Rapid Quench Technique Research Articles

Environment effect on the optical and photophysical investigation of Al(III)Porphyrins doped hybrid borate glasses

Hybrid borate glasses containing a series of Al(III)Porphyrins were prepared by rapid melt quench technique at 230 °C. The hybrid glass samples were characterized by X-ray diffraction, optical absorption, steady state and time resolved fluorescence emission. Upon exposure to UV light at 260 nm, the glass samples exhibit strong blue emission and red emission at 365 nm. The appearance of large stokes shift (Δ υ) and enhanced S 2 → S 0 emission at ∼495 nm indicates that structure of Al(III)Porphyrins were inherently modified in glass matrix. Time resolved fluorescence of the hybrid glasses shows three exponential decay with τ 1 = 0.11–0.59 ns, τ 2 = 3.13–3.95 ns and τ 3 = 8.13–9.56 ns. In the present study, we investigate the influence of glassy environment on the photophysical properties and the structure of Al(III)Porphyrins in borate glass was modeled through DFT calculations.

Energy Landscape of Adenylate Kinase: Phosphoryl Transfer and Conformational Transitions

Catalytic function of many enzymes is comprised of a number of microscopic steps including enzyme structural rearrangements and the chemical steps, in which bonds of the substrate(s) are broken/made to synthesize the product(s). Separation of these processes is a challenging task that hinders our understanding of enzyme catalysis. We have used nuclear magnetic resonance (NMR) and rapid-quenching techniques to independently study these processes in adenylate kinase (ADK) and to characterize their energetic contribution at atomic resolution. Adenylate kinase is an important enzyme that catalyzes a reversible reaction: 2ADP ↔ ATP +AMP, and is involved in maintaining energy homeostasis in a cell. Two binding sites of ADK and three different ligands result in a variety of biochemical states (determined by the bound ligands). Each of these states has different dynamic properties making the overall structural dynamics of ADK complex. We have tackled this problem by engineering a loss-of-function ADK mutant (with greatly reduced rate of turnover), which allowed us to “trap” the enzyme in well-defined biochemical states. Our results lead to a detailed energy profile of ADK, providing insights into the molecular mechanism of its functioning. This work reveals fundamental principles of enzyme catalysis and highlights the role of protein's intrinsic dynamics.

Optical and photophysical investigation of Meso, Proto and Hematoporphyrin(IX)dimethylester doped hybrid borate glasses

Hybrid borate glasses containing different concentrations (0.5–2.0 mg in 12 g of boric acid) of Mesoporphyrin(IX)dimethylester, Protoporphyrin(IX)dimethylester and Hematoporphyrin(IX)dimethylester were prepared by rapid melt quench technique at 230 °C. The hybrid glass samples were characterized by X-ray diffraction, optical absorption, steady state and time-resolved fluorescence emission. The optical absorption spectrum shows red-shift in Soret band along with change in Q-band pattern. The intensity of Q-band was found to increase with increase in the concentration of porphyrin in the glass. Steady state emission spectrum shows strong S 2→S 0 emission in the range 462–495 nm and blue shift in S 1→S 0 emission. Time-resolved fluorescence emission and fluorescence excitation spectra showed that different structures of porphyrins were exist in the glass samples. The variation in the spectral behaviour in the glass was correlated with those in solution medium and possible structures of porphyrin in borate glass were explored.

Structure and electrochemical performance of nickel hydroxide synthesized by rapid quench method

Abstract Nickel hydroxide with amorphous structure has been synthesized successfully by chemical precipitation method combined with rapid quench technique. The microstructure and morphology of the prepared samples were analyzed by XRD, Raman spectra, IR spectra, and SEM. The electrochemical performance of the sample was characterized by cyclic voltammetry, electrochemical impedance spectroscopy, and charge/discharge tests. The discharge capacity of the amorphous nickel hydroxide is 330.0 mAh g−1 at 0.2C, much higher than that of the theoretical capacity of β-nickel hydroxide (289.0 mAh g−1). Moreover, the amorphous nickel hydroxide exhibits higher electrochemical reaction reversibility, lower electrochemical impedance, and better cyclic stability compared with β-nickel hydroxide.

