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HLA-DM (DM) plays a critical role in Ag presentation to CD4 T cells by catalyzing the exchange of peptides bound to MHC class II molecules. Large lateral surfaces involved in the DM:HLA-DR (DR) interaction have been defined, but the mechanism of catalysis is not understood. In this study, we describe four small molecules that accelerate DM-catalyzed peptide exchange. Mechanistic studies demonstrate that these small molecules substantially enhance the catalytic efficiency of DM, indicating that they make the transition state of the DM:DR/peptide complex energetically more favorable. These compounds fall into two functional classes: two compounds are active only in the presence of DM, and binding data for one show a direct interaction with DM. The remaining two compounds have partial activity in the absence of DM, suggesting that they may act at the interface between DM and DR/peptide. A hydrophobic ridge in the DMβ1 domain was implicated in the catalysis of peptide exchange because the activity of three of these enhancers was substantially reduced by point mutations in this area.

To probe the mechanistic origins of convex Eyring plots that have been observed for alpha-chymotrypsin (alpha-CT)-catalyzed hydrolysis of specific p-nitroanilide substrates [Case, A., and Stein, R. L. (2003) Biochemistry 42, 3335-3348], we determined the temperature-dependence of (15)N-kinetic isotope effects for the alpha-CT-catalyzed hydrolysis of N-succinyl-Phe p-nitroanilide (Suc-Phe-pNA). To provide an interpretational context for these enzymatic isotope effects, we also determined 15N-KIE for alkaline hydrolysis of p-nitroacetanilide. In 0.002 and 2 N hydroxide (30 degrees C), 15N-KIE values are 1.035 and 0.995 (+/-0.001), respectively, and are consistent with the reported [HO-]-dependent change in rate-limiting step from leaving group departure from an anionic tetrahedral intermediate in dilute base, to hydroxide attack in concentrated base. For the alpha-CT-catalyzed hydrolysis of Suc-Phe-pNA, 15N-KIE is on kc/Km and thus reflects structural features of transition states for all reaction steps up to and including acylation of the active site serine. The isotope effect at 35 degrees C is 1.014 (+/-0.001) and suggests that in the transition state for this reaction, departure of leaving group from the tetrahedral intermediate is well advanced. Significantly, 15N-KIE does not vary over the temperature range 5-45 degrees C. This result eliminates one of the competing hypotheses for the convex Eyring plot observed for this reaction, that is, a temperature-dependent change in rate-limiting step within the chemical manifold of acylation, but supports a mechanism in which an isomerization of enzyme conformation is coupled to active site chemistry. We finally suggest that the near absolute temperature-independence of 15N-KIE may point to a unique transition state for this process.

Serine proteases catalyze the hydrolysis of amide bonds of their protein and peptide substrates through a mechanism involving the intermediacy of an acyl-enzyme. While the rate constant for formation of this intermediate, k(2), shows a dramatic dependence on peptide chain length, the rate constant for the intermediate's hydrolysis is relatively insensitive to chain length. To probe the mechanistic origins of this phenomenon, we determined temperature dependencies and solvent isotope effects for the alpha-chymotrypsin-catalyzed hydrolysis of Suc-Phe-pNA (K(s) = 1 mM, k(2) = 0.04 s(-)(1), and k(3) = 11 s(-)(1)), Suc-Ala-Phe-pNA (K(s) = 4 mM, k(2) = 0.9 s(-)(1), and k(3) = 42 s(-)(1)), and Suc-Ala-Ala-Pro-Phe-pNA (K(s) = 0.1 mM, k(2) = 98 s(-)(1), and k(3) = 71 s(-)(1)). We found that while the van't Hoff plots for K(s) and the Eyring plots for k(3) are linear for all three reactions, the Eyring plots for k(2) are convex, indicating that the process governed by k(2) is complex, possibly involving a coupling between active site chemistry and protein conformational isomerization. This interpretation is strengthened by solvent isotope effects on k(2) that are largely temperature-independent. Furthermore, the dependence of k(2) on peptide length is manifested entirely in the enthalpy of activation, suggesting a mechanism of catalysis by distortion. Taken together, this analysis of acylation suggests that extended substrates which can engage in subsite interactions are able to efficiently trigger the coupling mechanism between chemistry and a conformational isomerization that distorts the substrate and thereby promotes nucleophilic attack.

