The Saccharomyces cerevisiae quinone oxidoreductase Lot6p: stability, inhibition and cooperativity

Lot6p (EC 1.5.1.39; Ylr011wp) is the sole quinone oxidoreductase in the budding yeast, Saccharomyces cerevisiae. Using hexahistidine tagged, recombinant Lot6p, we determined the steady-state enzyme kinetic parameters with both NADH and NADPH as electron donors; no cooperativity was observed with these substrates. The NQO1 inhibitor curcumin, the NQO2 inhibitor resveratrol, the bacterial nitroreductase inhibitor nicotinamide and the phosphate mimic vanadate all stabilise the enzyme towards thermal denaturation as judged by differential scanning fluorimetry. All except vanadate have no observable effect on the chemical cross-linking of the two subunits of the Lot6p dimer. These compounds all inhibit Lot6p's oxidoreductase activity, and all except nicotinamide exhibit negative cooperativity. Molecular modelling suggests that curcumin, resveratrol and nicotinamide all bind over the isoalloxazine ring of the FMN cofactor in Lot6p. Resveratrol was predicted to contact an α-helix that links the two active sites. Mutation of Gly-142 (which forms part of this helix) to serine does not greatly affect the thermal stability of the enzyme. However, this variant shows less cooperativity towards resveratrol than the wild type. This suggests a plausible hypothesis for the transmission of information between the subunits and, thus, the molecular mechanism of negative cooperativity in Lot6p.

Development of Novel Activity-Based Probes for the Detection of Serine Proteases

Cystic Fibrosis (CF) is a genetic disease featuring a chronic cycle of inflammation and infection in the airways of sufferers. Mutations lead to altered ion transport, which in turn causes dehydrated airways and reduced mucociliary clearance which predisposes the patient to infection, resulting in a severe immune response and tissue destruction (1). Airway dehydration is primarily caused by the hyperabsorption of sodium by the epithelial sodium channel (ENaC) (2). ENaC is activated by the action of a number of predominantly trypsin-like Channel Activating Proteases (CAPs) including prostasin, matriptase and furin (3). Additional proteases known to activate ENaC include human airway trypsin (3), plasmin, neutrophil elastase and chymotrypsin (4).

Activity profiling is a valuable technique which involves the use of small inhibitory molecules called Activity-Based Probes (ABPs) which can be used to covalently label the active site of proteases and provide a range of information regarding its structure, catalytic mechanism, location and function within biological systems. The development of novel ABPs for CAPs, would enhance understanding of the role of these proteases in CF airways disease and in particular their role in ENaC activation and airway dehydration. This project investigates the application of a range of novel broad-spectrum ABPs targeting the various subclasses of serine proteases, to include those proteases involved in ENaC activation. Additionally, the application of more selective ABPs in detecting specific serine proteases is investigated.

Compounds were synthesised by Solid-Phase Peptide Synthesis (SPPS) using a standard Fmoc/tBu strategy. Kinetic evaluation of synthesised ABPs against various serine proteases was determined by fluorogenic steady-state enzyme assays. Furthermore, application of ABPs and confirmation of irreversible nature of the compounds was carried out through SDS-PAGE and electroblotting techniques.

Synthesised compounds showed potent irreversible inhibition of serine proteases within their respective targeting class (NAP855 vs Trypsin k3/Ki = 2.60 x 106 M-1 min-1, NFP849 vs Chymotrypsin k3/Ki = 1.28 x 106 M-1 min-1 and NVP800 vs Neutrophil Elastase k3/Ki = 6.41 x 104 M-1 min-1). Furthermore ABPs showed little to no cross-reactivity between classes and so display selectivity between classes. The irreversible nature of compounds was further demonstrated through labelling of proteases, followed by separation and detection via SDS-PAGE and electroblotting techniques. Targeted labelling of active proteases only, was demonstrated by failure of ABPs to detect previously inactivated proteases. Extension of the substrate recognition site within probes resulted in an increased potency and selectivity in the detection of the target proteases. Successful detection of neutrophil elastase from CF sputum samples by NVP800, demonstrated the application of compounds within biological samples and their potential use in identifying further proteases involved in ENaC activation and airway dehydration in CF patients.