Insights into the mechanisms of adenosylcobalamin (coenzyme B12)-dependent enzymes from rapid chemical quench experiments

Glutamate mutase is one of a group of adenosylcobalamin-dependent enzymes that use free radicals to catalyse unusual and chemically difficult rearrangements involving 1,2-migrations of hydrogen atoms. A key mechanistic feature of these enzymes is the transfer of the migrating hydrogen atom between substrate, coenzyme and product. The present review summarizes recent experiments from my laboratory that have used rapid chemical quench techniques to identify intermediates in the reaction and probe the mechanism of hydrogen transfer through a variety of pre-steady-state kinetic isotope effect measurements.

Paradoxical effects of endurance training and chronic hypoxia on myofibrillar ATPase activity

This study aimed to determine the changes in soleus myofibrillar ATPase (m-ATPase) activity and myosin heavy chain (MHC) isoform expression after endurance training and/or chronic hypoxic exposure. Dark Agouti rats were randomly divided into four groups: control, normoxic sedentary (N; n = 14), normoxic endurance trained (NT; n = 14), hypoxic sedentary (H; n = 10), and hypoxic endurance trained (HT; n = 14). Rats lived and trained in normoxia at 760 mmHg (N and NT) or hypobaric hypoxia at 550 mmHg (approximately 2,800 m) (H and HT). m-ATPase activity was measured by rapid flow quench technique; myosin subunits were analyzed with mono- and two-dimensional gel electrophoresis. Endurance training significantly increased m-ATPase (P < 0.01), although an increase in MHC-I content occurred (P < 0.01). In spite of slow-to-fast transitions in MHC isoform distribution in chronic hypoxia (P < 0.05) no increase in m-ATPase was observed. The rate constants of m-ATPase were 0.0350 +/- 0.0023 s(-1) and 0.047 +/- 0.0050 s(-1) for N and NT and 0.033 +/- 0.0021 s(-1) and 0.038 +/- 0.0032 s(-1) for H and HT. Thus, dissociation between variations in m-ATPase and changes in MHC isoform expression was observed. Changes in fraction of active myosin heads, in myosin light chain isoform (MLC) distribution or in MLC phosphorylation, could not explain the variations in m-ATPase. Myosin posttranslational modifications or changes in other myofibrillar proteins may therefore be responsible for the observed variations in m-ATPase activity.

Steady-State and Pre-steady-State Kinetic Analysis of Mycobacterium smegmatis Cysteine Ligase (MshC)

Mycobacterium tuberculosis and many other members of the Actinomycetes family produce mycothiol, i.e., 1-d-myo-inosityl-2-(N-acetyl-l-cysteinyl)amido-2-deoxy-alpha-d-glucopyranoside (MSH or AcCys-GlcN-Ins), to act against oxidative and antibiotic stress. The biosynthesis of MSH is essential for cell growth and has been proposed to proceed via a biosynthetic pathway involving four key enzymes, MshA-MshD. The MSH biosynthetic enzymes present potential targets for inhibitor design. With this as a long-term goal, we have carried out a kinetic and mechanistic characterization, using steady-state and pre-steady-state approaches, of the recombinant Mycobacterium smegmatis MshC. MshC catalyzes the ATP-dependent condensation of GlcN-Ins and cysteine to form Cys-GlcN-Ins. Initial velocity and inhibition studies show that the steady-state kinetic mechanism of MshC is a Bi Uni Uni Bi Ping Pong mechanism, with ATP binding followed by cysteine binding, release of PPi, binding of GlcN-Ins, followed by the release of Cys-GlcN-Ins and AMP. The steady-state kinetic parameters were determined to be kcat equal to 3.15 s-1, and Km values of 1.8, 0.1, and 0.16 mM for ATP, cysteine, and GlcN-Ins, respectively. A stable bisubstrate analogue, 5'-O-[N-(l-cysteinyl)sulfamonyl]adenosine, exhibits competitive inhibition versus ATP and noncompetitive inhibition versus cysteine, with an inhibition constant of approximately 306 nM versus ATP. Single-turnover reactions of the first and second half reactions were determined using rapid-quench techniques, giving rates of approximately 9.4 and approximately 5.2 s-1, respectively, consistent with the cysteinyl adenylate being a kinetically competent intermediate in the reaction by MshC.

