Chemical Quench Research Articles

Effect of the N-terminal extension in myosin essential light chain A1 on the mechanism of actomyosin ATP hydrolysis

Myosin essential light chains A1 and A2 are identical isoforms except for an extension of ∼40 amino acids at the N terminus of A1 that binds F-actin. The extension has no bearing on the burst hydrolysis rate (M-ATP → M-ADP-Pi) as determined by chemical quench flow (100μM isoenzyme). Whereas actomyosin-S1A2 steady state MgATPase (low ionic strength, 20 °C) is hyperbolically dependent on concentration: Vmax 7.6s-1, Kapp 6.4μM (F-actin) and Vmax 10.1s-1, Kapp 5.5μM (native thin filaments, pCa 4), the relationship for myosin-S1A1 is bimodal; an initial rise at low concentration followed by a decline to one-third the Vmax of S1A2, indicative of more than one rate-limiting step and A1-enforced flux through the slower actomyosin-limited hydrolysis pathway. In double-mixing stopped-flow with an indicator, Ca(II)-mediated activation of Pi dissociation (regulatedAM-ADP-Pi → regulatedAM-ADP+ Pi) is attenuated by A1 attachment to thin filaments (pCa 4). The maximum accelerated rates of Pi dissociation are: 81s-1(S1A1, Kapp 8.9μM) versus 129s-1(S1A2, Kapp 58μM). To investigate apomyosin-S1-mediated activation, thin filaments (EGTA) are premixed with a given isomyosin-S1 and double-mixing is repeated with myosin-S1A1 in the first mix. Similar maximum rates of Pi dissociation are observed, 44.5s-1(S1A1) and 47.1s-1(S1A2), which are lower than for Ca(II) activation. Overall, these results biochemically demonstrate how the longer light chain A1 can contribute to slower contraction and higher force and the shorter version A2 to faster contraction and lower force, consistent with their distribution in different types of striated muscle.

Demonstration of low-level biogenic fuel content using quench curve and direct liquid scintillation counting (LSC) methods

An investigation into the direct method for liquid scintillation counting (LSC) quantification of biogenic fuel content in fuel blendstock is presented. This method development intentionally used a colored matrix (∼99 wt%), fossil diesel fraction, and low-level biogenic fractions (∼1 wt%) to determine the applicability of the LSC technique in colored blend mixtures. LSC procedures for quench correction, includingtheuse ofan instrument internal standard (QuantulusSQP values), color quench curves,andaninternal14C standardspike on samples containing low-level amounts of biogenic gasoline, jet, and diesel mixed with fossil fuel, were compared.Samples were analyzed on both Perkin-ElmerQuantulusand Tri-Carb instruments, and the 14C contents were compared with those determined by accelerator mass spectrometry (AMS). Results from the Tri-Carb instrument showed that percent differences of <10 % compared to AMS-reported values are achievable at 5-hour count times despite colored samples. A comparison between the impact of chemical and color quenching in the fuel samples showed that color quenching in highly colored samples reduces efficiency significantly more than chemical quenching, indicating that chemical quench curves are not appropriate for highly colored biofuel/fossil-fuel blended samples. Results indicate that both the direct method with internal spike quench correction and the use of a color-quench curve provide accurate results for 1 % biogenic fuel blends.Additionally, we have explored the use of Fourier transform infrared (FTIR) spectroscopy in measuring the biogenic content of the colored blended fuel samples. Preliminary results show the presence of biogenic carbon-derived fingerprints that are absent in fossil-derived sample. However, further work is needed to develop an FTIR-based quantitative method.

Pre-Steady-State Reactivity of Peptidylglycine Monooxygenase Implicates Ascorbate in Substrate Triggering of the Active Conformer.