High molecular weight penicillin-binding proteins (PBPs) are bifunctional enzymes that build bacterial cell walls from the glycopeptide lipid II [GlcNAc-MurNAc(L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)-pyrophosphate-undecaprenol] by a process involving disaccharide polymerization and peptide cross-linking. The latter reaction involves acyl-transfer chemistry in which the penultimate (D)Ala first acylates the active-site serine, with release of the terminal (D)Ala, and is then transferred to the epsilon-amine of a Lys on a neighboring pentapeptide chain. These enzymes also catalyze hydrolysis of specific thioester substrates and acylation by beta-lactam antibiotics. In this paper, we explore these latter two reactions and report mechanistic experiments on the reaction of Streptococcus pneumoniae PBP 2x with N-benzoyl-(D)Ala-thioacetic acid [Bz-(D)Ala-(S)Gly] and penicillin G. For these experiments, we used PBP 2x, a soluble form of PBP 2x in which the transmembrane domain was deleted. The following results are significant: (1) pH dependencies for acylation of PBP 2x by penicillin G and Bz-(D)Ala-(S)Gly are identical, suggesting that the same ionizable residues are involved in both reactions and that these residues play the same catalytic role in the two processes. On the basis of these results, we propose a mechanistic model that is also consistent with recently published structural data [Gordon, E., et al. (2000) J. Mol. Biol. 299, 477-485]. (2) Pre-steady-state experiments for the PBP 2x-catalyzed hydrolysis of Bz-(D)Ala-(S)Gly at pH 6.5 indicate that k(c) is principally rate-limited by acylation with some contribution from deacylation. The contribution of these steps to rate limitation is pH-dependent, with acylation entirely rate-limiting at pH values less than 5.5 and deacylation principally rate-limiting above pH 8.5. (3) Results of solvent isotope effect and proton inventory experiments for acylation suggest a complex process that is at least partially rate-limited by chemistry with some involvement of changes in solvation and/or enzyme conformation. (4) Analysis of activation parameters suggests that during the acylation of PBP 2x by penicillin G the inherent chemical stability of penicillin's amide bond, as manifested in the enthalpy of activation, is offset by a favorable entropy term that reflects penicillin's rotationally constrained bicyclic system, which presumably allows a less energetically demanding entry into the transition state for acylation.

We have studied the mechanism of inhibition of the recombinant Rhodococcus proteasome by four different chemical classes of active site-directed small molecule inhibitors.Clasto-lactacystin β-lactone is a time-dependent inhibitor of the Rhodococcusproteasome’s ability to hydrolyze Suc-Leu-Leu-Val-Tyr-AMC, a substrate for this proteasome’s single type of active site, and proceeds with ak inact/[I] of 1,700m −1 s−1. Using peptide mapping of tryptic digests, LC/MS, and amino acid sequence analysis, we have established that the Oγ of the hydroxyl group on the N-terminal threonine of the β-subunit is the sole modification made by the β-lactone. Active site titrations of the Rhodococcus proteasome with reversible peptide aldehydes show the expected stoichiometry of one inhibitor molecule per β-subunit. Prior modification with β-lactone completely abrogates the binding of peptidyl boronic acid inhibitors, suggesting that these inhibitors also inactivate the enzyme by reacting with the Oγ moiety on Thr1. High performance liquid chromatography analysis of peptidyl vinyl sulfone-modified intactRhodococcus proteasome β-subunit and its tryptic peptides suggests that the peptidyl vinyl sulfone modifies a residue in the N-terminal 20 amino acids. This modification is also blocked by prior treatment with β-lactone.

The matrix metalloproteinase stromelysin-1 (MMP-3) is inhibited more strongly by peptidyl phosphinic acid 7 than by its corresponding phosphonamidate and phosphonate analogs. Extending a benzyl group at P′ 1 to a phenylethyl group in 8 further increases the potency (K i = 1.4 nM). Enhanced potency with an extended substituent into the P 3 region was observed.

Aroyl and arylacyl aminoalkyl substitutents at the P 1 position of N -carboxyalkyl dipeptides were found to enhance potency and selectivity for stromelysin-1 (MMP-3). In particular, the phthalimidobutyl and phenylpropanoylaminopropyl groups offered inhibitors of MMP-3 with K i 's of ∼ 10nM.

A series of N-carboxyalkyl dipeptides were synthesized to evaluate their inhibitory activities against human stromelysin-1(MMP-3), collagenase(MMP-1), and gelatinase-A(MMP-2). Structures with a homophenylalanine residue at P1′ substituted at the para position with small alkyl groups are potent inhibitors of (MMP-3) and (MMP-2) (Ki′ s 2–40 nM), but weak inhibitors of (MMP-1).

A series of N-carboxyalkyl peptides were prepared to test their inhibitory activity against human stromelysin (MMP-3), collagenase (MMP-1), and gelatinase A (MMP-2). Linear alkyl and ω-aminoalkyl residues were employed as replacements for a phenethyl group yielding inhibitors with in vitro activities comparable to their corresponding aromatic analogs.

A series of phosphinic acid-containing peptide inhibitors of human stromelysin-1 (MMP-3) were prepared. The P1 through P3 subsites were varied in a systematic manner on analogs possessing an invariant P1′-P3′ segment. The in vitro activity of these compounds as inhibitors of stromelysin and collagenase is discussed.