Direct Spectroscopic Evidence for a High-Spin Fe(IV) Intermediate in Tyrosine Hydroxylase

Tyrosine hydroxylase, a member of the aromatic amino acid hydroxylase family, uses a mononuclear Fe(II) and tetrahydropterin for hydroxylation of tyrosine to dihydroxyphenylalanine. Rapid-freeze quench Mossbauer spectroscopy has now provided direct evidence for the presence of an Fe(IV) intermediate in the reaction catalyzed by tyrosine hydroxylase. Rapid-quench techniques provide support for the kinetic competence of this species as the hydroxylating intermediate. This is the first direct evidence for a mononuclear Fe(IV) intermediate in an enzymatic aromatic hydroxylation reaction.

Paradoxical Effects Of Endurance Training And Chronic Hypoxia On Soleus Myofibrillar ATPase Activity

PURPOSE: The aim of this study was to determine the changes in soleus myofibrillar ATPase (m-ATPase) activity and MHC isoform expression after endurance training and/or chronic hypoxic exposure. METHODS: Dark Agouti rats were randomly divided into four groups: control, normoxic sedentary (N, n = 6); normoxic trained (NT, n = 6); hypoxic sedentary (H, n = 6) and hypoxic trained (HT, n = 6) group. Rats lived and trained in normoxia at 760 mmHg (N and NT), or hypobaric hypoxia at 550 mmHg; (≊ 2800 m) (H and HT). Training consisted of 5 sessions/week of treadmill run at 80% of maximal aerobic velocity (MAV) for five weeks. MAV was reached when the rat was not able to follow the incremen increase in speed imposed by the driven wheel and turned in the wheel more than three times. M-ATPase activity was measured by Rapid Flow Quench technique; myosin subunits were analyzed with mono- and two-dimensional gel electrophoresis. RESULTS: Endurance training significantly increased m-ATPase (P < 0.05), although no significant change in MHC isoform occurred in normoxia, there was a fast-to-slow shift in MHC isoform in hypoxia. Chronic hypoxia depressed m-ATPase (P < 0.05) in spite of a slow-to-fast transition in MHC isoform distribution. Indeed, the rate constants of m-ATPase (kF; s-1) for N and NT are respectively 0.032 ± 0.002 s-1 and 0.046 ± 0.003 s-1, while for H and HT 0.031 ±0.001 s-1 and 0.034 ± 0.004 s-1. CONCLUSION: Dissociation between variations in m-ATPase and changes in MHC isoform expression were observed. Changes in fraction of active myosin heads, in myosin light chain isoform (MLC) distribution or in MLC phosphorylation were not sufficient to explain the variations in m-ATPase. Myosin post-translational modifications or changes in other myofibrillar proteins may therefore be responsible for the observed variations in m-ATPase activity.

Evidence for Coupled Motion and Hydrogen Tunneling of the Reaction Catalyzed by Glutamate Mutase

Glutamate mutase is one of a group of adenosylcobalamin-dependent enzymes that catalyze unusual isomerizations that proceed through organic radical intermediates generated by homolytic fission of the coenzyme's unique cobalt-carbon bond. These enzymes are part of a larger family of enzymes that catalyze radical chemistry in which a key step is the abstraction of a hydrogen atom from an otherwise inert substrate. To gain insight into the mechanism of hydrogen transfer, we previously used pre-steady-state, rapid-quench techniques to measure the alpha-secondary tritium kinetic and equilibrium isotope effects associated with the formation of 5'-deoxyadenosine when glutamate mutase was reacted with [5'-(3)H]adenosylcobalamin and L-glutamate. We showed that both the kinetic and equilibrium isotope effects are large and inverse, 0.76 and 0.72, respectively. We have now repeated these measurements using glutamate deuterated in the position of hydrogen abstraction. The effect of introducing a primary deuterium kinetic isotope effect on the hydrogen transfer step is to reduce the magnitude of the secondary kinetic isotope effect to a value close to unity, 1.05 +/- 0.08, whereas the equilibrium isotope effect is unchanged. The significant reduction in the secondary kinetic isotope effect is consistent with motions of the 5'-hydrogen atoms being coupled in the transition state to the motion of the hydrogen undergoing transfer, in a reaction that involves a large degree of quantum tunneling.

