Comparison of alpha-chymotrypsin and subtilisin BPN': size and specificity of the active site

Influence of Leaving-Group Electronic Effect on alpha-Chymotrypsin: Catalytic Constants of Specific Substrates

Rate constants and binding constants for the alpha-chymotrypsin-catalyzed hydrolysis of N-acetyltyrosine, tryptophan, and phenylalanine anilides are presented. Both k(cat) and K(m) are independent of electronic effects in the substrate over a range of 9.8 orders of magnitude (as measured by pK of the leaving group). Similarly, K(m) is independent of charge and orientation about the alpha-carbon for various substrates and pseudo-substrates. These results are not consistent with the pretransition state protonation hypothesis; instead, they are discussed in terms of a tetrahedral intermediate that is thermodynamically less stable than the Michaelis complex.

Extremely high alkaline protease from a deep-subsurface bacterium, Alkaliphilus transvaalensis

A new high-alkaline protease (ALTP) was purified to homogeneity from a culture of the strictly anaerobic and extremely alkaliphilic Alkaliphilus transvaalensis. The molecular mass was 30 kDa on sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The enzyme showed the maximal caseinolytic activity higher than pH 12.6 in KCl-NaOH buffer at 40 degrees C. Hydrolysis of the oxidized insulin B-chain followed by mass spectrometric analysis of the cleaved products revealed that as many as 24 of the total 29 peptide bonds are hydrolyzed in a block-cutting manner, suggesting that ALTP has a widespread proteolytic functions. Calcium ion had no effect on the activity and stability of ALTP, unlike known subtilisins. The deduced amino acid sequence of the enzyme comprised 279 amino acids plus 97 prepropeptide amino acids. The amino acid sequence of mature ALTP was confirmed by capillary liquid chromatography coupled to tandem mass spectrometry, which was the 93% coverage of the deduced amino acid sequence. The mature enzyme showed moderate homology to subtilisin LD1 from the alkaliphilic Bacillus sp. strain KSM-LD1 with 64% identity, and both enzymes formed a new subcluster at an intermediate position among true subtilisins and high-alkaline proteases in a phylogenetic tree of subtilase family A. ALTP is the first high-alkaline protease reported from a strict anaerobe in this family.

Macromolecular Chromogenic Substrates for Measuring Proteinase Activity

Background: Proteinase activities are often measured using chromogenic substrates that are much smaller than physiological substrates.

Methods: The hydrodynamic size of macromolecular substrates (macrosubstrates) prepared by linking small chromogenic substrates to polyethylene glycol was determined by gel filtration. Efficiency of macrosubstrate cleavage by proteinases and α2-macroglobulin-proteinase complexes was monitored spectrophotometrically.

Results: Macrosubstrates had hydrodynamic radii of ∼20 Å, similar to proteins with a molecular weight of 18 000. Different macrosubstrates served as efficient substrates for chymotrypsin, trypsin, and thrombin. Linking small substrates to a polymer variably affected substrate efficiency, with the impact on activity ranging from a 60-fold decrease to a 30-fold increase. Proteinases complexed with α2-macroglobulin had ∼10-fold lower activity vs macrosubstrates than small substrates.

Conclusions: Macrosubstrates are efficient substrates that allow decreased measurement of sterically hindered proteinase molecules such as α2-macroglobulin-proteinase complexes. Thus, macrosubstrates may provide more accurate functional assays of proteinases such as coagulation factors.