Peptidylglycine monooxygenase (PHM) is essential for the posttranslational amidation of neuroendocrine peptides. An important aspect of the PHM mechanism is the complete coupling of oxygen reduction to substrate hydroxylation, which implies no oxygen reactivity of the fully reduced enzyme in the absence of peptidyl substrates. As part of studies aimed at investigating this feature of the PHM mechanism, we explored pre-steady-state kinetics using chemical quench (CQ) and rapid freeze-quench (RFQ) studies of the fully reduced ascorbate-free PHM enzyme. First, we confirmed the absence of Cu(I)-enzyme oxidation by O2 at catalytic rates in the absence of peptidyl substrate. Next, we investigated reactivity in the presence of the substrate dansyl-YVG. Surprisingly, when ascorbate-free di-Cu(I) PHM was shot against oxygenated buffer containing the dansyl-YVG substrate, <15% of the expected product was formed. Substoichiometric reactivity was confirmed by stopped-flow and RFQ EPR spectroscopy. Product generation reached a maximum of 70% by the addition of increasing amounts of the ascorbate cosubstrate in a process that was not the result of multiple turnovers. FTIR spectroscopy of the Cu(I)-CO reaction chemistry was then used to show that increasing ascorbate concentrations correlated with a substrate-induced Cu(I)M-CO species characteristic of an altered conformation. We conclude that ascorbate and peptidyl substrate work together to induce a transition from an inactive to an active conformation and suggest that the latter may represent the "closed" conformation (Cu-Cu of ∼4 Å) recently observed for both PHM and its sister enzyme DBM by crystallography.

Using kinetic isotope effects to probe the mechanism of adenosylcobalamin-dependent enzymes.

Adenosylcobalamin- (AdoCbl) dependent enzyme reactions involved the transfer of hydrogen atoms between the 5'-carbon of the coenzyme and the substrates and products of the reaction. Tritium and deuterium kinetic isotope effect measurements are, therefore, a valuable tool to probe the mechanisms of AdoCbl-dependent enzymes, as they can provide information about the reaction pathway and the rate-determining step. Furthermore, if the intrinsic kinetic isotope effect can be isolated, information on the nature of the transition state associated with hydrogen transfer can be obtained. In this chapter I present methods for the preparation of isotopically-labeled AdoCbl and their use in rapid chemical quench experiments that allow isotope effects on specific steps in the reaction to be isolated. These techniques are illustrated with examples from my laboratory's studies on the AdoCbl dependent enzyme, glutamate mutase.

Carbon-negative hydrogen: Exploring the techno-economic potential of biomass co-gasification with CO2 capture

The hydrogen economy is receiving increasing attention as a complement to electrification in the global energy transition. Clean hydrogen production is often viewed as a competition between natural gas reforming with CO2 capture and electrolysis using renewable electricity. However, solid fuel gasification with CO2 capture presents another viable alternative, especially when considering the potential of biomass to achieve negative CO2 emissions. This study investigates the techno-economic potential of hydrogen production from large-scale coal/biomass co-gasification plants with CO2 capture. With a CO2 price of 50 €/ton, the benchmark plant using commercially available technologies achieved an attractive hydrogen production cost of 1.78 €/kg, with higher CO2 prices leading to considerable cost reductions. Advanced configurations employing hot gas clean-up, membrane-assisted water-gas shift, and more efficient gasification with slurry vaporization and a chemical quench reduced the hydrogen production cost to 1.50–1.62 €/kg with up to 100% CO2 capture. Without contingencies added to the pre-commercial technologies, the lowest cost reduces to 1.43 €/kg. It was also possible to recover waste heat in the form of hot water at 120 °C for district heating, potentially unlocking further cost reductions to 1.24 €/kg. In conclusion, gasification of locally available solid fuels should be seriously considered next to natural gas and electrolysis for supplying the emerging hydrogen economy.

