A 13C-n.m.r. investigation of ionizations within a trypsin-inhibitor complex. Evidence that the pKa of histidine-57 is raised by interaction with the hemiketal oxyanion

Kinetic Studies of the Effect of pH on the Trypsin-Catalyzed Hydrolysis of N-α-benzyloxycarbonyl-l-lysine-p-nitroanilide: Mechanism of Trypsin Catalysis

The pH dependence of the trypsin-catalyzed hydrolysis of N-α-benzyloxycarbonyl-l-lysine p-nitroanilide has been studied at 25 °C. k _cat/K _M was maximal at alkaline pH values but decreased with decreasing pH. k _cat/K _M was dependent on free enzyme pK _a values of 6.75 ± 0.09 and 4.10 ± 0.13, which were assigned to the ionization of the active site histidine-57 and aspartate-189, respectively. Protonation of either group abolished catalytic activity. k _cat is shown to equal the acylation rate constant k ₂ over the pH range studied. k ₂ decreased on the protonation of two groups with pK _a values of 4.81 ± 0.15 and 4.23 ± 0.19. We assign the pK _a of 4.23 to the ionization of the aspartate-189 residue and the pK _a of 4.81 to the oxyanion of the tetrahedral intermediate formed during acylation. We conclude that during acylation, breakdown of the catalytic tetrahedral intermediate is rate-limiting and that there is a strong interaction between the imidazolium ion of histidine-57 and the oxyanion of the catalytic tetrahedral intermediate, which perturbs their pK _a values. From the pH dependence of k ₃, we conclude that deacylation depends on a pK _a of 6.41 ± 0.22 and that the ionization of the carboxylate group of aspartate-189 does not have a significant effect on the rate of deacylation (k ₃). A catalytic mechanism is proposed to explain the pH dependence of catalysis.

A new lysine derived glyoxal inhibitor of trypsin, its properties and utilization for studying the stabilization of tetrahedral adducts by trypsin

New trypsin inhibitors Z-Lys-COCHO and Z-Lys-H have been synthesised. Ki values for Z-Lys-COCHO, Z-Lys-COOH, Z-Lys-H and Z-Arg-COOH have been determined. The glyoxal group (-COCHO) of Z-Lys-COCHO increases binding ~300 fold compared to Z-Lys-H. The α-carboxylate of Z-Lys-COOH has no significant effect on inhibitor binding. Z-Arg-COOH is shown to bind ~2 times more tightly than Z-Lys-COOH. Both Z-Lys-13COCHO and Z-Lys-CO13CHO have been synthesized. Using Z-Lys-13COCHO we have observed a signal at 107.4 ppm by 13C NMR which is assigned to a terahedral adduct formed between the hydroxyl group of the catalytic serine residue and the 13C-enriched keto-carbon of the inhibitor glyoxal group. Z-Lys-CO13CHO has been used to show that in this tetrahedral adduct the glyoxal aldehyde carbon is not hydrated and has a chemical shift of 205.3 ppm. Hemiketal stabilization is similar for trypsin, chymotrypsin and subtilisin Carlsberg. For trypsin hemiketal formation is optimal at pH 7.2 but decreases at pHs 5.0 and 10.3. The effective molarity of the active site serine hydroxyl group of trypsin is shown to be 25300 M. At pH 10.3 the free glyoxal inhibitor rapidly (t1/2=0.15 h) forms a Schiff base while at pH 7 Schiff base formation is much slower (t1/2=23 h). Subsequently a free enol species is formed which breaks down to form an alcohol product. These reactions are prevented in the presence of trypsin and when the inhibitor is bound to trypsin it undergoes an internal Cannizzaro reaction via a C2 to C1 alkyl shift producing an α-hydroxycarboxylic acid.