Preparation of homogeneous Pb(Zr xTi 1− x)O 3 by a rapid-quenching technique and its compositional fluctuation

The effect of a rapid-quenching technique on the elimination of compositional fluctuation was investigated for a solid solution of PbZrO3–PbTiO3 system (PZT). A mixture of ZrO2 and TiO2 was rapidly quenched. The rapidly quenched materials were mixed with PbO and heated. PZT was formed without intermediate compounds. By using the Williamson–Hall method, it was found that PZT prepared using a rapid-quenching technique had almost no compositional fluctuation.

Crystal Structures Representing the Michaelis Complex and the Thiouronium Reaction Intermediate of Pseudomonas aeruginosa Arginine Deiminase

L-arginine deiminase (ADI) catalyzes the irreversible hydrolysis of L-arginine to citrulline and ammonia. In a previous report of the structure of apoADI from Pseudomonas aeruginosa, the four residues that form the catalytic motif were identified as Cys406, His278, Asp280, and Asp166. The function of Cys406 in nucleophilic catalysis has been demonstrated by transient kinetic studies. In this study, the structure of the C406A mutant in complex with L-arginine is reported to provide a snapshot of the enzyme.substrate complex. Through the comparison of the structures of apoenzyme and substrate-bound enzyme, a substrate-induced conformational transition, which might play an important role in activity regulation, was discovered. Furthermore, the position of the guanidinium group of the bound substrate relative to the side chains of His278, Asp280, and Asp166 indicated that these residues mediate multiple proton transfers. His278 and Asp280, which are positioned to activate the water nucleophile in the hydrolysis of the S-alkylthiouronium intermediate, were replaced with alanine to stabilize the intermediate for structure determination. The structures determined for the H278A and D280A mutants co-crystallized with L-arginine provide a snapshot of the S-alkylthiouronium adduct formed by attack of Cys406 on the guanidinium carbon of L-arginine followed by the elimination of ammonia. Asp280 and Asp166 engage in ionic interactions with the guanidinium group in the C406A ADI. L-arginine structure and might orient the reaction center and participate in proton transfer. Structure determination of D166A revealed the apoD166A ADI. The collection of structures is interpreted in the context of recent biochemical data to propose a model for ADI substrate recognition and catalysis.

Probing the role of tightly bound phosphoenolpyruvate in Escherichia coli 3-deoxy- d- manno-octulosonate 8-phosphate synthase catalysis using quantitative time-resolved electrospray ionization mass spectrometry in the millisecond time range

