two hydrolytic enzymes were compared by using hapten-analogous and truncated carbonate and ester substrates each containing a 4-nitrophenolate leaving group. Syntheses of the truncated substrates devoid of recognition features in the non-leaving group parts of the substrates are reported. The relatively high kinetic selectivity of the more active anti-phosphonate antibody preparation is considered to depend on a relatively rigid catalytic site with substantial reaction centre specificity together with other important recognition interactions with the extended non-leaving group part of the substrate. In contrast, the less catalytically active, more flexible anti-phosphate antibody exhibits much lower kinetic selectivity for the substrate reaction centre comparable with that of the hydrolytic enzymes with activity much less dependent on recognition interactions with the non-leaving group part of the substrate. The ways in which haptenic flexibility and IgG architecture might contribute to the differential kinetic selectivities are indicated.

scholarly journals Pseudomonas putida MPE, a manganese-dependent endonuclease of the binuclear metallophosphoesterase superfamily, incises single-strand DNA in two orientations to yield a mixture of 3′-PO4 and 3′-OH termini

2020 ◽  
Author(s):  
Shreya Ghosh ◽  
Anam Ejaz ◽  
Lucas Repeta ◽  
Stewart Shuman
Keyword(s):  
Pseudomonas Putida ◽  
Bound Water ◽  
Acid Catalyst ◽  
Nuclease Activity ◽  
Single Strand ◽  
Dna Endonuclease ◽  
Dependent Endonuclease ◽  
Leaving Group ◽  
Phosphodiester Hydrolysis ◽  
Hydrolysis Of

Abstract Pseudomonas putida MPE exemplifies a novel clade of manganese-dependent single-strand DNA endonuclease within the binuclear metallophosphoesterase superfamily. MPE is encoded within a widely conserved DNA repair operon. Via structure-guided mutagenesis, we identify His113 and His81 as essential for DNA nuclease activity, albeit inessential for hydrolysis of bis-p-nitrophenylphosphate. We propose that His113 contacts the scissile phosphodiester and serves as a general acid catalyst to expel the OH leaving group of the product strand. We find that MPE cleaves the 3′ and 5′ single-strands of tailed duplex DNAs and that MPE can sense and incise duplexes at sites of short mismatch bulges and opposite a nick. We show that MPE is an ambidextrous phosphodiesterase capable of hydrolyzing the ssDNA backbone in either orientation to generate a mixture of 3′-OH and 3′-PO4 cleavage products. The directionality of phosphodiester hydrolysis is dictated by the orientation of the water nucleophile vis-à-vis the OH leaving group, which must be near apical for the reaction to proceed. We propose that the MPE active site and metal-bound water nucleophile are invariant and the enzyme can bind the ssDNA productively in opposite orientations.

scholarly journals Phosphate-Catalyzed Succinimide Formation from an NGR-Containing Cyclic Peptide: A Novel Mechanism for Deammoniation of the Tetrahedral Intermediate

Molecules ◽  
2018 ◽  
Vol 23 (9) ◽  
pp. 2217 ◽  
Author(s):  
Ryota Kirikoshi ◽  
Noriyoshi Manabe ◽  
Ohgi Takahashi
Keyword(s):  
Conformational Changes ◽  
Density Functional ◽  
Cyclic Peptide ◽  
Density Functional Theory Method ◽  
Proton Exchange ◽  
Computational Method ◽  
Side Chain ◽  
Tetrahedral Intermediate ◽  
Rate Determining Step ◽  
Proton Source

Spontaneous deamidation in the Asn-Gly-Arg (NGR) motif that yields an isoAsp-Gly-Arg (isoDGR) sequence has recently attracted considerable attention because of the possibility of application to dual tumor targeting. It is well known that Asn deamidation reactions in peptide chains occur via the five-membered ring succinimide intermediate. Recently, we computationally showed by the B3LYP density functional theory method, that inorganic phosphate and the Arg side chain can catalyze the NGR deamidation using a cyclic peptide, c[CH2CO–NGRC]–NH2. In this previous study, the tetrahedral intermediate of the succinimide formation was assumed to be readily protonated at the nitrogen originating from the Asn side chain by the solvent water before the release of an NH3 molecule. In the present study, we found a new mechanism for the decomposition of the tetrahedral intermediate that does not require the protonation by an external proton source. The computational method is the same as in the previous study. In the new mechanism, the release of an NH3 molecule occurs after a proton exchange between the peptide and the phosphate and conformational changes. The rate-determining step of the overall reaction course is the previously reported first step, i.e., the cyclization to form the tetrahedral intermediate.

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