We have investigated the inhibition of the human matrix metalloproteinase stromelysin (SLN) by the N-(carboxyalkyl)dipeptide Ala[N]hPhe-Leu-anilide and find that it is a competitive, slow-binding inhibitor of this enzyme with Ki = 3 x 10(-8) M (pH 6.0, 25 degrees C). The dependence of k(obs), the observed first-order rate constant for the approach to steady state, on Ala[N]hPhe-Leu-anilide concentrations less than 10(-5) M is linear and suggests a simple, one-step mechanism with kon = 3.4 x 10(4) M-1 s-1 and k(off) = 1.2 x 10(-3) s-1 (pH 6.0, 25 degrees C). Using rapid kinetic techniques, we extended the concentration range of Ala[N]hPhe-Leu-anilide to 2 x 10(-3) M and found that the [Ala[N]hPhe-Leu-anilide] dependence of K(obs) suggests saturation kinetics with a Ki' near 5 x 10(-4) M. Detailed analysis of these data reveal that the dependence of k(obs) on [Ala[N]hPhe-Leu-anilide] is, in fact, sigmoidal. To probe the chemical mechanism of inhibition, we determined pH and temperature dependencies and solvent deuterium isotope effects. For k(on), delta H not equal to = 12.4 kcal/mol and -T delta S not equal to = 6.2 kcal/mol (T = 298 K; [I]steady-state = 10(-6) M), while for k(off), delta H not equal to = 12.5 kcal/mol and -T delta S not equal to = 8.9 kcal/mol (T = 298 K). pH dependencies of the kinetic parameters for inhibition are complex but reflect greater potency at lower pH and suggest a mechanism involving the same active-site groups that are involved in catalysis.(ABSTRACT TRUNCATED AT 250 WORDS)

Substrate specificity studies from this laboratory suggested that Ac-Pro-Leu-Ala-Nva-TrpNH2, and its thioester derivative, Ac-Pro-Leu-Ala-SNva-TrpNH2, would be substrates for stromelysin (SLN). In this paper, we report that both peptides are efficiently hydrolyzed not only by SLN but also by two other matrix metalloproteinases, collagenase and gelatinase, and by the bacterial metalloproteinase thermolysin. The pH-dependence of kc/Km for the SLN-catalyzed hydrolysis of Ac-Pro-Leu-Ala-SNva-TrpNH2 is identical to pH-dependencies for peptide hydrolysis and suggests no major mechanistic differences between thioester and amide hydrolysis by SLN.

Cdk5/p25 is a member of the cyclin-dependent, Ser/Thr kinase family and has been identified as one of the principle Alzheimer's disease-associated kinases that promote the formation of hyperphosphorylated tau, the major component of neurofibrillary tangles. We and others have been developing inhibitors of cdk5/p25 as possible therapeutic agents for Alzheimer's disease (AD). In support of these efforts, we examine the metal effect and solvent kinetic isotope effect on cdk5/p25-catalyzed H1P (a histone H-1-derived peptide) phosphorylation. Here, we report that a second Mg(2+) in addition to the one forming the MgATP complex is required to bind to cdk5/p25 for its catalytic activity. It activates cdk5/p25 by demonstrating an increase in k(cat) and induces a conformational change that favors ATP binding but has no effect on the binding affinity for the H1P peptide substrate. The binding of the second Mg(2+) does not change the binding order of substrates. The reaction follows the same rapid equilibrium random mechanism in the presence or absence of the second Mg(2+) as evidenced by initial velocity analysis and substrate analogue and product inhibition studies. A linear proton inventory with a normal SKIE of 2.0 +/- 0.1 in the presence of the second Mg(2+) was revealed and suggested a single proton transfer in the rate-limiting phosphoryl transfer step. The pH profile revealed a residue with a pK(a) of 6.5 that is most likely the general acid-base catalyst facilitating the proton transfer.

To probe the specificity of the metalloendoproteinase stromelysin toward peptide substrates, we determined kc/Km values for the stromelysin-catalyzed hydrolyses of peptides whose design was based loosely on the structure of a known SLN substrate, substance P (Arg-Pro-Lys-Pro-Gln-Gln-Phe-Phe-Gly-Leu-MetNH2, hydrolysis at Gln-Phe, kc/Km = 1700 M-1 s-1). Several noteworthy points emerge from this study: (i) Catalytic efficiency is dependent on peptide chain length with N-terminal truncation of substance P resulting in more pronounced rate-constant reductions than C-terminal truncation. These results suggest the existence of an extended active site for stromelysin. (ii) Preferences at positions P3, P2, P1, P1', and P2' are for the hydrophobic amino acids Pro, Leu, Ala, Nva, and Trp, respectively. (iii) Investigation of specificity at P3' supports our earlier hypothesis that SLN has a requirement for a hydrogen-bond donor at this position in its substrates. Based on these observations, we designed and had synthesized the fluorogenic substrate N-(2,4-dinitrophenyl)Arg-Pro-Lys-Pro-Leu-Ala-Nva-TrpNH2, whose stromelysin-catalyzed hydrolysis can be monitored continuously (kc/Km = 45,000 M-1 s-1).

The cyclosporin A binding protein, cyclophilin (CyP), and the FK-506 binding protein, FKBP, catalyze the cis-to-trans isomerization of Xaa-Pro bonds in peptides. To probe the mechanism of these reactions and their nonenzymatic counterparts, we determined the following: (1) substrate specificities of CyP and FKBP; (2) dependencies of k c /K m on pH and solvent deuterium; (3) secondary deuterium isotope effects; and (4) temperature-dependencies. The results indicate that for cis-to-trans isomerization of Suc-Ala-Xaa-cis-Pro-Phe-pNA, values of k c /K m for the CyP-catalyzed reactions show little dependence on Xaa

A structure-activity relationship study for a 2-chloroanilide derivative of pyrazolo[1,5-a]pyridine revealed that increased EphB3 kinase inhibitory activity could be accomplished by retaining the 2-chloroanilide and introducing a phenyl or small electron donating substituents to the 5-position of the pyrazolo[1,5-a]pyridine. In addition, replacement of the pyrazolo[1,5-a]pyridine with imidazo[1,2-a]pyridine was well tolerated and resulted in enhanced mouse liver microsome stability. The structure-activity relationship for EphB3 inhibition of both heterocyclic series was similar. Kinase inhibitory activity was also demonstrated for representative analogs in cell culture. An analog (32, LDN-211904) was also profiled for inhibitory activity against a panel of two hundred and eighty eight kinases and found to be quite selective for tyrosine kinases. Overall, these studies provide useful molecular probes for examining the in vitro, cellular and potentially in vivo kinase-dependent function of EphB3 receptor.