Dissecting the catalytic triad of a serine protease

Serine proteases are present in virtually all organisms and function both inside and outside the cell; they exist as two families, the 'trypsin-like' and the 'subtilisin-like', that have independently evolved a similar catalytic device characterized by the Ser, His, Asp triad, an oxyanion binding site, and possibly other determinants that stabilize the transition state (Fig. 1). For Bacillus amyloliquefaciens subtilisin, these functional elements impart a total rate enhancement of at least 10(9) to 10(10) times the non-enzymatic hydrolysis of amide bonds. We have examined the catalytic importance and interplay between residues within the catalytic triad by individual or multiple replacement with alanine(s), using site-directed mutagenesis of the cloned B. amyloliquefaciens subtilisin gene. Alanine substitutions were chosen to minimize unfavourable steric contacts and to avoid imposing new charge interactions or hydrogen bonds from the substituted side chains. In contrast to the effect of mutations in residues involved in substrate binding, the mutations in the catalytic triad greatly reduce the turnover number and cause only minor effects on the Michaelis constant. Kinetic analyses of the multiple mutants demonstrate that the residues within the triad interact synergistically to accelerate amide bond hydrolysis by a factor of approximately 2 X 10(6).

Crystal structure at 2.6 A resolution of the complex of subtilisin BPN' with streptomyces subtilisin inhibitor

The crystal structure of the complex of a bacterial alkaline serine proteinase, subtilisin BPN', with its proteinaceous inhibitor SSI (Streptomyces subtilisin inhibitor) was solved at 2.6 A resolution. Compared with other similar complexes involving serine proteinases of the trypsin family, the present structure is unique in several respects. (1) In addition to the usual antiparallel beta-sheet involving the P1, P2 and P3 residues of the inhibitor, the P4, P5 and P6 residues form an antiparallel beta-sheet with a previously unnoticed chain segment (residues 102 through 104, which was named the S4-6 site) of subtilisin BPN'. (2) The S4-6 site does not exist in serine proteinases of the trypsin family, whether of mammalian or microbial origin. (3) Global induced-fit movement seems to occur on SSI: a channel-like structure in SSI where hydrophobic side-chains are sandwiched between two lobes becomes about 2 A wider upon complexing with subtilisin. (4) The complex is most probably a Michaelis complex, as in most of the other complexes. (5) The main role of the "secondary contact region" of SSI seems to be to support the reactive site loop ("primary contact region"). Steric homology of the two contact regions between the inhibitors of the SSI family and the pancreatic secretory trypsin inhibitor-ovomucoid inhibitor family is so high that it seems to indicate divergent evolutionary processes and to support the general notion as to the relationship of prokaryotic and eukaryotic genes put forward by Doolittle (1978).

Kinetic studies on the chymotrypsin A alpha-catalyzed hydrolysis of a series of N-acetyl-L-phenylalanyl peptides

A series of N-acetyl-L-phenylalanyl peptides of general formula Ac-Phe-(Gly)n-NH2 (n = 0-2) has been synthesized to study the effect of leaving group chain length on the efficiency of chymotrypsin A alpha amidase and peptidase activities. The effect upon catalysis of hydrophobic side chains on the leaving group was investigated using similar substrates with one of the glycine residues selectively substituted by an alanine residue as in Ac-Phe-Ala-NH2, Ac-Phe-Ala-Gly-NH2, and Ac-Phe-Gly-Ala-NH2. Values of kcat and Km have been obtained from kinetic measurements at pH 8.00 and 25 degrees C. The results are shown to be consistent with binding schemes postulated from published model building studies. The catalytic reactions were studied over a range of temperature (15-35 degrees C) and in each case the Arrhenius law was obeyed. It was thus possible to obtain meaningful values for the thermodynamic functions of activation for the acylation step of the catalytic reaction. The results are shown to confirm the findings of postulated binding schemes but indicate that conclusions drawn from kinetic measurements at a single temperature may sometimes be misleading.

Kinetics of subtilisin and thiolsubtilisin

Subtilisin is a bacterial serine protease with a broad specificity in the S1 subsite. It has been very extensively studied using a variety of kinetic and physical techniques. A chemical derivative, thiolsubtilisin, has been subjected to similar studies in order to analyze the effects of the OH to SH conversion on enzyme activity. The native structure of thiolsubtilisin is indicated by a variety of physical techniques. Oligopeptides bind nearly equally well to both enzymes, and a peptide chloromethylketone is much more reactive to thiolsubtilisin than to subtilisin. Both enzymes have a similar level of activity towards activated nonspecific amides and esters. However, thiolsubtilisin is inactive towards highly specific peptide amides and esters. Thiolsubtilisin also does not show good binding to boronic and arsonic acids. The observation that these transition state analog inhibitors bind poorly to thiolsubtilisin while other compounds bind nearly equally well to both enzymes suggests that thiolsubtilisin may not be able to stabilize the transition state during acylation by specific substrates.

