Activation of the action of penicillopepsin on leucyl-tyrosyl-amide by a non-substrate peptide and evidence for a conformational change associated with a secondary binding site

Domain flexibility in aspartic proteinases

Comparison of the three-dimensional structures of native endothiapepsin (EC 3.4.23.6) and 15 endothiapepsin oligopeptide inhibitor complexes defined at high resolution by X-ray crystallography shows that endothiapepsin exists in two forms differing in the relative orientation of a domain comprising residues 190-302. There are relatively few interactions between the two parts of the enzyme; consequently, they can move as separate rigid bodies. A translational, librational, and screw analysis of the thermal parameters of endothiapepsin also supports a model in which the two parts can move relative to each other. In the comparison of different aspartic proteinases, the rms values are reduced by up to 47% when the two parts of the structure are superposed independently. This justifies description of the differences, including those between pepsinogen and pepsin (EC 3.4.34.1), as a rigid movement of one part relative to another although considerable distortions within the domains also occur. The consequence of the rigid body movement is a change in the shape of the active site cleft that is largest around the S3 pocket. This is associated with a different position and conformation of the inhibitors that are bound to the two endothiapepsin forms. The relevance of these observations to a model of the hydrolysis by aspartic proteinases is briefly discussed.

Effect of N-methylation on the modulation by synthetic peptides of the activity of the complement-factor-B-derived serine proteinase CVFBb

Although they share the active-site catalytic triad of less-specific enzymes such as trypsin and chymotrypsin, the serine proteinases of the complement and coagulation cascades each cleave a highly restricted set of substrates. Peptides with sequences similar to that at which C3 is cleaved by the alternative-pathway complement proteinase CVFBb were synthesized by solid-phase methodology and examined for their effects on the activity of this enzyme as measured by three different types of assays. It was found that a peptide methylated at the scissile bond was a far more effective inhibitor of the cleavage of the protein substrate C5 and of the lysis of guinea-pig erythrocytes by the alternative pathway than was the equivalent unmethylated peptide. Whereas the unmethylated peptide inhibited cleavage of the peptide substrate, the methylated peptide actually stimulated cleavage in this assay. This stimulation was found to be due to a 2.8-fold increase in kcat; the dissociation constant for the substrate was not altered significantly. One model consistent with this behaviour is that the binding of the activator peptide in the extended substrate-recognition region stabilizes a catalytically more active conformation of the active site. A small peptide substrate may have access to such an activated active site, whereas the larger substrate, C5, may be excluded from the site. These results demonstrate that the observed effect of a given compound on activity of an enzyme with an extended substrate-recognition region may depend upon the substrate.

Autocatalytic sets of proteins

This article investigates the possibility that the emergence of reflexively autocatalytic sets of peptides and polypeptides may be an essentially inevitable collective property of any sufficiently complex set of polypeptides. The central idea is based on the connectivity properties of random directed graphs. In the set of amino acid monomer and polymer species up to some maximum length, M, the number of possible polypeptides is large, but, for specifiable "legitimate" end condensation, cleavage and transpeptidation exchange reactions, the number of potential reactions by which the possible polypeptides can interconvert is very much larger. A directed graph in which arrows from smaller fragments to larger condensation products depict potential synthesis reactions, while arrows from the larger peptide to the smaller fragments depict the reverse cleavage reactions, comprises the reaction graph for such a system. Polypeptide protoenzymes are able to catalyze such reactions. The distribution of catalytic capacities in peptide space is a fundamental problem in its own right, and in its bearing on the existence of autocatalytic sets of proteins. Using an initial idealized hypothesis that an arbitrary polypeptide has a fixed a priori probability of catalyzing any arbitrary legitimate reaction to assign to each polypeptide those reactions, if any, which it catalyzes, the probability that the set of polypeptides up to length M contains a reflexively autocatalytic subset can be calculated and is a percolation problem on such reaction graphs. Because, as M increases, the ratio of reactions among the possible polypeptides to polypeptides rises rapidly, the existence of such autocatalytic subsets is assured for any fixed probability of catalysis. The main conclusions of this analysis appear independent of the idealizations of the initial model, introduce a novel kind of parallel selection for peptides catalyzing connected sequences of reactions, depend upon a new kind of minimal critical complexity whose properties are definable, and suggest that the emergence of self replicating systems may be a self organizing collective property of critically complex protein systems in prebiotic evolution. Similar principles may apply to the emergence of a primitive connected metabolism. Recombinant DNA procedures, cloning random DNA coding sequences into expression vectors, afford a direct avenue to test the distribution of catalytic capacities in peptide space, may provide a new means to select or screen for peptides with useful properties, and may ultimately lead toward the actual construction of autocatalytic peptide sets.