Substrate specificities, as reflected in kc/Km, were determined for the peptidyl prolyl cis-trans isomerase activities of cyclophilin and the FK-506 binding protein (FKBP). The substrates investigated were peptides of the general structure Suc-Ala-Xaa-Pro-Phe-p-nitroanilide, where Xaa = Gly, Ala, Val, Leu, Phe, His, Lys, on Glu. While kc/Km for cyclophilin-catalyzed isomerization shows little dependence on Xaa, kc/Km values for FKBP-catalyzed isomerization display a marked dependence on Xaa and vary over 3 orders of magnitude. An important outcome of this work is the discovery that Suc-Ala-Leu-Pro-Phe-pNA is a reactive substrate for FKBP (kc/Km = 640,000 M-1 s-1). This substrate can be used with FKBP concentrations that are low enough to allow, for the first time, accurate determinations of Ki values for tight-binding inhibitors of FKBP. Using this new assay, we found that FK-506 inhibits FKBP with Ki = 1.7 +/- 0.6 nM. The results of this work support the hypothesis that cyclophilin and FKBP are members of a family of peptidyl prolyl cis-trans isomerases and that the members of this family possess distinct substrate specificities that allow them to play diverse physiologic roles.

3-Amino-2-keto-7H-thieno[2,3-b]pyridin-6-one derivatives were discovered as moderately potent inhibitors of ubiquitin C-terminal hydrolase-L1 (UCH-L1) utilizing an assay that measures hydrolysis of the fluorogenic substrate Ub-AMC. SAR studies revealed that both the carboxylate at the 5-position and the 6-pyridone ring were critical for inhibitory activity. Furthermore, activity was dependent on the nature of the ketone substituent at the 2-position, with 4-Me-Ph and 2-naphthyl being best. Kinetic mechanism studies revealed that these compounds were uncompetitive inhibitors of UCH-L1, binding only to the Michaelis-complex and not to free enzyme. The active compounds were selective for UCH-L1, exhibiting neither inhibition of other cysteine hydrolases (e.g., UCH-L3, papain, isopeptidase T, caspase-3, and tissue transglutaminase) nor cytotoxicity in N2A cells.

Thieno[2,3-d]pyrimidin-4-one acylhydrazide derivatives were discovered as moderately potent inhibitors of TGase 2 (tissue transglutaminase) utilizing a fluorescence-based assay that measured TGase 2 catalyzed incorporation of the dansylated Lys derivative alpha-N-Boc-Lys-CH(2)-CH(2)-dansyl into the protein substrate N,N-dimethylated-casein. A SAR study revealed that the acylhydrazide thioether side-chain and the thiophene ring were critical to inhibitory activity.

Tissue transglutaminase (TGase) catalyzes transfer of gamma-acyl moieties of Gln residues in peptides or protein substrates to either water or amine nucleophiles through an acyl-enzyme intermediate formed from initial acyl-transfer to an active site Cys residue. Natural substrates for this enzyme include proteins (e.g., tau, alpha-synuclein, and huntingtin) whose TGase-promoted polymerization may be causative in neurodegenerative diseases. As part of a program to find inhibitors of TGase, we have undertaken kinetic and mechanistic studies of the enzyme from guinea pig (gpTGase) and humans (hTGase). Key findings of this study include: (i) gpTGase-catalyzed transamidation of Z-Gln-Gly by Gly-OMe proceeds essentially as described above but with the involvement of substrate inhibition by Gly-OMe. This phenomena, resulting from the binding of nucleophile to free enzyme, appears to be a common feature of TGase-catalyzed reactions. (ii) Solvent deuterium isotope effects for hydrolysis of Z-Gln-Gly by gpTGase are (D)(k(c)/K(m)) = 0.45 and (D)k(c) = 3.6. While the latter results from general catalysis of deacylation, the former originates purely from the reactant state, hydrogen fractionation factor of the active site thiol with no involvement of general catalysis of acylation. (iii) Studies of the transamidation of N,N-dimethylated casein by Gly-OMe and dansyl-cadaverine suggest a complex kinetic mechanism for both enzymes that reflects contributions from four reactions: Gln hydrolysis, intramolecular transpeptidation, intermolecular transpeptidation, and transamidation by added nucleophile.

