Substrate induced pK perturbations with chymotrypsin and the possible significance of nonproductive binding

Synthesis and crystal structures of a new series of intramolecular bridged alkylcobaloxime complexes

A new series of intramolecular bridged alkylcobaloxime complexes were prepared by heating a solution of aqua-(3-bromopropyl)cobaloxime (1) through an intramolecular nucleophilic substitution. They are characterized by EA, ESI-MS, and (1)H NMR. Crystal structures of Br(O-C(3)H(6)-(dmgH))(dmgH)Co(III) (2), [H(2)O(O-C(3)H(6)-(dmg))(dmgH(2))Co(III)]ClO(4) (3), [Py(O-C(3)H(6)-(dmg))(dmgH(2))Co(III)]ClO(4) (4), [Bzm(O-C(3)H(6)-(dmg))(dmgH(2))Co(III)]ClO(4) (5), and Im(O-C(3)H(6)-(dmg))(dmgH)Co(III) (6') were determined by X-ray diffraction. It is revealed that an intramolecular tri-methylene bridge exists between cobalt and one of the equatorial oxime oxygens forming a six-membered ring in the complexes. Additionally, the axial bases have some influences in their structure parameters, for example, Co-L bond lengths; folding angles in equatorial ligands; hydrogen atom positions in O-H-O bridge; and the orientations of those L planes with respect to the equatorial planes.

Insight into the catalysis of hydrolysis of four newly synthesized substrates by papain: a proton inventory study

We synthesized the following four new peptide substrates, Suc-Phe-Leu-pNA, Suc-Phe-Leu-NMec, Suc-Phe-Leu-ONPh, and Pht-Phe-Leu-pNA, and we applied the proton inventory method to their hydrolysis by papain. Useful relationships between the rate constants of the catalytic reaction have been established and contributed to the elucidation of the hydrolytic mechanism of papain. For all amide substrates, the parameter K(S) and the rate constants k(1), k(-)(1), and k(2) were estimated. Moreover, it was found that k(cat)/K(m) = k(1) for all four substrates, while two exchangeable hydrogenic sites, one in the ground state and another in the transition state, generate an inverse isotope effect during the reaction governed by this parameter. The proton inventories of both k(2) and k(3) are essentially linear, whatever the acyl moiety and/or the leaving group of the substrate. The proton inventories of K(S) are also essentially linear for all amide substrates, while the observed large isotope effect of about 3 to 9 originates from a single hydrogenic site in the product state. This latter, in agreement to both the small transition state fractionation factors found for k(cat)/K(m) (or k(1)) and the unit ground-state fractionation factors found for k(2), argues for the formation of a tetrahedral adduct during the reaction governed by the k(1) parameter. Furthermore, papain acts as a one-proton catalyst during acylation or deacylation, both of which proceed through similar concerted reaction pathways, where a nucleophilic attack is accompanied by the movement of one proton.

Synthesis and enzymic hydrolysis of cyclic peptides containing an anthranilic acid residue

Two cyclic peptides cyclo (Phe-MeAnt-Glyn) with MeAnt = 5-methyl-anthranilic acid residue, n = 4 (3b) and n = 6 (4b), have been synthesized in solution and their reaction with alpha-chymotrypsin analyzed. The polyglycyl chain was prepared by the phosphazo method; cyclization at the Gly-Phe site occurred in good yield using the azide method. Catalysis of the hydrolysis of peptides 3b and 4b by alpha-chymotrypsin was characterized at 37 degrees by the apparent second-order rate constants kcat/Km 0.12 and 1.15 M-1 S-1, respectively, in agreement with the usual acceleration observed upon enlargement of the size of the peptidic ring in cyclic peptides. alpha-Chymotrypsin specifically split the Phe-MeAnt amide bond in cyclopeptide 4b. This specific orientation suggests that analogous structures with a functionalized methylene group instead of the methyl substituent can be used in the design of suicide substrates for serine proteases.