A new chromophoric substrate for penicillopepsin and other fungal aspartic proteinases

The hexapeptide N-alpha-acetylalanylalanyl-lysyl-p- nitrophenylalanylalanylalanylamide has been synthesized and was found to be a good substrate for fungal aspartic proteinases that possess trypsinogen-activating activity, namely penicillopepsin, Rhizopus aspartic proteinase, Endothia aspartic proteinase and the aspartic proteinases from Aspergillus oryzae and Penicillium roqueforti. The peptide is rapidly cleaved between the lysine and p-nitrophenylalanine residues. Calf chymosin and human renin cleave the same bond, but only very slowly. The cleavage is accompanied by an absorbance decrease with a maximum at 296nm (Deltaepsilon -1800m(-1).cm(-1)). Pig pepsin and the aspartic proteinases from two Rhizomucor species cleave the peptide slowly on the carboxy side of p-nitrophenylalanine. For the five enzymes that hydrolysed the peptide rapidly, K(m) values range from 0.16 to 0.42mm and k(cat.) from 6 to 46.6s(-1) at pH 4.5 and 25 degrees C. A comparison of the kinetic parameters of the hexapeptide with those of the dipeptide N-alpha-acetyllysyl-p-nitrophenylalanylamide obtained with penicillopepsin shows that at pH 6.0 the catalytic rate constant k(cat.) is over 5000-fold greater for the hexapeptide, whereas the K(m) values are essentially the same, showing that the catalytic efficiency is strongly dependent on secondary binding. The new substrate with a p-nitrophenylalanine residue in the P'(1) position has advantages over previously used substrates for aspartic proteinases in that it offers a more sensitive spectrophotometric assay that is independent of pH up to 5.5 and can readily be used up to pH 7.0. The presence of lysine makes it very water-soluble. Stopped-flow spectrophotometric experiments with penicillopepsin gave clear evidence that the hydrolysis of the substrate by penicillopepsin is not accompanied by a ;burst' release of p-nitrophenylalanylalanylalanylamide.

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.

Inactivation of aspartyl proteinases by butane-2,3-dione. Modification of tryptophan and tyrosine residues and evidence against reaction of arginine residues

Butane-2,3-dione inactivates the aspartyl proteinases from Penicillium roqueforti and Penicillium caseicolum, as well as pig pepsin, penicillopepsin and Rhizopus pepsin, at pH 6.0 in the presence of light but not in the dark. The inactivation is due to a photosensitized modification of tryptophan and tyrosine residues. In the dark none of the amino acid residues, not even arginine residues, is modified even after several days. In the light one arginine residue in pig pepsin is lost at a rate that is comparable with the rate of inactivation; however, the loss of the single arginine residue in the aspartyl proteinase of P. roqueforti and the second arginine residue of pig pepsin is slower than the loss of activity; penicillopepsin is devoid of arginine. Loss of most of the activity is accompanied by the following amino acid losses: P. roqueforti aspartyl proteinase, about two tryptophan and six tyrosine residues; penicillopepsin, about two tryptophan and three tyrosine residues; pig pepsin, about four tryptophan and most of the tyrosine residues. Modification of histidine residues was too slow to contribute to inactivation. None of the other residues, including half-cystine and methionine residues (when present), was modified even after prolonged incubation. The inactivation of P. roqueforti aspartyl proteinase and pig pepsin appears due to non-specific modification of several residues. With penicillopepsin, however, the reaction is more limited and initially affects only those tryptophan and tyrosine residues that lie in the active-site groove. In the presence of pepstatin the rate of inactivation is considerably diminished. After prolonged reaction a general structural breakdown occurs.

Specificity of the acid protease from Monascus kaoliang towards the B-chain of oxidized insulin

The proteolytic specificity of the acid protease from Monascus kaoliang has been investigated using the B-chain of performic acid-oxidized insulin as peptide substrate. Six splittings were detected after 1 h digestion and 12 splittings were found after 12 h incubation at 37 degrees C, pH 4.8. The bonds most susceptible to the acton of M. kaoliang acid protease were Phe(24)-Phe(25), Leu(15)-Tyr(16) and Tyr(16)-Leu(17). Among the acid proteases compared, the specificity of M. kaoliang acid protease on the B-chain of oxidized insulin is more closely related to that of penicillopepsin with which it has ten cleavage sites in common. N-Acetyl-L-phenylalanyl-L-3,5-diiodotyrosine, a synthetic substrate for pepsin, was resistant to the hydrolysis of M. kaoliang acid protease.