Ionisations within a subtilisin-glyoxal inhibitor complex

Z-Ala-Pro-Phe-glyoxal (where Z is benzyloxycarbonyl) has been shown to be a competitive inhibitor of subtilisin with a K(i)=2.3+/-0.2 microM at pH 7.0 and 25 degrees C. Using Z-Ala-Pro-[2-(13)C]Phe-glyoxal we have detected a signal at 107.3 ppm by (13)C NMR, which we assign to the tetrahedral adduct formed between the hydroxy group of serine-195 and the (13)C-enriched keto-carbon of the inhibitor. The chemical shift of this signal is pH independent from pH 4.2 to 7.0 and we conclude that the oxyanion pK(a)<3. This is the first observation of oxyanion formation in a reversible subtilisin-inhibitor complex. The inhibitor is bound as a hemiketal which is in slow exchange with the free inhibitor. Inhibitor binding depends on a pK(a) of approximately 6.5 in the free enzyme and on a pK(a)<3.0 when the inhibitor is bound to subtilisin. Protonation of the oxyanion promotes the disassociation of the inhibitor. We show that oxyanion formation cannot be rate limiting during catalysis and that subtilisin stabilises the oxyanion by at least 45.1 kJ mol(-1). We conclude that if the energy required for oxyanion stabilisation is utilised as binding energy in drug design it should make a significant contribution to inhibitor potency.

13C-NMR study of the inhibition of delta-chymotrypsin by a tripeptide-glyoxal inhibitor

A new inhibitor, Z-Ala-Pro-Phe-glyoxal (where Z is benzyloxycarbonyl),has been synthesized and shown to be a competitive inhibitor of delta-chymotrypsin, with a K(i) of 25+/-8 nM at pH 7.0 and 25 degrees C. Z-Ala-Pro-[1-(13)C]Phe-glyoxal and Z-Ala-Pro-[2-(13)C]Phe-glyoxal have been synthesized, and (13)C-NMR has been used to determine how they interact with delta-chymotrypsin. Using Z-Ala-Pro-[2-(13)C]Phe-glyoxal we have detected a signal at 100.7 p.p.m. which we assign to the tetrahedral adduct formed between the hydroxy group of Ser-195 and the (13)C-enriched keto-carbon of the inhibitor. This signal is in a pH-dependent slow exchange with a signal at 107.6 p.p.m. which depends on a pK(a) of approximately 4.5, which we assign to oxyanion formation. Thus we are the first to detect an oxyanion pK(a) in a reversible chymotrypsin-inhibitor complex. A smaller titration shift of 100.7 p.p.m. to 103.9 p.p.m. with a pK(a) of approximately 5.3 is also detected due to a rapid exchange process. This pK(a) is also detected with the Z-Ala-Pro-[1-(13)C]Phe-glyoxal inhibitor and gives a larger titration shift of 91.4 p.p.m. to 97.3 p.p.m., which we assign to the ionization of the hydrated aldehyde hydroxy groups of the enzyme-bound inhibitor. Protonation of the oxyanion in the oxyanion hole decreases the binding efficiency of the inhibitor. From this decrease in binding efficiency we estimate that oxyanion binding in the oxyanion hole reduces the oxyanion pK(a) by 1.3 pK(a) units. We calculate that the pK(a)s of the oxyanions of the hemiketal and hydrated aldehyde moieties of the glyoxal inhibitor are both lowered by 6.4-6.9 pK(a) units on binding to chymotrypsin. Therefore we conclude that oxyanion binding in the oxyanion hole has only a minor role in decreasing the oxyanion pK(a). We also investigate how the inhibitor breaks down at alkaline pH, and how it breaks down at neutral pH in the presence of chymotrypsin.

13C NMR study of how the oxyanion pKa values of subtilisin and chymotrypsin tetrahedral adducts are affected by different amino acid residues binding in enzyme subsites S1-S4

A range of substrate-derived chloromethane inhibitors have been synthesized which have one to four amino acid residues. These have been used to inhibit both subtilisin and chymotrypsin. Using 13C NMR, we have shown that all except one of these inhibitors forms a tetrahedral adduct with chymotrypsin, subtilisin, and trypsin. From the pH-dependent changes in the chemical shift of the hemiketal carbon of the tetrahedral adduct, we are able to determine the oxyanion pKa in the different inhibitor derivatives. Our results suggest that in both the subtilisin and chymotrypsin chloromethane derivatives the oxyanion pKa is largely determined by the type of amino acid residue occupying the S1, subsite while binding in the S2-S4 subsites only has minor effects on oxyanion pKa values. Using free energy relationships, we determine that the different R groups of the amino acid residues binding in the S1 subsite only have minor effects on the oxyanion pKa values. We propose that the lower polarity of the chymotrypsin active site relative to that of the subtilisin active site explains why the oxyanion pKa is higher and more sensitive to the type of chloromethane inhibitor used in the chymotrypsin derivatives than in the subtilisin derivatives.