Optimized incorporation of an unnatural fluorescent amino acid affords measurement of conformational dynamics governing high-fidelity DNA replication

DNA polymerase from bacteriophage T7 undergoes large, substrate-induced conformational changes that are thought to account for high replication fidelity, but prior studies were adversely affected by mutations required to construct a Cys-lite variant needed for site-specific fluorescence labeling. Here we have optimized the direct incorporation of a fluorescent un-natural amino acid, (7-hydroxy-4-coumarin-yl)-ethylglycine, using orthogonal amber suppression machinery in Escherichia coli MS methods verify that the unnatural amino acid is only incorporated at one position with minimal background. We show that the single fluorophore provides a signal to detect nucleotide-induced conformational changes through equilibrium and stopped-flow kinetic measurements of correct nucleotide binding and incorporation. Pre-steady-state chemical quench methods show that the kinetics and fidelity of DNA replication catalyzed by the labeled enzyme are largely unaffected by the unnatural amino acid. These advances enable rigorous analysis to establish the kinetic and mechanistic basis for high-fidelity DNA replication.

Vránaite, ideally Al16B4Si4O38, a new mineral related to boralsilite, Al16B6Si2O37, from the Manjaka pegmatite, Sahatany Valley, Madagascar

The system B2O3-Al2O3-SiO2 (BAS) includes two ternary phases occurring naturally, boromullite, Al9BSi2O19, and boralsilite, Al46B6Si2O37, as well as synthetic compounds structurally related to mullite. The new mineral vranaite, a third naturally occurring anhydrous ternary BAS phase, is found with albite and K-feldspar as a breakdown product of spodumene in the elbaite-subtype Manjaka granitic pegmatite, Sahatany Valley, Madagascar. Boralsilite also occurs in this association, although separately from vrnnaite; both minerals form rare aggregates of subparallel prisms up to 100 p.m long. Vranaite is monoclinic, space group 121m, a= 10.3832(12), b= 5.6682(7), c= 10.8228(12) angstrom, beta = 90.106(11)degrees; V= 636.97(13) angstrom(3), Z= 1. In the structure [R-1, = 0.0416 for 550 F-o> 4 sigma F-o], chains of A106 octahedra run parallel to [010] and are cross-linked by Si207 disilicate groups, B03 triangles, and clusters of A104 and two A105 polyhedra. If all sites were filled (Al4 and Al5 to 50%), the formula becomes Al16B4Si4O38, close to Li1.08Be0.47Fe0.02Al14 65B3.89Si3.88O36.62 calculated from the analyses assuming cations sum to 24. The compatibility index based on the Gladstone-Dale relationship is 0.001 (superior). Assemblages with vranaite and boralsilite are inferred to represent initial reaction products of a residual liquid rich in Li, Be, Na, K, and B during a pressure and chemical quench, but at low H2O activities due to early melt contamination by carbonate in the host rocks. The two BAS phases are interpreted to have crystallized metastably in lieu of dumortierite in accordance with Ostwald Step Rule, possibly first as boron mullite, then as monoclinic phases. The presence of such metastable phases is suggestive that pegmatites crystallize, at least partially, by disequilibrium processes, with significant undercooling, and at high viscosities, which limit diffusion rates.

Adsorption of Alkali Metal by High-temperature Acid-treated Coal Char

Gas phase alkali metal compounds contribute to fouling, slagging, corrosion, and agglomeration problems in a gasifier system. Vapors of alkali metal compounds can be removed by quench of gases and the adsorption of char/ash in a chemical quench process. In the present study, an experimental investigation was performed to describe the properties of alkali vapor adsorption by the high-temperature coal char with NaCl as the alkali metal model compound. The experimental results may be helpful to control the alkali metal corrosion in coal gasifier.

The Reaction Mechanism of Methyl-Coenzyme M Reductase: HOW AN ENZYME ENFORCES STRICT BINDING ORDER