Quantitative Enzymology

Accurate measurement of the quantitative aspects of enzyme-catalysed reactions
is critical for a deeper understanding of their mechanisms, for their exploitation in biotechnology and for targeting enzymes by drug-like molecules. It is important to move beyond basic enzyme kinetics as encapsulated in the Michaelis-Menten equation. The type and magnitude of inhibition should be determined. Since the majority of enzyme-catalysed reactions involve more than one substrate, it is critical to understand how to treat these reactions quantitatively and how their kinetic behaviour depends on the type of mechanism occurring.
Some reactions do not conform to “standard” Michaelis-Menten treatment and exhibit phenomena such as cooperativity. Again it is important to put these phenomena onto a quantitative basis. Similarly the treatment of the effects of pH on enzymes is often vague and uninformative without a proper quantitative treatment. This review brings together tools and approaches for dealing with enzymes quantitatively together with original references for these approaches.

State defining experiment in chemical kinetics. Primary characterization of catalyst activity in a TAP experiment

This paper presents a new strategy, “state-by-state transient screening”, for kinetic characterization of states of a multicomponent catalyst as applied to TAP pulse-response experiments. The key idea is to perform an insignificant chemical perturbation of the catalytic system so that the known essential characteristics of the catalyst (e.g. oxidation degree) do not change during the experiment. Two types of catalytic substances can be distinguished: catalyst state substances, which determine the catalyst state, and catalyst dynamic substances, which are created by the perturbation. The general methodological and theoretical framework for multi-pulse TAP experiments is developed, and the general model for a one-pulse TAP experiment is solved. The primary kinetic characteristics, basic kinetic coefficients, are extracted from diffusion–reaction data and calculated as functions of experimentally measured exit-flow moments without assumptions regarding the detailed kinetic mechanism. The new strategy presented in this paper provides essential information, which can be a basis for developing a detailed reaction mechanism. The theoretical results are illustrated using furan oxidation over a VPO catalyst.

Structure and kinetics of phosphonopyruvate hydrolase from Variovorax sp. Pal2: New insight into the divergence of catalysis within the PEP mutase/isocitrate lyase superfamily .

Phosphonopyruvate (P-pyr) hydrolase (PPH), a member of the phosphoenolpyruvate (PEP) mutase/isocitrate lyase (PEPM/ICL) superfamily, hydrolyzes P-pyr and shares the highest sequence identity and functional similarity with PEPM. Recombinant PPH from Variovorax sp. Pal2 was expressed in Escherichia coli and purified to homogeneity. Analytical gel filtration indicated that the protein exists in solution predominantly as a tetramer. The PPH pH rate profile indicates maximal activity over a broad pH range.The steady-state kinetic constants determined for a rapid equilibrium ordered kinetic mechanism with Mg+2 binding first (Kd =140 ± 40 M), are kcat = 105 ± 2 s-1 and P-pyr Km = 5 ± 1 M. PEP (slow substrate kcat = 2 × 10-4 s-1), oxalate, and sulfopyruvate are competitive inhibitors with Ki values of 2.0 ± 0.1 mM, 17 ± 1 M, and 210 ± 10 M, respectively. Three PPH crystal structures have been determined, that of a ligand-free enzyme, the enzyme bound to Mg2+ and oxalate (inhibitor), and the enzyme bound to Mg2+ and P-pyr (substrate). The complex with the inhibitor was obtained by cocrystallization, whereas that with the substrate was obtained by briefly soaking crystals of the ligand-free enzyme with P-pyr prior to flash cooling. The PPH structure resembles that of the other members of the PEPM/ICL superfamily and is most similar to the functionally related enzyme, PEPM. Each monomer of the dimer of dimers exhibits an (/)8 barrel fold with the eighth helix swapped between two molecules of the dimer. Both P-pyr and oxalate are anchored to the active site by Mg2+. The loop capping the active site is disordered in all three structures, in contrast to PEPM, where the equivalent loop adopts an open or disordered conformation in the unbound state but sequesters the inhibitor from solvent in the bound state. Crystal packing may have favored the open conformation of PPH even when the enzyme was cocrystallized with the oxalate inhibitor. Structure alignment of PPH with other superfamily members revealed two pairs of invariant or conservatively replaced residues that anchor the flexible gating loop. The proposed PPH catalytic mechanism is analogous to that of PEPM but includes activation of a water nucleophile with the loop Thr118 residue.