Specificity in the hydrolysis of N-acyl-L-phenylalanine 4-nitroanilides by chymotrypsin

The affinity of N-acyl-L-phenylalanine 4-nitroanilides for chymotrypsin is enhanced as the hydrophobicity of non-amino acid residues in the P2-position of the substrates increases, whereas Kcat remains nearly constant. On the other hand, if alanine or leucine is in the P2-position Kcat increases with decreasing KM.

Catalysis and leaving group binding in anilide hydrolysis by chymotrypsin

The influence of the leaving group on the reactivity of specific anilides in alpha-chymotrypsin-catalyzed hydrolysis (chymotrypsin, EC 3.4.21.2) involves both its binding to the enzyme (steric effect) and electronic nature (electronic effect). These effects are considered in terms of the stereoelectronic theory for the formation and cleavage of the tetrahedral intermediate in acyltransfer reactions. The application of this theory to the enzyme hydrolysis leads to the conclusion that the nature of the reaction products and the effectiveness of the catalysis are controlled by the orientation of the leaving group nitrogen lone pair orbital. The leaving group binding affects the formation of a reactive conformation of the enzyme tetrahedral intermediate that is presumed to intervene between the Michaelis complex and the acylenzyme. The steric and electronic effects could be separated in a straightforward fashion only in the case of equal binding of the leaving groups to the leaving-group-binding site of alpha-chymotrypsin.

Design of new photoaffinity labels for ribosomal peptidyltransferase

The chemical syntheses of 6-azido-2'(3')-O-L-phenylalanylpurine ribonucleoside (4a), 2'(3')-O-(4-azido-L-phenylalanyl)adenosine (4b), and cytidylyl(3' leads to 5')-6-azido-2'(3')-O-L-phenylalanylpurine ribonucleoside (7) are described. 6-Azidopurine ribonucleoside 5'-triphosphate (10) was also synthesized starting from 6-methylmercaptopurine ribonucleoside. All of these compounds (4a, 4b, 7, and 10) are readily photolyzed by ultraviolet (UV) light. Compounds 4a, 4b, and 7 are active in the ribosomal peptidyltransferase-catalyzed release of the Ac-Phe residue from the Ac-Phe-tRNA-70S ribosome-poly(U) complex. It follows that the 6-azidopurine moiety of compounds 4a and 7, as well as the 4-azido-L-phenylalanine moiety of 4b, are recognized by the peptidyltransferase enzyme, and therefore these moieties are suggested for incorporation into tRNA as photoaffinity labeling reagents.

Binding rates, O--S substitution effects, and the pH dependence of chymotrypsin reactions

The pH dependence for acylation of alpha-chymotrypsin by N-acetyltryptophan p-nitrophenyl-, p-nitrothiophenyl-, ethyl-, and thiolethyl esters has been studied by the stopped-flow technique. Values for the acylation rate constant, k2, and the binding constant, KS, were obtained by using measurements of phenolate release, for the p-nitrophenyl esters, and proflavin displacement, for the ethyl esters. The oxygen esters tested have slightly higher k2 values, and substantially higher KS values relative to the analogous thiol esters. Whereas k2/KS for the thiolethyl ester is higher than that for the analogous oxygen ester, the k2/KS values for oxy- and thio-p-nitrophenyl esters are nearly identical. These data are interpreted to indicate rate-determining formation of a tetrahedral intermediate in acylation of alpha-chymotrypsin by p-nitrophenyl esters, and rate-determining breakdown of such an intermediate in the case of the ethyl esters. It is also concluded that the oxygen to sulfur substitution causes a substantial increase in the proportion of nonproductive binding in these substrates. pH dependent k2 and KS values were used to calculate values for k1 and k-1, the binding and debinding rate constants for the two p-nitrophenyl compounds. This is the first such calculation based on experimentally determined acylation rate constants.