Primary structure of porcine heart citrate synthase

The sequence of 437 amino acid residues of porcine heart citrate synthase [citrate oxaloacetate-lyase (pro-3S-CH2COO leads to acetyl-CoA), EC 4. 1. 3. 7] has been determined by the alignment of fragments generated by cleavage with cyanogen bromide and with trypsin. Isolation of the peptides was facilitated by recent developments in the high-performance liquid chromatography of peptide mixtures. The alignment of these peptides was consistent with that previously deduced from fragments derived by restricted cleavage of citrate synthase by limited proteolysis and cleavage of aspartyl-prolyl bonds and asparaginyl-glycyl bonds. The enzyme contains a modified amino acid, trimethyllysine, at residue 368, showing that the enzyme is subjected to post-translational modification.

The kinetics of hydrolysis of some extended N-aminoacyl-L-phenylalanine methyl esters by bovine chymotrypsin A-alpha. Evidence for enzyme subsite S5

A series of N-acetylated peptide methyl esters of general formula N-acetyl-(glycyl)n-L-phenylalanine methyl ester (n = 0--3) has been synthesized to study the effect of varying aminoacyl chain length on the efficiency of chymotrypsin A alpha (EC 3.4.21.1) catalysed ester hydrolysis. Values of kcat and Km for each substrate have been obtained from kinetic measurements at pH 8.00 and 25.0 degrees C. It has been found that for the first three members of the series (n = 0--2) there is an increase in kcat value as the aminoacyl chain length is increased. However, the kinetic constants (kcat and Km) for the third (n = 2) and fourth (n = 3) members of the series were found to be very similar. These results are shown to be consistent with a substrate binding scheme proposed for the isomeric enzyme chymotrypsin A gamma. The enzyme-catalysed reactions were also investigated over a range of temperature (15--35 degrees C). In each case the Arrhenius law was obeyed, within experimental error, and evaluation of meaningful values for the thermodynamic functions of activation (delta H++ and delta S++) was possible with certain assumptions. In contrast to the similarly of kinetic constants found for the third and fourth members of the substrate series, the corresponding values of delta H++ and delta S++ were markedly different. These results, together with those for the first two members of the series are interpreted in terms of a model binding system which is consistent with the existence of further enzyme subsites in the S4--S5 region.

Limited proteolysis of pig heart citrate synthase by subtilisin, chymotrypsin, and trypsin

Pig heart citrate synthase was subjected to limited proteolytic attack by subtilisin, chymotrypsin, and trypsin in the presence of palmitoyl-CoA. Initial proteolysis by all three proteolytic enzymes resulted in cleavage of the monomeric subunit (Mr 45 000 +/- 3000) into a large (Mr 35 000-38 500) and a small (Mr 9000 +/- 3000) into a large (Mr 35 000-38 500) and a small (Mr 9000-12 000) fragment. Further proteolysis of the large subunit produced a secondary fragment (Mr 31 000-36 000). The small (Mr 9000-12 000) fragment was stable in the presence of subtilisin but was substantially degraded by both chymotrypsin and trypsin. The actual molecular weight of fragments varied with the choice of the proteolytic enzyme. Limited proteolysis was absolutely dependent on the presence of palmitoyl-CoA and resulted in complete inhibition of the catalytic activity of the enzyme. Citrate, ammonium sulfate, and especially oxaloacetate provided complete protection against proteolysis whereas acetyl-CoA, CoASH, NADH, and ATP were ineffective. Reaction of rabbit anti-citrate synthase with citrate synthase and its proteolytic fragments indicated that the main antigenic region lay primarily in the small fragment. The products of subtilisin cleavage were isolated by gel filtration under denaturing conditions. The large (Mr 35 000-38 500) fragment contained the amino-terminal (approximately)336 amino acids and the small fragment contained the remaining carboxyl-terminal amino acids. The results are discussed in relation to the structure of citrate synthase.