A 13C-NMR study of the role of Asn-155 in stabilizing the oxyanion of a subtilisin tetrahedral adduct

By removing one of the hydrogen-bond donors in the oxyanion hole of subtilisin BPN, we have been able to determine how it affects the catalytic efficiency of the enzyme and the pKa of the oxyanion formed in a choloromethane inhibitor derivative. Variant 8397 of subtilisin BPN contains five mutations which enhance its stability. Site-directed mutagenesis was used to prepare the N155A mutant of this variant. The catalytic efficiencies of wild-type and variant 8397 are similar, but replacing Asn-155 with alanine reduces catalytic efficiency approx. 300-fold. All three forms of subtilisin were alkylated using benzyloxycarbonylglycylglycyl[2-13C]phenylalanylchloromethane++ + and examined by 13C-NMR. A single signal due to the 13C-enriched carbon was detected in all the derivatives and it was assigned to the hemiketal carbon of a tetrahedral adduct formed between the hydroxy group of Ser-221 and the inhibitor. This signal had chemical shifts in the range 98.3-103.6 p.p.m., depending on the pH. The titration shift of 4.7-4.8 p.p.m. was assigned to oxyanion formation. The oxyanion pKa values in the wild-type and 8397 variants were 6.92 and 7.00 respectively. In the N155A mutant of the 8397 variant the oxyanion pKa increased to 8.09. We explain why such a small increase is observed and we conclude that it is the interaction between the oxyanion and the imidazolium cation of the active-site histidine that is the main factor responsible for lowering the oxyanion pKa.

Determination of the ionization state of the active-site histidine in a subtilisin-(chloromethane inhibitor) derivative by 13C-NMR

Subtilisin BPN' has been alkylated using benzyloxycarbonyl-glycylglycyl[1-13C]phenylalanylchloromethane+ ++. Using difference 13C-NMR spectroscopy a single signal due to the 13C-enriched alpha-methylene carbon of the subtilisin-(chloromethane inhibitor) derivative was detected. No evidence for the denaturation/ autolysis of this derivative was obtained from pH 3.5 to 11.5. However, incubating at pH 12.75 or heating in the presence of SDS at pH 6.9 did denature this derivative. The negative titration shift of the alpha-methylene carbon of the denatured derivatives confirmed that the inhibitor had alkylated N-3 of the imidazole ring of the active-site histidine. The positive titration shift of 3.96 p.p.m. and the pKa of 7.04 obtained from studying the native subtilisin-(chloromethane inhibitor) derivative are assigned to oxyanion formation. We conclude that the pKa of the alkylated histidine residue in the native subtilisin-(chloromethane inhibitor) derivative must be > 12 and that subtilisin preferentially stabilizes the zwitterionic tetrahedral adduct consisting of the oxyanion and the imidazolium ion of the active-site histidine residue. We show that even before the oxyanion is formed the pKa of the active-site histidine must be much greater than that of the oxyanion in the zwitterionic tetrahedral adduct. We discuss the significance of our results for the catalytic mechanism of the serine proteinases.