We have developed an assay to continuously monitor the branched amino acid preferring peptidase (BrAAP) activity of the proteasome. This assay is based on the hydrolysis of the fluorogenic peptide, Abz-Gly-Pro-Ala-Leu-Ala-Nba (Abz is 2-aminobenzoyl and Nba is 4-nitrobenzylamide) which is cleaved exclusively at the Leu-Ala bond by the 20S proteasome with a kc/Km value of 13 000 M-1 s-1. Hydrolysis of this peptide is accompanied by an increase in fluorescence intensity (lambda ex = 340 nm, lambda em = 415 nm) due to release of the internally quenched 2-aminobenzoyl fluorescence that accompanies diffusion apart of the hydrolysis products, Abz-Gly-Pro-Ala-Leu and Ala-Nba. Using this assay, we examined inhibition of the BrAAP activity of the proteasome by a series of tripeptide aldehydes, Z-Leu-Leu-Xaa-H. When Xaa = Phe, (p-Cl)Phe, and Trp we observe biphasic or partial inhibition of the BrAAP activity. In contrast, when Xaa = Nva and Leu, simple inhibition kinetics are observed and allow us to calculate Ki values of 120 nM and 12 nM, respectively. The inhibitors that exhibit simple inhibition kinetics for BrAAP activity are also approximately equipotent for inhibition of the chymotrypsin-like (ChT-L) and peptidyl-glutamyl peptide hydrolyzing (PGPH) activities, dissociation constants varying by less than 25-fold, whereas the inhibitors that exhibit biphasic inhibition kinetics for BrAAP activity are300-fold more potent for inhibiting ChT-L activity than for PGPH activity. Inactivation of the BrAAP activity of the proteasome by clasto-lactacystin beta-lactone is also biphasic. beta-Lactone inactivates approximately 60% of the BrAAP activity rapidly, with kinetics indistinguishable from its inactivation of the chymotrypsin-like activity. The remaining 40% of the BrAAP activity is inactivated by beta-lactone at a 50-fold slower rate, with kinetics indistinguishable from its inactivation of the PGPH activity. These results suggest a mechanism in which hydrolysis of Abz-Gly-Pro-Ala-Leu-Ala-Nba (i.e., BrAAP activity) occurs at two different active sites in the 20S proteasome, and that these two active sites are the same ones that catalyze the previously described ChT-L and PGPH activities.

Deubiquitinating enzymes constitute a family of cysteine hydrolases that specifically cleave ubiquitin-derived substrates of general structure Ub-X, where X can be any number of leaving groups ranging from small thiols and amines to Ub and other proteins (Ub, ubiquitin). We have developed a general assay for deubiquitinating enzymes based on the substrate ubiquitin C-terminal 7-amido-4-methylcoumarin (Ub-AMC). Ub-AMC is efficiently hydrolyzed with liberation of highly fluorescent AMC by two rabbit reticulocyte deubiquitinating enzymes: isopeptidase T (IPaseT), a member of the gene family of ubiquitin-specific processing enzymes, and UCH-L3, a member of the family of ubiquitin C-terminal hydrolases. We used this new assay to probe kinetic and mechanistic aspects of catalysis by IPaseT and UCH-L3. Results from four series of experiments are discussed: (1) For UCH-L3, we determined steady-state kinetic parameters that suggest a diffusion-limited reaction of UCH-L3 with Ub-AMC. To probe this, we determined the viscosity dependence of kc/Km, as well as kc. We found complex viscosity dependencies and interpreted these in the context of a model in which association and acylation are viscosity-dependent but deacylation is viscosity-independent. (2) The kinetics of inhibition of UCH-L3 by ubiquitin C-terminal aldehyde (Ub-H) were determined and reveal a Ki that is less than 10(-14) M. Several mechanisms are considered to account for the extreme inhibition. (3) The IPaseT-catalyzed hydrolysis of Ub-AMC is modulated by Ub with activation at low [Ub] and inhibition at high [Ub]. (4) Finally, we compare kc/Km values for deubiquitinating enzyme-catalyzed hydrolysis of Ub-AMC and Z-Leu-Arg-Gly-Gly-AMC. For IPaseT, the ratio of rate constants is 10(4), while for UCH-L3 this ratio is > 10(7). These results suggest the following: (i) Deubiquitinating enzymes are able to utilize the free energy that is released from remote interactions with Ub-containing substrates for stabilization of catalytic transition states, and (ii) UCHs are more efficient at utilizing the energy from these interactions, presumably because they do not possess a binding domain for a Ub "leaving group".

