Acyl and amino intermediates in reactions catalysed by pig pepsin. Analysis of transpeptidation products

An artificial aspartic proteinase system

A series of aza crown ether derivatives with or without carboxyl groups in their side arms were synthesized and the former showed deacylation activities toward amino acid p-nitrophenyl ester hydrohalides. Substrate-selective phenomena were also observed. The relationship between the structures and deacylation activities of corresponding compounds suggested a nucleophilic catalytic mechanism. The results partially simulate some aspartic proteinases in the case of catalytic mechanism and are also useful for us to understand the detailed catalytic process of aspartic proteinases.

Mechanism of pepsin-catalyzed aminotranspeptidation reactions

1. The tetrapeptide Ala2-Nph2 (where Nph = p-nitrophenylalanyl) is treated by porcine pepsin to study the mechanism of aminotranspeptidation reactions. 2. The major initial product is Ala2-Nph and the major transpeptidation products are Nph2 and Nph3 accompanied by some Nph, a little Nph4, Ala2-Nph3 and Ala2-Nph4. 3. Oligomers of Nph greater than tetramers are formed near the end of the reaction. 4. In presence of [3H]Nph, no incorporation of Nph into the transpeptidation products is observed. 5. 18O-labeling shows extensive incorporation of 18O atoms from [18O]water in the carbonyl oxygens of Nph residues.

Oligo(methionyl) proteins. Enzymatic hydrolysis of the model isopeptides N epsilon-oligo(L-methionyl)-L-lysine

A number of model isopeptides containing oligo(methionine) chains varying in length (2-5 residues) covalently linked to the epsilon-amino group of lysine were synthesized by solid-phase procedures. Hydrolysis of these peptides by pepsin, chymotrypsin, cathepsin C (dipeptidyl peptidase IV) and intestinal aminopeptidase N was investigated using high-performance liquid chromatography to identify and quantify the hydrolysis products. Methionine oligomers grafted onto lysine were cleaved to tripeptides by pepsin. Chymotrypsin preferentially hydrolyzed the methionyl-methionine bond preceding the isopeptide bond. Cathepsin C released dimethionyl units from the covalently attached polymers. Intestinal aminopeptidase caused efficient hydrolysis of both peptides and isopeptide bonds although free methionine decreased the cleavage of the latter bond. Hydrophobic characteristics of oligo(methionine) chains promoted enzyme-catalyzed transpeptidations resulting probably from acyl-transfer-type reactions. Complementary hydrolysis of the isopeptides by these digestive enzymes suggests that covalent attachment of oligo(amino acid)s to food proteins may improve their nutritional value.

Surprising consequences of the tendency of pepsin to catalyze condensation reactions between small peptides

Pepsin catalyzes numerous acyl-transfer reactions. Are peptic acyl-enzyme intermediates involved in such reactions? To start, we examine the cleavage of Leu-Trp-Met-Arg at pH 3.4-4.5 in the presence of 25 mM tryptophanamide. Substantial amounts of Leu-TrpNH2 are generated. However, the appearance of this acyl-transfer product cannot be attributed to the intervention of Leu-pepsin and its trapping by tryptophanamide. Experiment proves that Leu-Trp-Met-Arg affords Leu3, which, in turn, reacts with tryptophanamide to produce Leu-TrpNH2. Both the formation of Leu3 from Leu-Trp-Met-Arg and the conversion of Leu3 + tryptophanamide into Leu-TrpNH2 can potentially implicate the generation and trapping of a Leu-pepsin intermediate. Does experiment support either possibility? The answer is no. Our data show that most of the Leu3 derived from Leu-Trp-Met-Arg stems from an autocatalytic condensation process whereby Leu3 already present speeds the conversion of the leucine residues of unreacted Leu-Trp-Met-Arg into more Leu3. Technical problems have prevented us from determining whether the first Leu3 formed results from the trapping of an acyl-enzyme intermediate. The generation of Leu-TrpNH2 from Leu3 was studied primarily via a more tractable analogous reaction: Leu-Trp-Leu + tryptophanamide leads to Leu-TrpNH2. The mechanism governing these transformations is highly complex. Its major feature is an initial condensation between two molecules of substrate. All the examples investigated further illustrate the marked tendency of pepsin to catalyze condensation reactions between suitably constructed small peptides. The prevalence of these reactions complicates the interpretation of much data bearing on pepsin's mechanism of action.

Conformational flexibility in the active sites of aspartyl proteinases revealed by a pepstatin fragment binding to penicillopepsin

Crystals of the molecular complex between the esterified tripeptide fragment of pepstatin and the aspartyl proteinase penicillopepsin are isomorphous with crystals of native penicillopepsin. The difference electron-density map at 1.8-A resolution, computed by using the amplitude differences and refined phases of reflections from the crystal of native penicillopepsin, unambiguously showed the binding mode of isovaleryl-Val-Val-StaOEt, where StaOEt is the ethyl ester of statine [(4S,3S)-4-amino-3-hydroxyl-6-methylheptanoic acid]. In addition, a major conformational change in penicillopepsin involving the large beta loop of residues from Trp-71 to Gly-83 (the so-called "flap" region) occurs as a result of this inhibitor binding. This structural movement provides the first confirmation of the importance of enzyme flexibility in the aspartyl proteinase mechanism. The 3-hydroxyl group of the Statine residue and the carbonyl oxygen atom of the ethyl ester are situated on either side of the approximate plane containing the hydrogen-bonded carboxyl groups of Asp-33 and Asp-213. The observed binding mode of the pepstatin tripeptide fragment is similar to that predicted for the binding of good substrates with penicillopepsin [James, M. N. G. (1980) Can. J. Biochem. 58, 251-271].

