Rapid Quench Studies Research Articles

Kinetic mechanism of protease inhibition by α1-antitrypsin

The native form of serine protease inhibitor (serpin) is kinetically trapped in a metastable state. Metastability in these proteins is critical to inhibit target protease by forming a stable covalent complex. Despite recent determination of the crystal structures of a Michaelis protease–serpin complex as well as a stable covalent complex, details on the kinetic mechanism remain unsolved. In this report, we examined the reaction mechanism of α1-antitrypsin toward elastase by a combination of stopped-flow experiments via fluorescence resonance energy transfer and rapid-quench studies. The results suggest a non-covalent complex intermediate other than Michaelis complex as an intermediate before the cleavage of P1–P1′ scissile bond, whose formation is the rate-determining step of the overall reaction. This rate-limiting step represents rearrangement of the reactive site loop, and is regulated by a salt bridge between E354 and R196. The ionic interaction is unique to α1-antitrypsin, which suggests that protease inhibition mechanisms are varied among serpins.

Arginine deiminase uses an active-site cysteine in nucleophilic catalysis of L-arginine hydrolysis.

Arginine deiminase (EC 3.5.3.6) catalyzes the hydrolysis of l-arginine to citrulline and ammonium ion, which is the first step of the microbial l-arginine degradation pathway. The deiminase conserves the active-site Cys-His-Asp motif found in several related enzymes that catalyze group-transfer reactions from the guanidinium center of arginine-containing substrates. For each of these enzymes, nucleophilic catalysis by the conserved Cys has been postulated but never tested. In this communication we report the results from rapid quench studies of single-turnover reactions carried out with recombinant Pseudomonas aeruginosa arginine deiminase and limiting [14C-1]l-arginine. The citrulline-formation and arginine-decay curves measured at 25 degrees C were fitted to yield apparent rate constants k = 3.6 +/- 0.1 s-1 and k = 4.2 +/- 0.1 s-1, respectively. The time course for the formation (k =13 s-1) and decay (k = 6.5 s-1) of 14C-labeled enzyme defined a kinetically competent intermediate. Under the same reaction conditions, the Cys406Ser mutant failed to form the 14C-labeled enzyme intermediate. These results, along with the recently reported enzyme X-ray structure (Galkin, A.; Kulakova, L.; Sarikaya, E.; Lim, K.; Howard, A.; Herzberg, O. J. Biol. Chem. 2004, 279, 14001-14008, evidence a reaction pathway in which l-arginine deimination proceeds via a covalent enzyme intermediate formed by ammonia displacement from the arginine guanidinum carbon by the active-site Cys406.

D-Ala–d-X ligases: evaluation of d-alanyl phosphate intermediate by MIX, PIX and rapid quench studies

Background: The d-alanyl–d-lactate (d-Ala–d-Lac) ligase is required for synthesis of altered peptidoglycan (PG) termini in the VanA phenotype of vancomycin-resistant enterococci (VRE), and the d-alanyl–d-serine (d-Ala–d-Ser) ligase is required for the VanC phenotype of VRE. Here we have compared these with the Escherichia colid-Ala–d-Ala ligase DdlB for formation of the enzyme-bound d-alanyl phosphate, d-Ala1-PO32– (d-Ala1-P), intermediate.Results: The VanC2 ligase catalyzes a molecular isotope exchange (MIX) partial reaction, incorporating radioactivity from 14C-d-Ser into d-Ala–14C-d-Ser at a rate of 0.7 min−1, which approaches kinetic competence for the reversible d-Ala1-P formation from the back direction. A positional isotope exchange (PIX) study with the VanC2 and VanA ligases displayed a d-Ala1-dependent bridge to nonbridge exchange of the oxygen-18 label of [γ-18O4]-ATP at rates of up to 0.6 min−1; this exchange was completely suppressed by the addition of the second substrate d-Ser or d-Lac, respectively, as the d-Ala1-P intermediate was swept in the forward direction. As a third criterion for formation of bound d-Ala1-P, we conducted rapid quench studies to detect bursts of ADP formation in the first turnover of DdlB and VanA. With E. coli DdlB, there was a burst amplitude of ADP corresponding to 26–30% of the DdlB active sites, followed by the expected steady-state rate of 620–650 min−1. For d-Ala–d-Lac and d-Ala–d-Ala synthesis by VanA, we measured a burst of 25–30% or 51% of active enzyme, respectively.Conclusions: These three approaches support the rapid (more than 1000 min−1), reversible formation of the enzyme intermediate d-Ala1-P by members of the d-Ala–d-X (where X is Ala, Ser or Lac) ligase superfamily.