Methyl-coenzyme M reductase (MCR) is a nickel tetrahydrocorphinoid (coenzyme F430) containing enzyme involved in the biological synthesis and anaerobic oxidation of methane. MCR catalyzes the conversion of methyl-2-mercaptoethanesulfonate (methyl-SCoM) and N-7-mercaptoheptanoylthreonine phosphate (CoB7SH) to CH4 and the mixed disulfide CoBS-SCoM. In this study, the reaction of MCR from Methanothermobacter marburgensis, with its native substrates was investigated using static binding, chemical quench, and stopped-flow techniques. Rate constants were measured for each step in this strictly ordered ternary complex catalytic mechanism. Surprisingly, in the absence of the other substrate, MCR can bind either substrate; however, only one binary complex (MCR·methyl-SCoM) is productive whereas the other (MCR·CoB7SH) is inhibitory. Moreover, the kinetic data demonstrate that binding of methyl-SCoM to the inhibitory MCR·CoB7SH complex is highly disfavored (Kd = 56 mM). However, binding of CoB7SH to the productive MCR·methyl-SCoM complex to form the active ternary complex (CoB7SH·MCR(Ni(I))·CH3SCoM) is highly favored (Kd = 79 μM). Only then can the chemical reaction occur (kobs = 20 s(-1) at 25 °C), leading to rapid formation and dissociation of CH4 leaving the binary product complex (MCR(Ni(II))·CoB7S(-)·SCoM), which undergoes electron transfer to regenerate Ni(I) and the final product CoBS-SCoM. This first rapid kinetics study of MCR with its natural substrates describes how an enzyme can enforce a strictly ordered ternary complex mechanism and serves as a template for identification of the reaction intermediates.

Progress in the experimental observation of thiamin diphosphate-bound intermediates on enzymes and mechanistic information derived from these observations

Thiamin diphosphate (ThDP), the vitamin B1 coenzyme is an excellent representative of coenzymes, which carry out electrophilic catalysis by forming a covalent complex with their substrates. The function of ThDP is to greatly increase the acidity of two carbon acids by stabilizing their conjugate bases, the ylide/carbene/C2-carbanion of the thiazolium ring and the C2α-carbanion/enamine, once the substrate binds to ThDP. In recent years, several ThDP-bound intermediates on such pathways have been characterized by both solution and solid-state methods. Prominent among these advances are X-ray crystallographic results identifying both oxidative and non-oxidative intermediates, rapid chemical quench followed by NMR detection of several intermediates which are stable under acidic conditions, solid-state NMR and circular dichroism detection of the states of ionization and tautomerization of the 4′-aminopyrimidine moiety of ThDP in some of the intermediates. These methods also enabled in some cases determination of the rate-limiting step in the complex series of steps. This review is an update of a review with the same title published by the authors in 2005 in this Journal. Much progress has been made in the intervening decade in the identification of the intermediates and their application to gain additional mechanistic insight.

Metal stopping reagents facilitate discontinuous activity assays of the de novo purine biosynthesis enzyme PurE

The conversion of 5-aminoimidazole ribonucleotide (AIR) to 4-carboxy-AIR (CAIR) represents an unusual divergence in purine biosynthesis: microbes and nonmetazoan eukaryotes use class I PurEs while animals use class II PurEs. Class I PurEs are therefore a potential antimicrobial target; however, no enzyme activity assay is suitable for high throughput screening (HTS). Here we report a simple chemical quench that fixes the PurE substrate/product ratio for 24h, as assessed by the Bratton–Marshall assay (BMA) for diazotizable amines. The ZnSO4 stopping reagent is proposed to chelate CAIR, enabling delayed analysis of this acid-labile product by BMA or other HTS methods.

A Diiron(III,IV) Imido Species Very Active in Nitrene‐Transfer Reactions

Metal-catalyzed nitrene transfer reactions arouse intense interest as clean and efficient procedures for amine synthesis. Efficient Rh- and Ru-based catalysts exist but Fe alternatives are actively pursued. However, reactive iron imido species can be very short-lived and getting evidence of their occurrence in efficient nitrene-transfer reactions is an important challenge. We recently reported that a diiron(III,II) complex is a very efficient nitrene-transfer catalyst to various substrates. We describe herein how, by combining desorption electrospray ionization mass spectrometry, quantitative chemical quench experiments, and DFT calculations, we obtained conclusive evidence for the occurrence of an {Fe(III) Fe(IV) NTosyl} intermediate that is very active in H-abstraction and nitrene-transfer reactions. DFT calculations revealed a strong radical character of the tosyl nitrogen atom in very low-lying electronic configurations of the Fe(IV) ion which are likely to confer its high reactivity.