Escherichia coli 3-deoxy- d- manno-octulosonate 8-phosphate (KDO8P) synthase catalyzes the condensation of phosphoenolpyruvate (PEP) and d-arabinose 5-phosphate (A5P) to produce KDO8P and inorganic phosphate. The enzyme is often isolated with varying amounts of tightly bound PEP substrate. To better understand the role of tightly bound PEP in E. coli KDO8P synthase catalysis, a combination of transient kinetic methodologies including rapid chemical quench and mass spectrometry techniques such as time-resolved electrospray ionization mass spectrometry (ESI-TOF MS) were used to study the enzyme purified both in the PEP-bound state and in the unbound state. Pre-steady state burst and single-turnover experiments using radiolabeled [1- 14C] and [ 32P]A5P revealed significant kinetic differences between these enzyme preparations. The active sites concentrations for the bound and unbound states of the enzyme were almost the same (∼100%) and the product release for both states of the enzyme was rate limiting. However, the rate constant of product formation for the PEP-bound enzyme (125 s −1) was higher than that of the unbound enzyme (46 s −1). This was further confirmed by single-turnover experiments using radiolabeled [ 32P]A5P. Interestingly, when PEP was removed from the PEP-bound enzyme and external PEP was added before the kinetic experiments, both the pre-steady state burst and the single-turnover kinetic parameters were similar to those of the enzyme purified in the unbound state. The rate constants of product formation were determined as 44 s −1 (burst experiment) and 48 s −1 (single-turnover experiment). The reaction kinetics of the E. coli KDO8P synthase was also followed by time-resolved ESI mass spectrometry. To validate the suitability of this technique for conducting enzyme kinetics, the standard reaction of p-nitrophenyl acetate hydrolysis by chymotrypsin was analyzed by stopped-flow and time-resolved ESI-TOF MS. The rate constant of p-nitrophenol formation followed by stopped-flow spectrophotometry matched perfectly the rate constant of acetyl–chymotrypsin intermediate formation followed by time-resolved ESI-TOF MS (0.1 s −1). The catalytic properties of the PEP-bound and unbound states of the E. coli KDO8P synthase were then studied on a millisecond time scale. The changes in the intensity of E•PEP, E•KDO8P, and E•intermediate complexes as a function of time were quantified and the reaction kinetics were modeled using KinTekSim simulation software. An analysis of the reaction kinetics established the kinetic competence of the intermediate based upon the rate constants for substrate decay and product formation. The ability of time-resolved ESI-TOF MS to detect and monitor the kinetics for the reaction intermediate constitutes a significant advantage over the traditional rapid chemical quench technique. For all three states of the enzyme (PEP-bound, unbound, and PEP removed from the PEP-bound state) the rate constants obtained by time-resolved ESI-TOF MS matched the pre-steady state rates determined by rapid chemical quench. A comparison of reaction time courses for each state of the enzyme revealed that, in the case of PEP-bound enzyme, the enzymatic reaction reached completion faster than that for the unbound state. In summary, these studies led to the conclusion that bound PEP has an important role in catalysis, maintaining the enzyme in a conformational state optimal for catalytic activity, and established the kinetic competence of the reaction intermediate. This technique has broad applicability for the kinetic analysis of any enzyme system where the substrates, products, or intermediates are eluding the common detection techniques or as a method alternative to the widely used radioactivity assays.

Pre-steady-state measurement of intrinsic secondary tritium isotope effects associated with the homolysis of adenosylcobalamin and the formation of 5'-deoxyadensosine in glutamate mutase.

Glutamate mutase is one of a group of adenosylcobalamin-dependent enzymes that catalyze a variety of reactions that proceed through organic radical intermediates generated by homolytic fission of coenzyme's unique cobalt-carbon bond. For all the enzymes that have been examined, the homolysis step is kinetically indistinguishable from abstraction of hydrogen from the substrate (or protein), implying that deoxyadenosyl radical is formed only as a fleeting intermediate. To examine how these two steps are coupled together, we have used pre-steady-state, rapid quench techniques to measure the alpha-secondary tritium isotope effect associated with the formation of 5'-deoxyadenosine when the enzyme is reacted with [5'-(3)H]-adenosylcobalamin and L-glutamate. Surprisingly, a large inverse equilibrium isotope effect of 0.72 +/- 0.04 was found for the overall reaction, indicating that the 5'-C-H bonds become significantly stiffer on going from adenosylcobalamin to 5'-deoxyadenosine, even though the 5'-carbon remains formally sp(3) hybridized. The kinetic isotope effect for the formation of 5'-deoxyadenosine was 0.76 +/- 0.02, which suggests a late transition state for the reaction.

Timing of epimerization and condensation reactions in nonribosomal peptide assembly lines: kinetic analysis of phenylalanine activating elongation modules of tyrocidine synthetase B.

The cyclic decapeptide antibiotic tyrocidine has D-Phe residues at positions 1 and 4, produced during peptide chain growth from L-Phe residues by 50 kDa epimerase (E) domains embedded, respectively, in the initiation module (TycA) and the TycB3 module of the three-subunit (TycABC), 10-module nonribosomal peptide synthetase. While the initiation module clearly epimerizes the aminoacyl thioester Phe1-S-TycA intermediate, the timing of epimerization versus peptide bond condensation at internal E domains has been less well characterized in nonribosomal peptide synthetases. In this study, we use rapid quench techniques to evaluate a three-domain (ATE) and a four-domain version (CATE) of the TycB3 module and a six-domain fragment (ATCATE) of the TycB2(-3) bimodule to measure the ability of the E domain in the TycB3 module to epimerize the aminoacyl thioester Phe-S-TycB3 and the dipeptidyl-S-enzyme (L-Phe-L-Phe-S-TycB3 if L-Phe-D-Phe-S-TycB3). The chiralities of the Phe-S-enzyme and Phe-Phe-S-enzyme species over time were determined by hydrolysis and chiral TLC separations, allowing for the clear conclusion that epimerization in the internal TycB3 module occurs preferentially on the peptidyl-S-enzyme rather than the aminoacyl-S-enzyme, by a factor of about 3000/1. In turn, this imposes constraints on the chiral selectivity of the condensation (C) domains immediately upstream and downstream of E domains. The stereoselectivity of the upstream C domain was shown to be L-selective at both donor and acceptor sites ((L)C(L)) by site-directed mutagenesis studies of an E domain active site residue and using the small-molecule surrogate D-Phe-Pro-L-Phe-N-acetylcysteamine thioester (D-Phe-Pro-L-Phe-SNAC) and D-Phe-Pro-D-Phe-SNAC as donor probes.