In this paper, we report kinetic studies for the chymotryptic activity of the 20S proteasome. Major observations include the following: (1) Reaction progress curves that are recorded at concentrations of Suc-Leu-Leu-Val-Tyr-AMC greater than about 40 microM are biphasic and characterized by initial velocities that decay by a first-order process to final, steady-state velocities. (2) Also at [Suc-Leu-Leu-Val-Tyr-AMC] > 40 microM, initial and steady-state velocities are smaller than predicted from simple, Michaelis-Menten kinetics. (3) The first-order rate constant for the approach to steady-state has a complex dependence on substrate concentration and decreases sigmoidally as substrate concentration increases. These results indicate that the 20S proteasome is a hysteretic enzyme and is subject to substrate inhibition. To explain these observations we propose a minimal kinetic model with two critical mechanistic features: (1) the 20S proteasome has two cooperative active sites for Suc-Leu-Leu-Val-Tyr-AMC and (2) there are two interconvertible conformers of active 20S proteasome. To probe this mechanism in greater detail, we explored the kinetic mechanism of inhibition of the 20S proteasome-catalyzed hydrolysis of Suc-Leu-Leu-Val-Tyr-AMC by the peptide aldehyde, Ac-Leu-Leu-Nle-H. Our studies reveal a nonlinear dependence of reciprocal steady-state velocity on inhibitor concentration (i.e., parabolic inhibition) as well as a nonlinear dependence of the apparent inhibitor dissociation constant on substrate concentration. Both of these observations are explained by binding of inhibitor at multiple sites on the enzyme. Taken together, the results of this study indicate that the 20S proteasome is a conformationally flexible protein that can adjust to the binding of ligands and that has multiple and cooperative active sites. These results support a view of the proteasome's substrate specificity in which (1) substrates are recognized and hydrolyzed by more than one active site; (2) each active site can bind substrates that possess a variety of P1 residues; and (3) the P1 residue plays a relatively minor role as a specificity determinant. Finally, we interpret the results of this study to suggest that, in vivo, the 20S proteasome requires conformational plasticity for its interactions with regulatory complexes and, after it has combined with appropriate regulatory complexes, to catalyze hydrolysis of proteins.

Publisher Summary This chapter describes the mechanism of both enzymatic and non-enzymatic prolyl isomerization. Non-enzymatic prolyl isomerization and rotation about amide bonds are reviewed. Amide rotation is mechanistically related to prolyl isomerization and serves as a useful model for prolyl isomerization. A common mechanism for these reactions and a structure for the rate-limiting transition state are reviewed. The chapter also discusses on what is known of enzyme-catalyzed prolyl isomerization. The chemistry of non-enzymatic prolyl isomerizations and the mechanisms of the non-enzymatic catalysis of this reaction dictate the catalytic strategy that is used by prolyl isomerases. Finally, it leads to a mechanistic proposal for enzymatic prolyl isomerization. The catalytic strategy that an enzyme develops over the evolutionary time is dictated by the chemistry of the reaction being catalyzed. The prolyl isomerases are able to stabilize the non-enzymatic transition state without formation of covalent intermediates. Based on a k cat value of 10 4 sec -1 for CyP and a k uncut of 10 -2 sec -1 for the cis -to-trans isomerization of Suc-Ala-Ala- cis- Pro-Phe-pNA, an acceleration factor, k cat /k uncut of 10 6 , is calculated that corresponds to a transition state stabilization free energy of over 8 kcal/mol 3 . The energetic price to distort the Xaa-Pro bond out of planarity must ultimately be paid by favorable transition state interactions.

To probe the mechanism of stromelysin (SLN)-catalyzed peptide hydrolysis, we determined the pH dependence of kc/Km and solvent deuterium isotope effects on kc and kc/Km. pH dependencies of kc/Km were determined for the SLN-catalyzed hydrolysis of three peptides: Arg-Pro-Lys-Pro-Gln-Gln-Phe-Phe-Gly-Leu-Nle-NH2,Arg-Pro-Ala-Pro-Gln-Gln- Phe-Phe - Gly-Leu-NleNH2, and N-acetyl-Arg-Pro-Ala-Pro-Gln-Gln-Phe-Phe-Gly-Leu-Nle-NH2 (cleavage at Gln-Phe bond). The pH dependencies are all bell-shaped with shoulders that extend from pH 7.5 to 8.5. The existence of a shoulder indicates that the reaction mechanism involves at least two routes to products. These curves are governed by three proton ionizations with pKa values of 5.4, 6.1, and 9.5. The solvent isotope effect measurements provided the following values: D(kc/Km) = 0.80 +/- 0.05 and D(kc) = 1.58 +/- 0.05. That D(kc/Km) and D(kc) are different suggests that the rate-limiting transition states for the processes governed by kc/Km and kc cannot be the same. We use these results, together with analogy to thermolysin catalysis, to develop a mechanism for SLN catalysis.

Cyclophilin, the cytosolic binding protein for the immunosuppressive drug cyclosporin A, has recently been shown to be identical with peptidyl prolyl cis-trans isomerase [Fischer, G., Wittmann-Liebold, B., Lang, K., Kiefhaber, T., & Schmid, F.X. (1989) Nature 337, 476; Takahashi, N., Hayano, T., & Suzuki, M. (1989) Nature 337, 473]. To provide a mechanistic framework for studies of the interaction of cyclophilin with cyclosporin, we investigated the mechanism of the PPI-catalyzed cis to trans isomerization of Suc-Ala-Xaa-cis-Pro-Phe-pNA (Xaa = Ala, Gly). Our mechanistic studies of peptidyl prolyl cis-trans isomerase include the determination of steady-state kinetic parameters, pH and temperature dependencies, and solvent and secondary deuterium isotope effects. The results of these experiments support a mechanism involving catalysis by distortion in which the enzyme uses free energy released from favorable, noncovalent interactions with the substrate to stabilize a transition state that is characterized by partial rotation about the C-N amide bond.