Active centers of alpha-chymotrypsin and of Streptomyces griseus proteases 1 and 3. S2-P2 enzyme-substrate interactions

A number of peptides of the general formula Ac-Pro-Ala-X-Phe-NH2, where X = Gly, Ala, Leu, Phe or Pro, have been synthesized for the study of S2-P2 enzyme-substrate interactions in three serine proteases: alpha-chymotrypsin and Streptomyces griseus proteases 1 and 3. All three enzymes interacted favorably with those peptides with hydrophobic, non-aromatic, P2 amino acid residues, leucine being optimal. The increase in kcat/Km on going from the P2 glycine to the P2 leucine peptide was 30-fold in alpha-chymotrypsin and greater than 150-fold and 350-fold in the Streptomyces enzymes, being due to both increased affinities and higher acylation rates. Hydrophobic S2-P2 interactions, particularly in S. griseus proteases 1 and 3, appear to be the most important enzyme-substrate interactions apart from S1-P1. The kinetic data is discussed in relation to the tertiary structures of the active centers of the enzymes.

alpha-Chymotrypsin as the catalyst for peptide synthesis

alpha-Chymotrypsin (EC 3.4.21.1)-catalysed syntheses of peptides were performed with various N-acylated amino acid or peptide esters as donors, and amino acid derivatives, peptides or their derivatives as acceptors. Under optimal conditions the synthesis was almost quantitative. As acceptor nucleophiles, free amino acids or the ester derivatives were inadequate, but amino acid amides or hydrazides, di- or tri-peptides, or the amides, hydrazides and esters of the peptides were useful. The nucleophile specificity for synthesis was markedly similar to the leaving-group specificity in hydrolysis; hydrophobic or bulky amino acid residues were most effecient at both P1' and P2' positions [notation of Schechter & Berger (1967) Biochem. Biophys. Res. Commun. 27, 157-162], but L-proline as well as D-amino acid residues were the worst choices. The synthesis was further dependent on the solubility of the products synthesized; a higher yield of products was expected with lower solubility. As donor esters, good substrates were all useful. Accordingly, fragment condensation was possible by using N-acylated peptide esters and various peptides. The present study suggested that alpha-chymotrypsin may become a useful tool for peptide synthesis.

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.

Secondary and conformational specificities of trypsin and chymotrypsin

Specific and non-specific trypsin substrates of known structure have been examined for common features. This analysis suggests that trypsin has a specificity for a particular conformation near the scissile bond which I denote as a conformational specificity. This conformation is a bent left-handed helix at the third and fourth (P3 and P4) amino acid positions toward the amino terminus from the scissile bond which I denote as a conformational specificity. This conformation is a bent left-handed show a high frequency of proline and glycine at these positions consistent with the left-handed helical conformation. This apparent secondary specificity for a particular substrate residue other than that at the primary position is not related to the nature of the residues at the third and fourth positions. Rather, these residues determine the bend of left-handed helix which has the effect of exposing main chain hydrogen-bonding groups of the substrate peptide chain to hydrogen-bonding groups on the enzyme. Thus, the secondary specificity of trypsin is not sequence-specific, but is for peptide main chain in the third and fourth positions and is determined by the tertiary structure of the substrate. This hypothesis for conformational and secondary specificity in trypsin can be extended to chymotrypsin. It also provides a means for the regulation of certain processes in vivo catalyzed by other proteases.