15N and 1H NMR spectroscopy of the catalytic histidine in chloromethyl ketone-inhibited complexes of serine proteases

The hemiketal hydroxyl groups in chloromethyl ketone (cmk) complexes of trypsin and chymotrypsin have been reported to ionize to the oxyanion with pK(a) values 2-4 pK(a) units below expectations for such a functional group on the basis of the behavior of the hemiketal carbon atom in 13C NMR spectra [Finucane, M. D., & Malthouse, J. P. G. (1992) Biochem. J. 286, 889-900]. The low pK(a) indicates the enzymes selectively stabilize the oxyanion form of the bound inhibitor, and therefore that cmk complexes may be good models of enzyme-mediated transition-state stabilization. However, the 13C NMR studies could not rule out His57 as the titrating group. Here we report the behavior of the ring 15N atoms of His57 in the Ala-Ala-Pro-Val-cmk complex of alpha-lytic protease. Both N(delta 1) and N(epsilon 2) of His57 respond to an ionization with a pK(a) of approximately 7.5, but His57 itself does not titrate as N(epsilon 2) remains alkylated and N(delta 1) remains bonded to a proton over the entire pH range. The species titrating with a pK(a) of approximately 7.5 must therefore be the hemiketal hydroxyl. The results also show that the 1H NMR signal from the proton in the Asp-His hydrogen bond behaves in a characteristic manner in cmk complexes and can be used diagnostically to confirm that His57 does not titrate and to measure the pK(a) of the hemiketal hydroxyl in cmk-protease complexes without resorting to 15N-labeling. We have used the behavior of this signal to directly confirm that His57 does not titrate in the trypsin and chymotrypsin complexes that were the subjects of the original 13C NMR studies.

A study of the stabilization of the oxyanion of tetrahedral adducts by trypsin, chymotrypsin and subtilisin

Subtilisin and delta-chymotrypsin have been alkylated using 2-13C-enriched benzyloxycarbonylglycylglycylphenylalanylchloromethane. A single signal due to the 13C-enriched carbon was detected in both the intact subtilisin and delta-chymotrypsin derivatives. The signal titrated from 98.9 p.p.m. to 103.6 p.p.m. with a pKa value of 6.9 in the subtilisin derivative and it is assigned to a tetrahedral adduct formed between the hydroxy group of serine-221 and the inhibitor. The signal in the delta-chymotrypsin derivative titrated from 98.5 p.p.m. to 103.2 p.p.m. with a pKa value of 8.92 and it is assigned to a tetrahedral adduct formed between the hydroxy group of serine-195 and the inhibitor. In both derivatives the titration shift is assigned to the formation of the oxyanion of the tetrahedral adduct. delta-Chymotrypsin has been inhibited by benzyloxycarbonylphenylalanylchloromethane and two signals due to 13C-enriched carbons were detected. One of these signals titrated from 98.8 p.p.m. to 103.6 p.p.m. with a pKa value of 9.4 and it was assigned in the same way as in the previous delta-chymotrypsin derivative. The second signal had a chemical shift of 204.5 +/- 0.5 p.p.m. and it did not titrate from pH 3.5 to 9.0. This signal was assigned to alkylated methionine-192. We discuss how subtilisin and chymotrypsin could stabilize the oxyanion of tetrahedral adducts.

A study of the stabilization of tetrahedral adducts by trypsin and delta-chymotrypsin