A Diiron(III,IV) Imido Species Very Active in Nitrene‐Transfer Reactions

AbstractMetal‐catalyzed nitrene transfer reactions arouse intense interest as clean and efficient procedures for amine synthesis. Efficient Rh‐ and Ru‐based catalysts exist but Fe alternatives are actively pursued. However, reactive iron imido species can be very short‐lived and getting evidence of their occurrence in efficient nitrene‐transfer reactions is an important challenge. We recently reported that a diiron(III,II) complex is a very efficient nitrene‐transfer catalyst to various substrates. We describe herein how, by combining desorption electrospray ionization mass spectrometry, quantitative chemical quench experiments, and DFT calculations, we obtained conclusive evidence for the occurrence of an {FeIIIFeIVNTosyl} intermediate that is very active in H‐abstraction and nitrene‐transfer reactions. DFT calculations revealed a strong radical character of the tosyl nitrogen atom in very low‐lying electronic configurations of the FeIV ion which are likely to confer its high reactivity.

Position of Phenylalanine in the Relay Loop is Important for Myosin Motor Action

We have scanned phenylalanine in the relay loop of Dictyostelium discoideum myosin to study the role of the relay loop in the myosin ATPase actin activation. It is known that C-terminus of the relay loop is on the actin binding interface. Myosin crystal structures show that F506 of the relay loop interacts with F487 of the relay helix in the post-recovery stroke structural state. This interaction is absent in the pre-recovery stroke state due to the linear shift of the relay loop along the relay helix. We hypothesized that actin binding facilitates this conformational change in the relay loop-helix region, thus activating myosin ATPase rate. The goal of the phenylalanine scan was to simulate the loop-helix shift and populate myosin pre- or post-recovery stroke structural states, mimicking proposed effect of actin binding. Two myosin mutants were designed (F506A:D505F and F506A:G507F), along with the wild type myosin (F506) placing phenylalanine in the three consecutive positions within the relay loop. We have used transient time-resolved FRET, myosin intrinsic fluorescence, pyrene labeled actin, and chemical quench to characterize myosin kinetics in detail and conclude on the role of F506 in myosin relay loop. Supported by NIH AR59621.

Molecular Basis for the Resistance of Human Mitochondrial 2-Cys Peroxiredoxin 3 to Hyperoxidation

Peroxiredoxins (Prxs) detoxify peroxides and modulate H2O2-mediated cell signaling in normal and numerous pathophysiological contexts. The typical 2-Cys subclass of Prxs (human Prx1-4) utilizes a Cys sulfenic acid (Cys-SOH) intermediate and disulfide bond formation across two subunits during catalysis. During oxidative stress, however, the Cys-SOH moiety can react with H2O2 to form Cys sulfinic acid (Cys-SO2H), resulting in inactivation. The propensity to hyperoxidize varies greatly among human Prxs. Mitochondrial Prx3 is the most resistant to inactivation, but the molecular basis for this property is unknown. A panel of chimeras and Cys variants of Prx2 and Prx3 were treated with H2O2 and analyzed by rapid chemical quench and time-resolved electrospray ionization-TOF mass spectrometry. The latter utilized an on-line rapid-mixing setup to collect data on the low seconds time scale. These approaches enabled the first direct observation of the Cys-SOH intermediate and a putative Cys sulfenamide (Cys-SN) for Prx2 and Prx3 during catalysis. The substitution of C-terminal residues in Prx3, residues adjacent to the resolving Cys residue, resulted in a Prx2-like protein with increased sensitivity to hyperoxidation and decreased ability to form the intermolecular disulfide bond between subunits. The corresponding Prx2 chimera became more resistant to hyperoxidation. Taken together, the results of this study support that the kinetics of the Cys-SOH intermediate is key to determine the probability of hyperoxidation or disulfide formation. Given the oxidizing environment of the mitochondrion, it makes sense that Prx3 would favor disulfide bond formation as a protection mechanism against hyperoxidation and inactivation.