Kinetics of inhibition have been determined for the interaction of human leukocyte elastase (HLE) with two series of peptide trifluoromethyl ketones (TFMKs): X-Val-CF3,X-Pro-Val-CF3,X-Val-Pro-Val-CF3, and X-Lys(Z)-Val-Pro-Val-CF3, where X is MeOSuc or Z. These compounds are "slow-binding" inhibitors of HLE and, thus, allow the determination of Ki, the dissociation constant for the stable complex of inhibitor and enzyme, as well as kon and koff, the rate constants for formation and decomposition of this complex. Maximal potency is reached with Z-Lys(Z)-Val-Pro-Val-CF3, which displays a Ki less than 0.1 nM. Upon binding to HLE, these compounds undergo addition by the hydroxyl of the active site serine to form a hemiketal. The evidence supporting a hemiketal intermediate includes Ki values of 1.6 and 80,000 nM for Z-Val-Pro-Val-CF3 and its alcohol analogue, linear free energy correlations between inhibitory potency and catalytic efficiency for structurally related TFMKs and substrates, and the pH dependence of kon for the inhibition of HLE by Z-Val-Pro-Val-CF3, which is sigmoidal and displays a pKa of 6.9. Hemiketal formation is probably not rate limiting, however. Kinetic solvent isotope effects of unity suggest that kon cannot be rate limited by a reaction step, like hemiketal formation, that is subject to protolytic catalysis. A general mechanism that is consistent with these results is one in which formation of the hemiketal is rapid and is followed or preceded by a slow step that rate limits kon.(ABSTRACT TRUNCATED AT 250 WORDS)

The microbial, peptide-derived aldehyde chymostatin is a potent, competitive inhibitor of chymotrypsin and cathepsin G: Ki = 4 X 10(-10) and 1.5 X 10(-7) M, respectively. Et is "slow-binding inhibitor" of both proteases and, as such, allows determination of rate constants for its association with and dissociation from these proteases. Inhibition kinetics indicate second-order rate constants for the association of chymostatin with chymotrypsin and cathepsin G of 360,000 and 2000 M-1 S-1, respectively and a first-order rate constant for the dissociation of both protease-chymostatin complexes of approximately 0.0002 s-1. Thus, the extreme difference in potency of chymostatin as an inhibitor of chymotrypsin and cathepsin G originates entirely in Kon. Solvent deuterium isotope effects (SIE) were determined to probe the reaction step that rate limits Kon. For the reaction of chymotrypsin with chymostatin, the SIE for Kon is 1.6 +/- 0.1, while for the reaction of chymotrypsin with the peptide substrates Ala-Ala-Phe-pNA and Suc-Ala-Ala-Pro-Phe-pNA, the SIE's for Kc/Km are 2.8 +/- 0.2 and 1.9 +/- 0.1, respectively. These results suggest that Kon for the association of chymotrypsin with chymostatin is at least partially rate limited by a reaction step involving proton transfer. Combined with results for the inhibition of chymotrypsin by Bz-Phe-H [Kennedy, W.P., & Schultz, R. M. (1979) Biochemistry 18, 349-356], these data suggest a mechanism for inhibition by chymostatin involving the general-base-catalyzed formation of an enzyme-bound hemiacetal, followed by a conformational change of this intermediate that produces the final, stable complex of enzyme and inhibitor.(ABSTRACT TRUNCATED AT 250 WORDS)

Acyl-enzymes of human leukocyte elastase (HLE) were generated in situ during the hydrolysis of peptide thiobenzyl esters and served as substrates for aminolysis by a variety of amino acid amides and short peptide nucleophiles. For amino acid amides, there is a positive correlation between nucleophilic reactivity toward N-methoxysuccinyl (MeOSuc)-Ala-Ala-Pro-Val-HLE and the hydrophobicity of the side chain. For peptides, nucleophilicity toward MeOSuc-Ala-Ala-Pro-Val-HLE decreases dramatically with increasing chain length. Combined, these results suggest that substrate specificity for the P1' residue may be more dependent on side chain hydrophobicity than on specific, structural features of the side chain and there may be no important binding interactions available past S1'. Kinetic parameters were also determined for the nucleophilic reactions of PheNH2 and TyrNH2 with MeOSuc-Pro-Val-HLE, MeOSuc-Ala-Pro-Val-HLE, MeOSuc-Ala-Ala-Pro-Val-HLE, and MeOSuc-Ala-Ala-Pro-Ala-HLE. Reactivity of these acyl-enzymes toward nucleophilic attack displays no dependence on peptide chain length but does increase significantly for the substrate with Ala at P1. This same correlation between reactivity and acyl-enzyme structure is also seen for nucleophilic attack by water.

Valine-derived benzoxazinones have been synthesized and found to be competitive, slow-binding inhibitors of human leukocyte elastase (HLE). Steady-state inhibition constants Ki are dependent on aryl substitution and reach a maximum of potency of 0.5 nM with the 5-Cl compound 6. UV-spectral data for the interaction of HLE and the unsubstituted inhibitor 3 indicate that the stable complex formed between enzyme and inhibitor is an acyl-enzyme that can either undergo ring closure, to reform intact benzoxazinone, or hydrolysis, to liberate an N-acylanthranilic acid. "Burst" kinetic data, derived from the direct observation of the interaction of HLE and 3, are consistent with results of the inhibition of catalysis experiments.