Negative apparent kinetic order in steady-state kinetics of the water-gas shift reaction over a Pt-CeO2 catalyst

The kinetics of the water-gas shift reaction Were Studied on a 0.2% Pt/CeO2 catalyst between 177 and 300 degrees C over a range of CO and steam pressures. A rate decrease with increasing partial pressure of CO was experimentally observed over this sample, confirming that a negative order in CO can occur under certain conditions at low temperatures. The apparent reaction order of CO measured at 197 degrees C was about -0.27. This value is significantly larger than that (i.e, -0.03) reported by Ribeiro and co-workers [A.A. Phatak, N. Koryabkina, S. Rai, J.L. Ratts, W. Ruettinger, R.J. Farrauto, G.E. Blau, W.N. Delgass, F.H. Ribeiro, Catal. Today 123 (2007) 224] at a similar temperature. A kinetic peculiarity was also evidenced, i.e. a maximum of the reaction rate as a function of the CO concentration or possibly a kinetic break, which is sometimes observed in the oxidation of simple molecules. These observations support the idea that competitive adsorption of CO and H2O play an essential role in the reaction mechanism. (C) 2008 Elsevier B.V. All rights reserved.

OBSERVATION OF BIPHASIC KINETICS IN LIGHT-INDUCED SPIN-STATE CROSSOVER IN AN IRON(II) COMPLEX IN SOLUTION

Relaxation of the 1A1 half arrow right over half arrow left 5T2 spin equilibrium in acetonitrile of the complex of Fe(II) with the multidentate pyridyl macrocyclic ligand N,N',N''-tris(2-pyridylmethyl)-1,4,7-triazacyclodecane (tp[10]aneN3) after perturbation by a pulsed laser provides the first example of biphasic kinetics for spin crossover in solution with a fast (tau

Kinetics of liquid phase semiconductor photoassisted reactions: Supporting observations for a pseudo-steady-state model

The kinetics of liquid phase semiconductor photocatalytic and photoassisted reactions are an area of some debate, reignited recently by an article by Ollis(1) in which he proposed a simple pseudo- steady- state model to interpret the Langmuir- Hinshelwood type kinetics, commonly observed in such systems. In the current article, support for this model, over other models, is provided by a reinterpretation of the results of a study, reported initially in 1999,2 of the photoassisted mineralization of 4- chlorophenol, 4-CP, by titania films and dispersions as a function of incident light intensity, I. On the basis of this model, these results indicate that 4- CP is adsorbed more strongly on P25 TiO2 when it is in a dispersed, rather than a film form, due to a higher rate constant for adsorption, k(1). In addition, the kinetics of 4- CP removal appear to depend on I-beta where, beta = 1 or 0.6 for when the TiO2 is in a film or a dispersed form, respectively. These findings are discussed both in terms of the pseudo- steady- state model and other popular kinetic models.

Extraction of electrode kinetic parameters from microdisc voltammetric data measured under transport conditions intermediate between steady-state convergent and transient linear diffusion as typically applies to room temperature ionic liquids

The extraction of electrode kinetic parameters for electrochemical couples in room-temperature ionic liquids (RTILs) is currently an area of considerable interest. Electrochemists typically measure electrode kinetics in the limits of either transient planar or steady-state convergent diffusion for which the voltammetic response is well understood. In this paper we develop a general method allowing the extraction of this kinetic data in the region where the diffusion is intermediate between the planar and convergent limits, such as is often encountered in RTILs using microelectrode voltammetry. A general working surface is derived, allowing the inference of Butler-Volmer standard electrochemical rate constants for the peak-to-peak potential separation in a cyclic voltammogram as a function of voltage scan rate. The method is applied to the case of the ferrocene/ferrocenium couple in [C(2)mim][N(Tf)(2)] and [C(4)mim][N(Tf)(2)].