The Kinetic Mechanism of the Human Bifunctional Enzyme ATIC (5-Amino-4-imidazolecarboxamide Ribonucleotide Transformylase/Inosine 5′-Monophosphate Cyclohydrolase): A SURPRISING LACK OF SUBSTRATE CHANNELING

5-Amino-4-imidazolecarboxamide ribonucleotide transformylase/IMP cyclohydrolase (ATIC) is a bifunctional protein possessing two enzymatic activities that sequentially catalyze the last two steps in the pathway for de novo synthesis of inosine 5'-monophosphate. This bifunctional enzyme is of particular interest because of its potential as a chemotherapeutic target. Furthermore, these two catalytic activities reside on the same protein throughout all of nature, raising the question of whether there is some kinetic advantage to the bifunctionality. Rapid chemical quench, stopped-flow absorbance, and steady-state kinetic techniques were used to elucidate the complete kinetic mechanism of human ATIC. The kinetic simulation program KINSIM was used to model the kinetic data obtained in this study. The detailed kinetic analysis, in combination with kinetic simulations, provided the following key features of the enzyme reaction pathway. 1) The rate-limiting step in the overall reaction (2.9 +/- 0.4 s(-1)) is likely the release of tetrahydrofolate from the formyltransferase active site or a conformational change associated with tetrahydrofolate release. 2) The rate of the reverse transformylase reaction (6.7 s(-1)) is approximately 2-3-fold faster than the forward rate (2.9 s(-1)), whereas the cyclohydrolase reaction is essentially unidirectional in the forward sense. The cyclohydrolase reaction thus draws the overall bifunctional reaction toward the production of inosine monophosphate. 3) There was no kinetic evidence of substrate channeling of the intermediate, the formylaminoimidazole carboxamide ribonucleotide, between the formyltransferase and the cyclohydrolase active sites.

Structural and magnetic properties of metastableFe1-xSix (0.15

Fe1-xSix (0.15<x<0.375) alloys have been prepared bya rapid-quenching technique. X-ray diffraction patterns show thatthese alloys consist of submicron grains between 100 and300 nm. The DO3 cubic symmetry could be obtained for Sicontent up to 34 at.% Si. This feature is particularlyinteresting since alloys containing more than 26 at.% Si and cast with usual techniques consist of a mixture of Fe3Siand Fe5Si3. The magnetization, Curie temperatureand resistivity data for these fine-grained alloys areconsistent with those for bulk alloys for Si content below 25at.% Si. In contrast, the structural and physical data forsingle-phase alloys with 28-34 silicon content are reported forthe first time. Within this composition range, the magnetizationand Curie point values roughly correspond to those suggestedby the extrapolation of existing data. However, theresistivity shows an unexpected marked increase above 25 at.% Si. The values of resistivity, magnetization and effectiveanisotropy of soft-magnetic nanocrystalline Fe2Si are found to be 200 µΩ cm, 0.6 T and 15 kJ m-3respectively, suggesting that this alloy has potential for high-frequency applications.

Steady-state and pre-steady-state kinetic analysis of Mycobacterium tuberculosis pantothenate synthetase.