delta-Chymotrypsin has been alkylated by 1-13C- and 2-13C-enriched tosylphenylalanylchloromethane. In the intact inhibitor derivative, signals due to the 1-13C- and 2-13C-enriched carbon atoms have chemical shifts which titrate from 55.10 to 59.50 p.p.m. and from 99.10 to 103.66 p.p.m. respectively with similar pKa values of 8.99 and 8.85 respectively. These signals are assigned to a tetrahedral adduct formed between the hydroxy group of serine-195 and the inhibitor. An additional signal at 58.09 p.p.m. and at 204.85 p.p.m. in the 1-13C- and 2-13C-enzyme-inhibitor derivatives respectively does not titrate when the pH is changed and it is assigned to alkylated methionine-192. On denaturation/autolysis of the 1-13C-enriched enzyme-inhibitor derivative these signals associated with the intact inhibitor derivative are no longer detected, and a new signal, which titrates from 56.28 to 54.84 p.p.m. with a pKa of 5.26, is detected. The titration shift of this signal is assigned to the deprotonation of the imidazolium cation of alkylated histidine-57 in the denatured/autolysed enzyme-inhibitor derivative. Model compounds which form stable hydrates and hemiketals in aqueous solutions have been synthesized. By comparing the 13C titration shifts of these model compounds with those of the 13C enriched trypsin- and delta-chymotrypsin-inhibitor derivatives, we deduce that, in both of the intact enzyme-inhibitor derivatives, the zwitterionic tetrahedral adduct containing the imidazolium cation of histidine-57 and the hemiketal oxyanion predominates at alkaline pH values. It is estimated that in both the trypsin and delta-chymotrypsin-inhibitor derivatives the concentration of this zwitterionic tetrahedral adduct is 10,000-fold greater than it would be in water. We conclude that the pKa of the oxyanion of the hemiketal in the presence of the imidazolium cation of histidine-57 is 7.9 and 8.9 in the trypsin and delta-chymotrypsin-inhibitor derivatives respectively and that the pKa of the imidazolium cation of histidine-57 is greater than 7.9 and greater than 8.9 when the oxyanion is present as its conjugate acid, whereas, when the oxyanion is present, the pKa of the imidazolium cation is greater than 11 in both enzyme-inhibitor derivatives. We discuss how these enzymes preferentially stabilize zwitterionic tetrahedral adducts in the intact enzyme-inhibitor derivatives and how they could stabilize similar tetrahedral intermediates during catalysis. It is suggested that substrate binding could raise the pKa of the imidazolium cation of histidine-57 before tetrahedral-intermediate formation which would explain the enhanced nucleophilicity of the hydroxy group of serine-195.(ABSTRACT TRUNCATED AT 400 WORDS)

A study of the relaxation parameters of a 13C-enriched methylene carbon and a 13C-enriched perdeuteromethylene carbon attached to chymotrypsin

L-1-Chloro-4-phenyl-3-tosylamido[1-13C]butan-2-one (Tos-[1-13C]Phe-CH2Cl) and Tos-[1-13C,2H2]Phe-CH2Cl were prepared and used to alkylate delta-chymotrypsin. The relaxation parameters of the 13C-n.m.r. signal resulting from the alkylation of histidine-57 in both enzyme-inhibitor complexes were determined at 1.88 T and 6.34 T as well as the spin-lattice relaxation times of the backbone alpha-carbon atoms of the unenriched Tos-Phe-CH2-delta-chymotrypsin complex. It is concluded that the species examined do not have significant internal librational motions and that the rotational correlation time of the monomeric enzyme-inhibitor complex is 16.0 +/- 3.2 ns. The signal from the 13C-enriched atom of Tos-[1-13C,2H2]Phe-CH2Cl is split into a quintet (JCD = 23 Hz) whereas in the Tos-[1-13C,2H2]Phe-CH2-delta-chymotrypsin complex the signal from the 13C-enriched inhibitor carbon atom is decoupled. This decoupled signal had linewidths of 16 +/- 3 Hz and 52 +/- 2 Hz at 1.88 T and 6.34 T respectively, whereas linewidths at 40 +/- 2 Hz and 53 +/- 4 Hz were obtained for the same signal in the Tos-[1-13C]Phe-CH2-delta-chymotrypsin complex at 1.88 T and 6.34 T respectively. Therefore whereas deuteration produces a 2.5-fold reduction in linewidth at 1.88 T there is no significant decrease in the linewidth at 6.34 T. This result is explained by using the rigid rotor model, which predicts that the quadrupolar spin-lattice relaxation rate will be faster at low field strengths, resulting in more efficient deuterium decoupling by scalar relaxation of the second kind at lower field strengths. It is also predicted that deuterium decoupling by scalar relaxation will become less efficient as rotational correlation times increase. The consequences of these predictions for the detection of 13C-enriched atomic probes of proteins are discussed. It is also shown that a spin-echo pulse sequence can be used to remove signals due to protonated carbon atoms without attenuating the signal due to deuterated carbon atoms.