Escherichia coli dimethylallyl diphosphate:tRNA dimethylallyltransferase: pre-steady-state kinetic studies

Escherichia coli dimethylallyl diphosphate:tRNA dimethylallyltransferase (DMAPP-tRNA transferase) catalyzes the first step in the biosynthesis of the hypermodified A37 residue in tRNAs that read codons beginning with uridine. The mechanism of the enzyme-catalyzed reaction was studied by isotope trapping, pre-steady-state rapid quench, and single turnover experiments. Isotope trapping indicated that the enzyme·tRNA complex is catalytically competent, whereas the enzyme·DMAPP complex is not. The results are consistent with an ordered sequential mechanism for substrate binding where tRNA binds first. The association and dissociation rate constants for the enzyme·tRNA binary complex are 1.15±0.33×10 7 M −1 s −1 and 0.06±0.01 s −1, respectively. Addition of DMAPP gives an enzyme·tRNA·DMAPP ternary complex in rapid equilibrium with the binary complex and DMAPP. Rapid quench studies yielded a linear profile ( k cat=0.36±0.01 s −1) with no evidence for buildup of enzyme-bound product. Product release from DMAPP-tRNA transferase is therefore not rate-limiting. The Michaelis constant for tRNA and the equilibrium dissociation constant for DMAPP calculated from the individual rate constants determined here are consistent with values obtained from a steady-state kinetic analysis.

Antichymotrypsin Interaction with Chymotrypsin: INTERMEDIATES ON THE WAY TO INHIBITED COMPLEX FORMATION

Serpins form enzymatically inactive covalent complexes (designated E*I*) with their target proteinases, corresponding most likely to the acyl enzyme that resembles the normal intermediate in substrate turnover. Formation of E*I* involves large changes in the conformation of the reactive center loop (residues P17 to P9') and of the serpin molecule in general. The "hinge" region of the reactive center loop, including residues P10-P14, shows facile movement in and out of beta-sheet A, and this movement appears to be crucial in determining whether E*I* is formed (the inhibitor pathway) or whether I is rapidly hydrolyzed to I* (the substrate pathway). Here, we report stopped-flow and rapid quench studies investigating the pH dependence of the conversion of the alpha1-antichymotrypsin.alpha-chymotrypsin encounter complex, E.I, to E*I*. These studies utilize fluorescent derivatives of cysteine variants of alpha1-antichymotrypsin at the P11 and P13 residues. Our results demonstrate three identifiable intermediates, EIa, EIb, and EIc, between E.I and E*I* and permit informed speculation regarding the nature of these intermediates. Partitioning between inhibitor and substrate pathways occurs late in the process of E*I* formation, most likely from a species occurring between EIc and E*I*.

Mechanistic studies on full length and the catalytic domain of the tandem SH2 domain-containing protein tyrosine phosphatase: analysis of phosphoenzyme levels and Vmax stimulatory effects of glycerol and of a phosphotyrosyl peptide ligand.

SHP-1, a protein tyrosine phosphatase containing two tandem SH2 domains, is autoinhibited at rest by its N-terminal SH2 (N-SH2) domain. Relief from autoinhibition and a subsequent 10-60-fold increase in V(max) have been observed upon N-SH2 domain engagement by a specific phosphotyrosyl ligand or upon deletion of the SH2 domains to yield the catalytic PTPase domain. In this study, we observed that glycerol and propane-1,2-diols, at concentrations of 4-6 M, accelerated the k(cat) of the full length enzyme by 47-fold and of the PTPase domain by 8-fold. Glycerol also increases the rate of proteolytic cleavage between the SH2 and catalytic PTPase domains. In stopped-flow studies using p-nitrophenyl phosphate (pNPP) as a substrate, a burst of p-nitrophenolate in the full length enzyme was not observed; however, a 50-70% stoichiometric burst was observed with the PTPase domain. Rapid quench studies using [32P]pNPP as a substrate showed a very low level of covalent [32P]phosphocysteinyl enzyme intermediate accumulation: 0.06% in the full length enzyme and 1% in the PTP domain. Stimulation by glycerol reduced the accumulating levels of phosphocysteinyl enzyme in both cases of full length SHP-1 and the PTPase domain; however, glycerol is not acting as a cosubstrate since no glycerophosphate product was detectable. It is likely that, for full length SHP-1, with pNPP as a model substrate, enzyme-substrate complex (ES) accumulates in its basal autoinhibited state, whereas enzyme-product complex (EP(i)) accumulates in its pY ligand-bound activated state. Glycerol probably relaxes the compact structure of SHP-1 and the PTP domain, thereby accelerating the catalytic rates in both cases by increasing forward reaction rates of ES and EP(i).

Location of the catalytic site for phosphoenolpyruvate formation within the primary structure of Clostridium symbiosum pyruvate phosphate dikinase. 1. Identification of an essential cysteine by chemical modification with [1-14C]bromopyruvate and site-directed mutagenesis.