Roles of Pyrophosphorolysis in Transcription Initiation

RNA polymerase can cleave NMP at 3'end of nascent RNA by adding pyrophosphate (PPi) to the NMP, and produces NTP. This reaction called pyrophosphorolysis is a chemically reverse reaction of RNA elongation. During transcription elongation, pyrophosphorolysis is typically 10∧3-10∧4-fold slower than RNA elongation under physiological [NTP] and [PPi]. This is required for a processivity of transcription elongation. However, pyrophosphorolysis during transcription initiation prior to formation of a processive elongation complex is not well characterized. We made an initiation complex of E. coli RNA polymerase that retains 9-nt RNA by transcribing the RNA from a psbA2 promoter. We analyzed the rates of pyrophosphorolysis with 50 μM PPi and 1-nt RNA elongation with 500 μM GTP by a rapid chemical quench flow. Surprisingly, the promoter-initiated complex had a fraction that performs pyrophosphorolysis 10-fold faster than elongation in the substrate concentrations that are similar to physiological ones. We could not observe the fraction in a complex assembled with synthetic RNA and DNA oligos in which a transcription initiation factor σ is released (Sidorenkov et al., Mol Cell 1998). Thus, the rapid pyrophosphorolysis appears to be specific for the promoter initiated complex. A mechanism of the rapid pyrophosphorolysis and its involvement in proofreading are discussed.

Isotope Effects Suggest a Stepwise Mechanism for Berberine Bridge Enzyme

The flavoprotein Berberine Bridge Enzyme (BBE) catalyzes the regioselective oxidative cyclization of (S)-reticuline to (S)-scoulerine in an alkaloid biosynthetic pathway. A series of solvent and substrate deuterium kinetic isotope effect studies were conducted to discriminate between a concerted mechanism, in which deprotonation of the substrate phenol occurs before or during the transfer of a hydride from the substrate to the flavin cofactor and substrate cyclization, and a stepwise mechanism, in which hydride transfer results in the formation of a methylene iminium ion intermediate that is subsequently cyclized. The substrate deuterium isotope effect of 3.5 on k(red), the rate constant for flavin reduction, is pH-independent, indicating that C-H bond cleavage is rate-limiting during flavin reduction. Solvent isotope effects on k(red) are equal to 1 for both wild-type BBE and the E417Q mutant, indicating that solvent exchangeable protons are not in flight during or before flavin reduction, thus eliminating a fully concerted mechanism as a possibility for catalysis by BBE. An intermediate was not detected by rapid chemical quench or continuous-flow mass spectrometry experiments, indicating that it must be short-lived.

Kinetic Analysis of DNA Strand Joining by Chlorella Virus DNA Ligase and the Role of Nucleotidyltransferase Motif VI in Ligase Adenylylation

Chlorella virus DNA ligase (ChVLig) is an instructive model for mechanistic studies of the ATP-dependent DNA ligase family. ChVLig seals 3'-OH and 5'-PO(4) termini via three chemical steps: 1) ligase attacks the ATP α phosphorus to release PP(i) and form a covalent ligase-adenylate intermediate; 2) AMP is transferred to the nick 5'-phosphate to form DNA-adenylate; 3) the 3'-OH of the nick attacks DNA-adenylate to join the polynucleotides and release AMP. Each chemical step requires Mg(2+). Kinetic analysis of nick sealing by ChVLig-AMP revealed that the rate constant for phosphodiester synthesis (k(step3) = 25 s(-1)) exceeds that for DNA adenylylation (k(step2) = 2.4 s(-1)) and that Mg(2+) binds with similar affinity during step 2 (K(d) = 0.77 mM) and step 3 (K(d) = 0.87 mM). The rates of DNA adenylylation and phosphodiester synthesis respond differently to pH, such that step 3 becomes rate-limiting at pH ≤ 6.5. The pH profiles suggest involvement of one and two protonation-sensitive functional groups in catalysis of steps 2 and 3, respectively. We suggest that the 5'-phosphate of the nick is the relevant protonation-sensitive moiety and that a dianionic 5'-phosphate is necessary for productive step 2 catalysis. Motif VI, located at the C terminus of the OB-fold domain of ChVLig, is a conserved feature of ATP-dependent DNA ligases and GTP-dependent mRNA capping enzymes. Presteady state and burst kinetic analysis of the effects of deletion and missense mutations highlight the catalytic contributions of ChVLig motif VI, especially the Asp-297 carboxylate, exclusively during the ligase adenylylation step.