C-H bond activation over metal oxides: A new insight into the dissociation kinetics from density functional theory

The C-H activation on metal oxides is a fundamental process in chemistry. In this paper, we report a density functional theory study on the process of the C-H activation of CH4 on Pd(111), Pt(111), Ru(0001), Tc(0001), Cu(111), PdO(001), PdO(110), and PdO(100). A linear relationship between the C-H activation barrier and the chemisorption in the dissociation final state on the metal surfaces is obtained, which is consistent with the work in the literature. However, the relationship is poor on the metal oxide surfaces. Instead, a strong linear correlation between the barrier and the lattice O-H bond strength is found on the oxides. The new linear relationship is analyzed and the physical origin is identified. (c) 2008 American Institute of Physics.

Dependence of the kinetics of liquid-phase photocatalyzed reactions on oxygen concentration and light intensity

The initial kinetics of the oxidation of 4-chlorophenol, 4-CP, photocatalyzed by titania films and aqueous dispersions were studied as a function of oxygen partial pressure, P-O2, and incident light intensity, I. The reaction conditions were such that the kinetics were independent of [4-CP] but strongly dependent on PO2-a situation that allowed investigation of the less-often studied kinetics of oxygen reduction. The observed kinetics fit a pseudo-steady-state model in which the oxygen is Langmuir-adsorbed on the titania photocatalyst particles before being reduced by photogenerated electrons. The maximum rate of photocatalysis depends directly on I-beta, where, beta = 1 for films and 0.7 for dispersions of titania, indicating that the kinetics are dominated by the surface reactions of the photogenerated electrons and holes for the films and by direct recombination for the powder dispersions. Using the pseudo-first-order model, for both titania films and dispersions, the apparent Langmuir adsorption constant, K-LH, derived from a Langmuir-Hinshelwood analysis of the kinetics, appears to be largely independent of incident light intensity, unlike KLH for 4-CP Consequently, similar values are obtained for the Langmuir adsorption constant, K-ads, extracted from a pseudosteady-state analysis of the kinetics for oxygen on TiO2 dispersions and films in aqueous solution (i.e., ca. 0.0265 +/- 0.005 kPa(-1)), and for both films and dispersions, oxygen appears to be weakly adsorbed on TiO2 compared with 4-CP, at a rate that would take many minutes to reach equilibrium. The value of Kads for oxygen on titania particles dispersed in solution is ca. 4.7 times lower than that reported for the dark Langmuir adsorption isotherm; possible causes for this difference are discussed. (c) 2006 Elsevier Inc. All rights reserved.

Solid-state sodium-selective sensors based on screen-printed Ag/AgCl reference electrodes

The potentiometric and AC impedance characteristics of all solid-state sodium-selective electrodes based on planar screen-printed Ag/AgCl electrodes are described. Two solid-state designs have been investigated. The first was based on the deposition of a sodium-selective PVC membrane directly on top of a screen-printed Ag/AgCl electrode, The second design included a NaCl doped hydrogel layer, between the PVC and Ag\AgCl layers. The hydrogel provides a mechanism to relieve any blockage to charge transfer occurring when PVC membranes are used directly on top of Ag/AgCl and also improves adhesion between the two layers. Results suggest the electrodes display Fast ion exchange kinetics, low noise and drift. The performance compares favorably to that of a conventional ion-selective electrode with internal filling solution.