Diastereotopic covalent binding of the natural inhibitor leupeptin to trypsin: detection of two interconverting hemiacetals by solution and solid-state NMR spectroscopy

The naturally occurring peptidyl protease inhibitor leupeptin (N-acetyl-L-leucyl-L-leucyl-L-argininal) has been prepared labeled with 13C at the argininal carbonyl. 13C chemical shift data for the trypsin-leupeptin inhibitor complex in the pH range 3.0-7.6 reveal the presence of two pH-dependent covalent complexes, suggestive of two interconverting diastereomers at the new asymmetric tetrahedral center created by covalent addition of Ser195 to either side of the 13C-enriched aldehyde of the inhibitor. At pH 7 two signals are observable at delta 98.8 and delta 97.2 (84:16 ratio), while at pH 3.0 the latter signal predominates. In the selective proton 13C-edited NOE spectrum of the major diastereomer at pH 7.4, a strong NOE is observed between the hemiacetal proton of the inhibitor and the C2 proton of His57 of the enzyme, thus defining the stereochemistry of the high pH complex to the S configuration in which the hemiacetal oxygen resides in the oxyanion hole. pH titration studies further indicate that the 13C chemical shift of the S diastereomer follows a titration curve with a pKa of 4.69, the magnitude of which is consistent with direct titration of the hemiacetal oxygen. Similar pH-dependent chemical shifts were obtained by using CPMAS 13C NMR, providing evidence for the existence of the same diastereomeric equilibrium in the solid state.

Inactivation of the RTEM-1 cysteine beta-lactamase by iodoacetate. The nature of active-site functional groups and comparisons with the native enzyme

The pH-rate profile for inactivation of the RTEM-1 cysteine beta-lactamase by iodoacetate supports previous evidence [Knap & Pratt (1989) Proteins Struct. Funct. Genet. 6, 316-323] for the activation of the active-site thiol group by adjacent functional groups. The enhanced reactivity of iodoacetate, with respect to that of iodoacetamide, suggests the influence of a positive charge in the active site. The reactivity of iodoacetate is not affected by dissociation of an active-site functional group of pKa 6.7, which increases the reactivity of neutral reagents, probably because of a compensation phenomenon; it is, however, lost on dissociation of an acid of pKa 8.1. It is concluded that the active cysteine beta-lactamase has four functional groups at the active site, one nucleophilic thiolate of Cys-70, one neutral acid (most probably the carboxy group of Glu-166, from the crystal structures) and two cationic residues (most probably Lys-73 and Lys-234). A comparison of these results with the pH-dependence of reactivity of the native RTEM-2 beta-lactamase suggests that the active form of the latter enzyme is also monocationic, although the nucleophile (Ser-70) is likely to be neutral in this case and the carboxylic acid dissociated. A mechanism of class A beta-lactamase catalysis is discussed where the Glu-166 carboxylate acts as a general base/acid catalyst and Lys-73 is principally required for electrostatic stabilization of the anionic tetrahedral intermediate.

A 13C-n.m.r. investigation of the ionizations within an inhibitor--alpha-chymotrypsin complex. Evidence that both alpha-chymotrypsin and trypsin stabilize a hemiketal oxyanion by similar mechanisms

13C-n.m.r. was used to investigate the structure of the inhibitor enzyme complex formed when alpha-chymotrypsin is alkylated by L-1-chloro-4-phenyl-3-tosylamido-[2-13C]butan-2-one. Two signals are detected. The one at 204.82 +/- 0.11 p.p.m. does not titrate from pH 3 to 9 and is assigned to alkylated methionine-192. The second signal titrates from 99.08 p.p.m. to 103.44 p.p.m. with pKa 8.67. This signal is assigned to a tetrahedral adduct formed between the hydroxy group of serine-195 and the inhibitor. The titration shift of the tetrahedral adduct is ascribed to the ionization of the hemiketal hydroxy group. It is proposed that the resulting oxyanion is stabilized by interaction with the imidazolium ion of histidine-57. It is argued that this interaction must raise the pKa of at least 70% of histidine-57 to greater than 11. On denaturation/autolysis of the inhibitor-enzyme complex neither of the signals associated with the intact complex is detected, but a new signal is observed that titrates from 203.52 p.p.m. to 206.08 p.p.m. with pKa = 5.27. This titration shift is assigned to the ionization of the imidazolium ion of alkylated histidine, confirming that the inhibitor has alkylated histidine-57. The significance of these results for the catalytic mechanism of the serine proteinases is discussed.