Pyruvate phosphate dikinase (PPDK) catalyzes the interconversion of adenosine 5'-triphosphate (ATP), orthophosphate (Pi), and pyruvate with adenosine 5'-monophosphate (AMP), pyrophosphate (PPi), and phosphoenolpyruvate (PEP). The reaction takes place according to the following steps: (1) E+ATP+P(i)<-->E-PP.AMP.P(i), (2) E-PP.AMP.P(i)<-->E-P+AMP+PP(i), and (3) E-P+pyruvate<-->E+PEP, where E represents free enzyme; E-PP, pyrophosphorylenzyme; and E-P, phosphorylenzyme. Steps 1 and 2 comprise the nucleotide partial reaction, and step 3 comprises the pyruvate partial reaction. The present studies were carried out to locate amino acid residues within the primary structure of Clostridium symbiosum PPDK participating in the catalysis of the pyruvate partial reaction. The enzyme was treated with the affinity label [1-14C]bromopyruvate, reduced with NaBH4, proteolyzed with trypsin, and chromatographed on an HPLC column. The radiolabeled tryptic peptide isolate was sequenced to reveal Cys 831 as the site of alkylation. Using PCR techniques Cys 831 was replaced by Ala, and the C831A PPDK mutant formed was then subjected to kinetic analysis. Rapid quench studies of single turnover reactions on the enzyme showed that the mutant is as efficient as wild-type PPDK in catalyzing the nucleotide partial reaction while it is unable to catalyze the pyruvate partial reaction. These results were interpreted as evidence for a role of Cys 831 in pyruvate/PEP binding and/or catalysis.

Formation and utilization of formyl phosphate by N10-formyltetrahydrofolate synthetase: evidence for formyl phosphate as an intermediate in the reaction

N10-Formyltetrahydrofolate synthetase from bacteria and yeast catalyzes a slow formate-dependent ADP formation in the absence of H4folate. The synthesis of formyl phosphate by the enzyme was detected by trapping the intermediate as formyl hydroxamate. That the "formate kinase" activity was part of the catalytic center of N10-formyltetrahydrofolate synthetase was shown by demonstrating coordinate inactivation of the "kinase" and synthetase activities by heat and a sulfhydryl reagent, similar effects of monovalent cations, similar Km values for substrates, and similar Ki values for the inhibitor phosphonoacetaldehyde for both activities. The relative rates of the kinase activities for the bacterial and yeast enzymes are about 10(-4) and 4 x 10(-6) of their respective synthetase activities. These slow rates for the kinase reaction can be explained by the slow dissociation of ADP and formyl phosphate from the enzyme. This conclusion is supported by rapid-quench studies where a "burst" of ADP formation (6.4 s-1) was observed that is considerably faster than the steady-state rate (0.024 s-1). The demonstration of enzyme-bound products by a micropartition assay and the lack of a significant formate-stimulated exchange between ADP and ATP provide further evidence for the slow release of the products from the enzyme. The synthesis of N10-CHO-H4folate when H4folate was added to the E-formyl phosphate-ADP complex is also characterized by a "burst" of product formation. The rate of this burst phase at 5 degrees C occurs with a rate constant of 18 s-1 compared to 14 s-1 for the overall reaction at the same temperature. These results provide further evidence for formyl phosphate as an intermediate in the reaction and are consistent with the sequential mechanism of the normal catalytic pathway. Positional isotope exchange experiments using [beta,gamma-18O]ATP showed no evidence for exchange during turnover experiments in the presence of either H4folate or the competitive inhibitor pteroyltriglutamate. The absence of scrambling of the 18O label as observed by 31P NMR suggests that the central complex may impose restraints to limit free rotation of the P beta oxygens of the product ADP.

Isotope, pulse-chase, stopped-flow, and rapid quench studies on the kinetic mechanism of bovine dihydropteridine reductase.

The kinetics of the reduction of quinonoid 2-amino-4-hydroxy-6, 7-dimethyldihydropteridine (DMPH2) catalyzed by bovine liver dihydropteridine reductase were examined with NADH, (S)-NADD, (S)-NADT, and [3H]-NADH as substrates. No significant deuterium isotope effect was observed on either Km or Vm, indicating that hydrogen transfer is not a major rate-limiting step of the reaction. Tritium from (S)-NADT is transferred to an exchangeable position of the pteridine product without significant isotopic discrimination. The ratio of tritium released into solvent to NAD+ produced is approximately 1.0 in the steady state as well as in the first enzyme turnover as determined by pulse-chase experiments. Pulse-chase methods also showed that the binary complex E.NADH is fully functional and can be completely converted to products prior to NADH dissociation in the presence of saturating DMPH2. The concentration of DMPH2 giving half-maximal trapping of E.NADH is identical with its Km as determined by steady-state kinetics. Stopped-flow kinetic measurements gave no evidence for a burst of NADH utilization. This was further demonstrated by rapid quench experiments which demonstrated a pre-steady-state rate nearly identical with that of the steady state. The above results are consistent with nonequilibrium ordered binding of substrates and with a rate-limiting isomerization in the ternary complex which precedes hydrogen transfer.