Structural and kinetic characterization of the LPS biosynthetic enzyme D-alpha,beta-D-heptose-1,7-bisphosphate phosphatase (GmhB) from Escherichia coli

Lipopolysaccharide is a major component of the outer membrane of gram-negative bacteria and provides a permeability barrier to many commonly used antibiotics. ADP-heptose residues are an integral part of the LPS inner core, and mutants deficient in heptose biosynthesis demonstrate increased membrane permeability. The heptose biosynthesis pathway involves phosphorylation and dephosphorylation steps not found in other pathways for the synthesis of nucleotide sugar precursors. Consequently, the heptose biosynthetic pathway has been marked as a novel target for antibiotic adjuvants, which are compounds that facilitate and potentiate antibiotic activity. D-alpha,beta-D-heptose-1,7-bisphosphate phosphatase (GmhB) catalyzes the third essential step of LPS heptose biosynthesis. This study describes the first crystal structure of GmhB and enzymatic analysis of the protein. Structure-guided mutations followed by steady state kinetic analysis, together with established precedent for HAD phosphatases, suggest that GmhB functions through a phosphoaspartate intermediate. This study provides insight into the structure-function relationship of GmhB, a new target for combatting gram-negative bacterial infection.

Size-fitting of Intravaginal Rings for Macaques and in vitro Release Kinetics of Zinc Finger Inhibitors

Background: Small molecule inhibitors of the zinc finger domain (ZFI) in the nucleocapsid protein (NCp7) of HIV-1 are potent inhibitors of HIV and SIV
replication and may have utility as topical products to prevent infection. Furthermore, intravaginal rings (IVRs) were developed as coitally-independent,
sustained release devices which could be used for administration of HIV microbicides. The aims of these studies were to demonstrate that IVRs sized for
macaques are practical and compatible with the current generation of thioester-based NCp7 inhibitors.

Methods: Non-medicated silicone elastomer vaginal rings of various sizes thought to be applicable for macaques were prepared and tested for vaginal fit in Pigtailed and Chinese Rhesus macaques. Macaques were monitored for 8 weeks for mucosal disruption by colposcopy and proinflammatory cytokine markers in cervical vaginal lavages (CVL) using Luminex bead-based technology. Three different ZFIs (compounds 52, 89 and 122, each derived from an N-substituted S-acyl-2-mercaptobenzamide thioester scaffold) were loaded at 50 mg into an optimal matrix-type ring design. In vitro continuous release studies were then conducted over 28 days and analyzed by HPLC. Rate of release was determined by linear regression analysis.

Results: Qualitative evaluation at the time of ring insertion suggested that the 25 mm ring provided optimal fit in both macaque species. All rings remained in
place during the study period (2 to 4 weeks), and the animals did not attempt to remove the rings. No tissue irritation was observed, and no signs of physical
discomfort were noted. Also, no significant induction of cervicovaginal proinflammatory markers was observed during the 8-week period during and following ring insertion. One Pigtailed macaque showed elevated IL-8 levels in the CVL during the period when the ring was in place; however, these levels were comparable to those observed in two control macaques. In vitro release of the ZFIs peaked at day 1 and then continually declined to near steady-state rates between 20-30 mcg/day. The percent release after 14 days was 2.9, 2.0 and 0.9 for ZFI 89, 52 and 122, respectively.

Conclusions: IVRs of 25mm diameter, determined to be the optimal size for macaques, were well tolerated and did not induce inflammation. Release of all ZFI compounds followed t 0.5 kinetics. These findings suggest that efficacy testing in primate models is warranted to fully evaluate the potential to prevent
transmission.

The use of Short Time on Stream (STOS) transient kinetics to investigate the role of hydrogen in enhancing NOx reduction over silver catalysts

The role of hydrogen in promoting the reduction by ammonia of NOx on silver catalysts has been investigated using a Short Time on Stream (STOS) technique to allow differentiation between potentially reactive intermediates and relatively inactive spectator species. Under these conditions, we have used DRIFTS to identify surface nitrate species that are formed and removed on a timescale of seconds. This is in contrast to nitrate species observed under normal steady-state conditions which can continue to form over many tens of minutes. Since this timescale of seconds is very similar to the response rate at which the NH3/NOx to N-2 reaction is accelerated when H-2 is added, or decelerated when H-2 is removed, we conclude that this fast-forming and fast disappearing nitrate species is most probably adsorbed on or close to the active Ag sites. The removal of such a blocking nitrate species from the active sites can explain the effect of H-2 in greatly increasing the rate of the overall de-NOx reaction.