Mechanism of acid protease catalysis based on the crystal structure of penicillopepsin

A proposed mechanism for the catalytic hydrolysis of peptide bonds by acid proteases is similar in many respects to the Zn-carbonyl mechanism previously derived for carboxypeptidase A. In the acid proteases the electrophilic component is the proton shared by Asp-32 and Asp-215; Tyr-75 donates its proton to the amide nitrogen of the scissile bond and an OH- ion from a water molecule bound between the carboxyl group of Asp-32 and the substrate attacks the carbonyl carbon atom.

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.

X-ray analysis and circular dichroism of the acid protease from Endothia parasitica and chymosin

The structure of an acid proteinase from Endothia parasitica has been solved by x-ray diffraction using multiple isomorphous replacement. A 3 A resolution map was interpreted in terms of a bilobal structure with a long 25 A cleft. The secondary structure is mostly distorted beta-sheet. The circular dichroism was measured and model curves for different secondary structures were fitted by least squares indicating a large component of beta-structure. The structure was seen to be homologous with that of the acid proteinase from R. Chinensis and hence with pepsin and chymosin. A rotation function against diffraction data from chymosin crystals confirm confirm this and suggested an approach to the solution of this structure.

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.

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

The action of pig pepsin on a variety of small peptides including Leu-Trp-Met-Arg, Leu-Trp-Met, Leu-Leu-NH2, benzyloxycarbonyl-Phe-Leu and Gly-Leu-Tyr was studied. Leu-Leu-Leu was found to be the major product from the substrates Leu-Trp-Met-Arg and Leu-Trp-Met, indicating that the predominant reaction at pH 3.4 was a transpeptidation of the acyl-transfer type. Leu-Leu-Leu was also formed in high yield by amino transfer from benzyloxycarbonyl-Phe-Leu. Like the amino-transfer reactions the acyl transfer proceeded via a covalent intermediate, since [14C]leucine was not incorporated into transpeptidation products and did not exchange with enzyme-bound leucine in the presence of acceptors. With Leu-Trp-Met both acyl and amino transpeptidation products, namely Leu-Leu, Leu-Leu-Leu, Met-Met and Met-Met-Met, were formed in addition to methionine and leucine. With Leu-Trp-Met-Arg (1 mM) the pH optimum for the rates of hydrolysis and acyl transfer is about pH 3.4. At this pH the rate of acyl transfer exceeds that of hydrolysis; at pH 2, however, hydrolysis was faster than transfer. A comparison of the effect of the length of substrates and products on the reaction rates allows the conclusion that the binding site can extend over eight to nine amino acid residues. Although the experiments provide no conclusive evidence for or against the involvement of amino and/or acyl intermediates in the hydrolysis of long peptides and proteins, the high yield of transpeptidation reactions of both types observed with some substrates suggests a major role for the intermediates in pepsin-catalysed reactions. The results also show that when pig pepsin is used for the digestion of proteins for sequence work, the likelihood of the formation of transpeptidation products is considerable. In this way peptides not present in the original sequence could easily form in a reasonably good yield.

Acyl intermediates in penicillopepsin-catalysed reactions and a discussion of the mechanism of action of pepsins

Penicillopepsin catalyses transpeptidation reactions involving the transfer of the N-terminal amino acids of suitable substrates via covalent acyl intermediates to acceptor peptides, usually the substrate. The major products obtained when Phe-Tyr-Thr-Pro-Lys-Ala and Met-Leu-Gly were used as substrates were Phe-Phe and Met-Met respectively. With Met-Leu-Gly the tetrapeptide Met-Met-Leu-Gly was observed as probable intermediate. Co-incubation of Leu-Tyr-Leu and Phe-Tyr-Thr-Pro-Lys-Ala led to the formation of Leu-Phe and Phe-Leu as well as Leu-Leu and Phe-Phe. No reaction was observed with tripeptides in which the first or second amino acid is glycine. It appears that two amino aicds with large hydrophobic residues are needed for the transpeptidation reaction. Nucleophilic compounds other than peptides, such as hydroxylamine, aliphatic alcohols and dinitrophenylhydrazine, were not acceptors for the acyl group. Leucine, phenylalanine and leucine methyl ester also had no effect on the reaction. The transpeptidation reaction proceeded readily at pH 3.6 and 4.7. At pH 6.0 the reaction was slow and at pH 1.9 little or no transpeptidation was observed. Porcine pepsin catalyses similar transpeptidation reactions. Sequence studies show that porcine pepsin and penicillopepsin are homologous. The present study also suggests that they have a very similar mechanism. Evidence available at this time indicates that the mechanism of these enzymes is complex and may be modulated by secondary substrate-enzyme interactions. A hypothesis is presented which proposes that pepsin-catalysed reactions proceed via different covalent intermediates (amino-intermediates or acylintermediates) depending on the nature of the substrate. The possibility that some reactions do not involve covalent intermediates is also discussed.