Comparison of pepsins isolated from porcine, bovine and Penicillium jathiuellum

1. The reactivities of pepsins, isolated from three different sources (porcine, bovine, and Penicillium jathiuelum), toward ester and peptide substrates were compared. 2. Porcine pepsin showed the highest activity followed by penicillopepsin with bovine pepsin being the least active. 3. The esterase activity of penicillopepsin was greater than that of porcine pepsin with bovine pepsin again showing the least activity. 4. The CD spectra indicate that porcine and bovine pepsin have similar conformations, even though bovine pepsin shows less ellipticity at 220 nm. 5. Penicillopepsin showed a completely opposite sign in the near-u.v. region of the CD spectrum. 6. The far-u.v. region of the CD spectrum of penicillopepsin strongly suggests a beta-sheet structure. 7. Previously reported X-ray crystallographic data suggest that porcine pepsin has a compact three-dimensional structure, while the structures of bovine and penicillopepsins are partially unfolded.

Enzyme-catalyzed condensation reactions which initiate rapid peptic cleavage of substrates. 1. How the structure of an activating peptide determines its efficiency

The addition of a small peptide can significantly increase the rate at which pepsin cleaves a substrate at pH 4.5. Why? In order to find out, we have determined spectrophotometrically the relative ability of over a dozen peptides to speed the initial rate of disappearance of Phe-Trp-NH2 and Leu-Trp-Met-Arg. Here are some of the criteria which establish the reliability of the acquired kinetic data: (1) rates depend linearly on [E] and , to a good approximation, on [activator], (2) measurements with both substrates yield the same ranking for the activators tested; (3) high-pressure liquid chromatographic investigations independently confirm conclusions derived from the spectrophotometric studies. The best activators found were Z-Ala-Phe and Ala-Leu. At 3.2 mM they are respectively 60 and 30 times more effective than an equal concentration of A-(Ala)2. The two-step mechanism given below (for Phe-Trp-NH2) best explains the structural specificity found, as well as other observations on the nature of these activated cleavages. It assumes that reaction commences when pepsin catalyzes synthesis of a peptide bond between activator and substrate. The polypeptide so formed subsequently undergoes scission at a different bond. The modified activator liberated, here designated Z-AA2-AA1-Phe, can eventually provide a variety of reaction products, as the succeeding paper demonstrates.

Penicillopepsin from Penicillium janthinellum crystal structure at 2.8 A and sequence homology with porcine pepsin

The polypeptide chain of the acid protease penicillo pepsin folds via an 18-stranded mixed beta-sheet into two distinct lobes separated by a 30-A long groove which is the extended substrate binding site. The catalytic residues Asp-32 and Asp-215 are located in this groove and their carboxyl groups are in intimate contact. Alignment of the amino acid sequence with that of pepsin shows regions of high homology.

Penicillopepsin: 2.8 A structure, active site conformation and mechanistic implications

The crystal structure of penicillopepsin, an extracellular acid protease isolated from the mold Penicillium janthinellum, has been determined at 2.8 A resolution by the method of multiple isomorphous replacement. The resulting electron density map computed from the native structure factor amplitudes and MIR phases has an overall mean figure of merit of 0.90. The molecule is decidedly nonspherical, with the majority of residues in beta-structure. There is an 18-stranded mixed beta-sheet which forms the structural core in the region of the active site. This site, identified by the covalent binding of two EPNP molecules to Asp-32 and Asp-215, is located in a deep groove which divides the molecule into two approximately equal lobes. Both aspartic acid residues in the active site are in intimate contact with one another and the carboxyl group of Asp-32 makes two other important hydrogen-bonded contacts: one with Ser-35 and the other with the main chain peptide bond between Thr-216 and Gly-217. A proposed mechanism for acid protease catalysis is similar in many aspects to that proposed for carboxypeptidase A. The electrophilic component which polarizes the substrate carbonyl bond in the acid proteases is the proton shared between the beta-carboxyl groups of Asp-32 and Asp-215. The beta-carboxyl group of Asp-32 removes a proton from a water molecule bound between this side chain and the substrate; the resultant OH- attacks the carbonyl carbon atom of the substrate molecule. The phenolic -OH group of Tyr-75 donates its proton to the amide nitrogen of the scissile bond of the substrate.

Effects of secondary binding by activator and inhibitor peptides on covalent intermediates of pig pepsin

A number of peptides were found to increase the activity of pig pepsin towards small synthetic substrates. The activators increase transpeptidation of both the acyl-transfer and the amino-transfer types by as much as 45-fold. The effect on hydrolysis varies from inhibition to modest activation, but is always less than the effect on transpeptidation. The kinetics of substrate cleavage are the converse of non-competitive inhibition and show an increase in kcat. and no effect on Km values. Lineweaver-Burk plots of results obtained in the presence of the activators indicate a substrate activation at high substrate concentration. This appears to be a co-operative effect, since it is not observed in the absence of the activators. The activation is greatest at pH 4.7, less at pH 3.4, and at pH 2.0 is observable only with some of the activator peptides. The results show directly the effect of secondary binding on the catalytic efficiency of pepsin. The most effective activators are those that are most hydrophobic. The results suggest that binding in the secondary binding sites causes an increase in hydrophobicity in the catalytic site which results in increased stability of the acyl and amino intermediates, and preferential reaction with acceptors other than water. The implication that the present results strengthen the case for a role of covalent intermediates in the hydrolysis of good substrates (high kcat. values) is discussed.