Subsite mapping of enzymes. Depolymerase computer modelling

We have developed a depolymerase computer model that uses a minimization routine. The model is designed so that, given experimental bond-cleavage frequencies for oligomeric substrates and experimental Michaelis parameters as a function of substrate chain length, the optimum subsite map is generated. The minimized sum of the weighted-squared residuals of the experimental and calculated data is used as a criterion of the goodness-of-fit for the optimized subsite map. The application of the minimization procedure to subsite mapping is explored through the use of simulated data. A procedure is developed whereby the minimization model can be used to determine the number of subsites in the enzymic binding region and to locate the position of the catalytic amino acids among these subsites. The degree of propagation of experimental variance into the subsite-binding energies is estimated. The question of whether hydrolytic rate coefficients are constant or a function of the number of filled subsites is examined.

The active centers of Streptomyces griseus protease 3 and alpha-chymotrypsin. Enzyme-substrate interactions beyond subsite S'1

A series of N-acetylated tetra- to heptapeptide amides has synthesized for the study of enzyme-substrate interactions beyond the S1' subsite in Streptomyces griseus Protease 3 (SGP3) and alpha-chymotrypsin (EC 3.4.21.1). Evidence was obtained that S2'-P2' enzyme-substrate interactions can play a significant role for the rate of substrate hydrolysis in both enzymes. No important interaction could be demonstrated beyond the nitrogen atom of residue P3'. This provides supplementary evidence that the active site of SGP3 extends over 6-7 subsites and that of alpha-chymotrypsin over 5-6 subsites. SGP3 is a considerably more efficient protease than alpha-chymotrypsin, kcat/Km being approximately 5-10(6) S-1-M-1 for the best substrates, thus being about 100 times higher than for alpha-chymotrypsin. However, an analysis of the kinetic data indicates that, for both enzymes, the acylation rates for the best peptide substrates approach their deacylation rates.

Subsite mapping of enzymes: collecting and processing experimental data--a case study of an amylase-malto-oligosaccharide system

Two research groups have independently developed the theory and experimental methodology for quantitatively assessing substrate monomer-subsite binding-energies for depolymerases. When the two approaches are applied to the same enzyme-substrate system they yield surprisingly divergent results. This paper outlines the application of the two approaches to an amylase-maltooligosaccharide system and points out the more important areas of disagreement. We show that by proper data-management, the conflicts between the tow laboratories are basically resolved. The complexities of the subsite model demand extensive data-gathering and exacting data-processing and verification that the computed model-parameters can faithfully reproduce the experimental data.

Regulation of neutral protease productivity in Bacillus subtilis: transformation of high protease productivity

A transformable strain of Bacillus subtilis 6160, a derivative of B. subtilis 168, produces three kinds of casein hydrolytic enzymes (alkaline protease, neutral protease, and esterase) in a culture medium. B. natto IAM 1212 produces 15 to 20 times as much total proteolytic activity as does B. subtilis. Extracellular proteases produced by the two strains were separated into each enzyme fraction by diethylaminoethyl-Sephadex A-50 column chromatography. The difference in the total protease activities of extracellular proteases between the two strains was due to the amount of neutral protease. The ratios of neutral protease activity to alkaline protease activity (N/A) were 1.1 in B. subtilis 6160 and 13.0 in B. natto IAM 1212. Enzymological and immunological properties of alkaline protease and neutral protease obtained from the two strains were quite similar or identical, respectively. Specific activities measured by an immunological analysis of the two neutral proteases against casein were also equal. A genetic character of high protease productivity in B. natto IAM 1212 was transferred to B. subtilis 6160 by the deoxyribonucleic acid-mediated transformation. Among 73 transformants that acquired high protease productivity, 69 produced a higher amount of neutral protease and the ratios of N/A were changed to 15 to 60. Three other strains were transformed in the productivity of neutral protease and alpha-amylase simultaneously, and one showed considerable change in the production of alkaline protease and neutral protease. The specific activities (casein hydrolytic activities/enzyme molecules) of neutral proteases from the representative four transformants were equal to those of the two parental strains. These results suggested the presence of a specific gene(s) that participated in the productivity of neutral protease in B. subtilis.