Pantothenate synthetase (EC 6.3.2.1), encoded by the panC gene, catalyzes the essential ATP-dependent condensation of D-pantoate and beta-alanine to form pantothenate in bacteria, yeast and plants. Pantothenate synthetase from Mycobacterium tuberculosis was expressed in E. coli, purified to homogeneity, and found to be a homodimer with a subunit molecular mass of 33 kDa. Initial velocity, product, and dead-end inhibition studies showed the kinetic mechanism of pantothenate synthetase to be Bi Uni Uni Bi Ping Pong, with ATP binding followed by D-pantoate binding, release of PP(i), binding of beta-alanine, followed by the release of pantothenate and AMP. Michaelis constants were 0.13, 0.8, and 2.6 mM for D-pantoate, beta-alanine, and ATP, respectively, and the turnover number, k(cat), was 3.4 s(-1). The formation of pantoyl adenylate, suggested as a key intermediate by the kinetic mechanism, was confirmed by (31)P NMR spectroscopy of [(18)O]AMP produced from (18)O transfer using [carboxyl-(18)O]pantoate. Single-turnover reactions for the formation of pyrophosphate and pantothenate were determined using rapid quench techniques, and indicated that the two half-reactions occurred with maximum rates of 1.3 +/- 0.3 and 2.6 +/- 0.3 s(-)(1), respectively, consistent with pantoyl adenylate being a kinetically competent intermediate in the pantothenate synthetase reaction. These data also suggest that both half-reactions are partially rate-limiting. Reverse isotope exchange of [(14)C]-beta-alanine into pantothenate in the presence of AMP was observed, indicating the reversible formation of the pantoyl adenylate intermediate from products.

Nucleotide release and associated conformational changes regulate function in the COOH-terminal Src kinase, Csk.

The COOH-terminal Src kinase (Csk) regulates a broad array of cellular processes via the specific phosphorylation and downregulation of Src family protein kinases. While Csk has been a topic for steady-state kinetic studies, the individual steps associated with substrate phosphorylation have not been investigated. To understand active-site phenomena, pre-steady-state and transient-state kinetic methods were applied to develop a catalytic pathway for substrate processing. Rapid quench flow techniques show that the phosphorylation of a substrate peptide, generated from a random library, occurs in two kinetic phases: a rapid, exponential "burst" phase followed by a slow, linear phase. The amplitude of the burst phase increases as a function of enzyme concentration, indicating that the biphasic kinetics are not the result of product inhibition. Analysis of the burst rate as a function of substrate concentration indicates that the phosphoryl transfer step is fast (k3 > or = 140 s(-1) and highly favorable (k3/k-3 > or = 6). The apparent dissociation rate constant for ADP (0.6 s(-1), measured using stopped-flow kinetic methods and a fluorescent trapping agent, mant-ATP, is close to kcat. Since the substrate dissociation constant is high, the release of phosphopeptide is not likely to limit turnover. These findings indicate that Csk rapidly delivers the gamma-phosphate of ATP to the substrate and rapidly releases the phosphoproduct. Overall rate limitation in the steady state is then attributed to the slow, net dissociation of ADP. Viscosometric studies suggest that this final event in the catalytic cycle is coupled with slow conformational changes.

Kinetic analysis of three activated phenylalanyl intermediates generated by the initiation module PheATE of gramicidin S synthetase.

The three-domain initiation module PheATE (GrsA) of Bacillus brevis gramicidin S synthetase catalyzes the activation, thiolation and epimerization of L-phenylalanine (L-Phe), the first amino acid incorporated into the decapeptide antibiotic gramicidin S. There are three activated intermediates in the PheATE catalyzed chemical pathway: L-phenylalanyl-adenosine-5'-monophosphate diester (L-Phe-AMP), L-Phe-S-4'-phosphopantetheine(Ppant)- and D-Phe-S-4'-Ppant-acyl enzyme. In this study, we examined PheATE in single-turnover catalysis using rapid chemical quench techniques. Kinetic modeling of the process of disappearance of the substrate L-Phe, transient appearance and disappearance of L-Phe-AMP and the ad seriatim formation and equilibration of the L- and D-Phe-S-Ppant-acyl enzyme adducts allowed evaluation of the microscopic rate constants for the three chemical reactions in the initiation module PheATE. This study provides the first transient-state kinetic analysis of a nonribosomal peptide synthetase (NRPS) module.