Temporal Resolution of Autophosphorylation for Normal and Oncogenic Forms of EGFR and Differential Effects of Gefitinib

Epidermal growth factor receptor (EGFR) is a member of the ErbB family of receptor tyrosine kinases (RTK). EGFR overexpression or mutation in many different forms of cancers has highlighted its role as an important therapeutic target. Gefitinib, the first small molecule inhibitor of EGFR kinase function to be approved for the treatment of nonsmall cell lung cancer (NSCLC) by the FDA, demonstrates clinical activity primarily in patients with tumors that harbor somatic kinase domain mutations in EGFR. Here, we compare wild-type EGFR autophosphorylation kinetics to the L834R (also called L858R) EGFR form, one of the most common mutations in lung cancer patients. Using rapid chemical quench, time-resolved electrospray mass spectrometry (ESI-MS), and Western blot analyses, we examined the order of autophosphorylation in wild-type (WT) and L834R EGFR and the effect of gefitinib (Iressa) on the phosphorylation of individual tyrosines. These studies establish that there is a temporal order of autophosphorylation of key tyrosines involved in downstream signaling for WT EGFR and a loss of order for the oncogenic L834R mutant. These studies also reveal unique signature patterns of drug sensitivity for inhibition of tyrosine autophosphorylation by gefitinib: distinct for WT and oncogenic L834R mutant forms of EGFR. Fluorescence studies show that for WT EGFR the binding affinity for gefitinib is weaker for the phosphorylated protein while for the oncogenic mutant, L834R EGFR, the binding affinity of gefitinib is substantially enhanced and likely contributes to the efficacy observed clinically. This mechanistic information is important in understanding the molecular details underpinning clinical observations as well as to aid in the design of more potent and selective EGFR inhibitors.

Identification of an Acyl-Enzyme Intermediate in a meta-Cleavage Product Hydrolase Reveals the Versatility of the Catalytic Triad

Meta-cleavage product (MCP) hydrolases are members of the α/β-hydrolase superfamily that utilize a Ser-His-Asp triad to catalyze the hydrolysis of a C-C bond. BphD, the MCP hydrolase from the biphenyl degradation pathway, hydrolyzes 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid (HOPDA) to 2-hydroxypenta-2,4-dienoic acid (HPD) and benzoate. A 1.6 Å resolution crystal structure of BphD H265Q incubated with HOPDA revealed that the enzyme's catalytic serine was benzoylated. The acyl-enzyme is stabilized by hydrogen bonding from the amide backbone of 'oxyanion hole' residues, consistent with formation of a tetrahedral oxyanion during nucleophilic attack by Ser112. Chemical quench and mass spectrometry studies substantiated the formation and decay of a Ser112-benzoyl species in wild-type BphD on a time scale consistent with turnover and incorporation of a single equivalent of (18)O into the benzoate produced during hydrolysis in H(2)(18)O. Rapid-scanning kinetic studies indicated that the catalytic histidine contributes to the rate of acylation by only an order of magnitude, but affects the rate of deacylation by over 5 orders of magnitude. The orange-colored catalytic intermediate, ES(red), previously detected in the wild-type enzyme and proposed herein to be a carbanion, was not observed during hydrolysis by H265Q. In the newly proposed mechanism, the carbanion abstracts a proton from Ser112, thereby completing tautomerization and generating a serinate for nucleophilic attack on the C6-carbonyl. Finally, quantification of an observed pre-steady-state kinetic burst suggests that BphD is a half-site reactive enzyme. While the updated catalytic mechanism shares features with the serine proteases, MCP hydrolase-specific chemistry highlights the versatility of the Ser-His-Asp triad.