Steady-state kinetic parameters were determined for the human leukocyte elastase catalyzed hydrolysis of a series of peptide-based thiobenzyl esters and p-nitroanilides. The peptide units are MeOSuc-Val, MeOSuc-Alan-Pro-Val (n = 0-2), and MeOSuc-Alan-Pro-Ala (n = 1 or 2). The results of this study suggest five important mechanistic features for HLE. Few important remote subsite contacts are established in the Michaelis complex. Full recognition and tight binding of the substrate occurs in the transition state for acylation. The P3-S3 interaction is critical during acylation. Subsite contacts are unimportant in deacylation. P1 specificity is regulated by peptide length. An important steady-state kinetic consequence of this specificity is that the rate-limiting step of kc for p-nitroanilide hydrolysis changes from acylation to deacylation as the peptide chain is lengthened.

Steady-state kinetic parameters were determined at pH 7.4 and 25 °C for the human leukocyte elastase-catalyzed hydrolysis of several N -carbobenzoxy- l -amino acid p -nitrophenyl esters. The substrate specificity for these esters was quite broad, and included the Gly, Phe, and Tyr derivatives. Together with reports of a much narrower P-1 specificity for peptide-based substrates, these results suggest that interactions remote from the scissle bond between enzyme and substrate regulate primary specificity. Also, it was found that k c and k c K m did not exhibit the same dependence on substrate structure. This is interpreted to suggest that there are significant differences in P-1 specificity between acylation and deacylation for leukocyte elastase-catalyzed reactions.

To probe the substrate specificity of the human metalloproteinase stromelysin (SLN), we determined values of kc/Km for the SLN-catalyzed hydrolysis of substance P (Arg-Pro-Lys-Pro-Gln-Gln-Phe-Phe-Gly-Leu-MetNH2; SP; kc/Km = 1790 +/- 140 M-1 s-1), 15 analogues of SP, and 17 other peptides. We found a remarkably narrow substrate specificity for SLN: while SP and its analogues could serve as substrates for SLN (hydrolysis occurred exclusively at the Gln6-Phe7 bond), peptides that were not direct analogues could not (kc/Km less than 3 M-1 s-1). From the study of the SLN-catalyzed hydrolysis of SP and its analogues, the following findings emerged: (1) Decreasing the length of SP results in decreases in kc/Km. (2) Conservative amino acid replacements near the scissle bond of SP decrease kc/Km. (3) The SP analogue in which Gly9 is replaced with sarcosine (N-methylglycine) is not hydrolyzed by SLN (kc/Km less than 3 M-1 s-1). (4) Several SP analogues that are not hydrolyzed by SLN are inhibitors of the enzyme. The complexes formed from interaction of SLN with these peptides have dissociation constants that are similar to the Km value for the complex of SLN and SP. Combined, these results suggest that SLN uses the energy that is available from favorable interactions with its substrate to stabilize catalytic transition states but not the Michaelis complex or other stable-state complexes.

The oxygenation of arachidonic acid (AA) by guinea-pig neutrophil 5-lipoxygenase terminates prematurely at a substrate utilization of only 50%. In the presence of dithiothreitol (DTT), reaction progress continues longer but still terminates prematurely, at about 70% substrate turnover. The addition of more substrate during the first 60 seconds of the initial reaction resulted in continued product formation. However, at times after 120 seconds, the addition of more AA could not produce additional product formation. Together, these results indicate a time-dependent (t1/2 = 0.5-1.0 min), irreversible loss of enzyme activity. To determine if the product 5-hydroperoxy-6,8,11,14-eicosatetraenoic acid (5-HPETE) mediates the inactivation, it was tested for its ability to irreversibly inhibit the enzyme and found to inactivate 5-lipoxygenase with Ki = 0.05 +/- 0.01 microM and ki = 1.4 +/- 0.4 min-1. DTT changed the apparent affinity of 5-HPETE (Ki = 0.33 +/- 0.09 microM) but had no effect on the rate of inactivation (ki = 1.26 +/- 0.62 min-1). In contrast, the hydroxy derivative of 5-HPETE, 5-hydroxy-6,8,11,14-eicosatetraenoic acid (5-HETE), is a reversible, time-independent inhibitor with Ki = 6.3 +/- 0.9 microM regardless of DTT. The ability of thiols to protect 5-lipoxygenase from production inactivation is due, at least in part, to a non-enzymatic reaction between DTT and 5-HPETE that converts the hydroperoxy acid to a material that can no longer inactivate the enzyme.

The new α-amino acid, 2-amino-4-(3-pyridyl)butyric acid (4)[abbreviation, Ala(3 Pm)], has been synthesized and resolved. The N-t-butoxycarbonyl derivative of the L-amino-acid has been used in the picolyl ester ‘handle’ method to synthesize Boc-Ala(3 Pm)-Ala-Ala-Ala-Lys(Z)-OPic (8)(Pit = 4-picolyl) and its N-acetyl analogue (9), Boc-Ala(3 Pm)-Ala-Ala-D-Ala-Lys(Z)-OPic (10), and Boc-Ala(3 Pm)-Ala-Ala-Val-Lys(Z)-OPic (11). Compounds (8), (9), and (11) are weak inhibitors of human leucocytic elastase.