Divergence of chemical function in the alkaline phosphatase superfamily: Structure and mechanism of the P-C bond cleaving enzyme phosphonoacetate hydrolase

Phosphonates constitute a class of natural products that mimic the properties of the more common organophosphate ester metabolite yet are not readily degraded owing to the direct linkage of the phosphorus atom to the carbon atom. Phosphonate hydrolases have evolved to allow bacteria to utilize environmental phosphonates as a source of carbon and phosphorus. The work reported in this paper examines one such enzyme, phosphonoacetate hydrolase. By using a bioinformatic approach, we circumscribed the biological range of phosphonoacetate hydrolase to a select group of bacterial species from different classes of Proteobacteria. In addition, using gene context, we identified a novel 2-aminoethylphosphonate degradation pathway in which phosphonoacetate hydrolase is a participant. The X-ray structure of phosphonoformate-bound phosphonoacetate hydrolase was determined to reveal that this enzyme is most closely related to nucleotide pyrophosphatase/diesterase, a promiscuous two-zinc ion metalloenzyme of the alkaline phosphatase enzyme superfamily. The X-ray structure and metal ion specificity tests showed that phosphonoacetate hydrolase is also a two-zinc ion metalloenzyme. By using site-directed mutagenesis and P-32-labeling strategies, the catalytic nucleophile was shown to be Thr64. A structure-guided, site-directed mutation-based inquiry of the catalytic contributions of active site residues identified Lys126 and Lys128 as the most likely candidates for stabilization of the aci-carboxylate dianion leaving group. A catalytic mechanism is proposed which combines Lys12/Lys128 leaving group stabilization with zinc ion activation of the Thr64 nucleophile and the substrate phosphoryl group.

Structure activity studies of mast cell activation and hypotension induced by neuropeptide Y (NPY), centrally truncated and C-terminal NPY analogues

1 Neuropeptide-induced histamine release is thought to occur via receptor-independent mechanisms, with net charge and lipophilicity being important factors.

Computational learning of the conditional phase-type (C-Ph) distribution: Learning C-Ph distributions

This paper presents a new algorithm for learning the structure of a special type of Bayesian network. The conditional phase-type (C-Ph) distribution is a Bayesian network that models the probabilistic causal relationships between a skewed continuous variable, modelled by the Coxian phase-type distribution, a special type of Markov model, and a set of interacting discrete variables. The algorithm takes a dataset as input and produces the structure, parameters and graphical representations of the fit of the C-Ph distribution as output.The algorithm, which uses a greedy-search technique and has been implemented in MATLAB, is evaluated using a simulated data set consisting of 20,000 cases. The results show that the original C-Ph distribution is recaptured and the fit of the network to the data is discussed.

Structure-based design of HSPA5 inhibitors: From peptide to small molecule inhibitors

<p>We identified nine small-molecule hit compounds of Heat shock 70 kDa protein 5 (HSPA5) from cascade in silico screening based on the binding modes of the tetrapeptides derived from the peptide substrate or inhibitors of Escherichia coli HSP70. Two compounds exhibit promising inhibition activities from cancer cell viability and tumor inhibition assays. The binding modes of the hit compounds provide a platform for development of selective small molecule inhibitors of HSPA5. (C) 2013 Elsevier Ltd. All rights reserved.</p>

Asymmetric Total Synthesis of (+)-Inthomycin C Via O-Directed Free Radical Alkyne Hydrostannation with Ph₃SnH and Catalytic Et₃B: Reinstatement of the Zeeck-Taylor (3<em>R</em>)-Structure for (+)-Inthomycin C

A new pathway to (+)-inthomycin C is reported that exploits an O-directed free radical hydrostannation reaction on (−)-12 and a Stille cross-coupling as key steps. Significantly, the latter process was effected on 19 where a gauche-pentane repulsive interaction could interfere. Our stereochemical studies on the alkynol (−)-12 and the enyne (+)-7 confirm that Ryu and Hatakeyama’s (3S)-stereochemical revision of (+)-inthomycin C is invalid and that Zeeck and Taylor’s original (3R)-stereostructure for (+)-inthomycin C is correct.<br/>

Advanced Ceramic Substrate with Ordered and Designed Micro-Structure for Applications in Automotive Catalysts

This study describes an innovative monolith structure designed for applications in automotive catalysis using an advanced manufacturing approach developed at Imperial College London. The production process combines extrusion with phase inversion of a ceramic-polymer-solvent mixture in order to design highly ordered substrate micro-structures that offer improvements in performance, including reduced PGM loading, reduced catalyst ageing and reduced backpressure.<br/><br/>This study compares the performance of the novel substrate for CO oxidation against commercially available 400 cpsi and 900 cpsi catalysts using gas concentrations and a flow rate equivalent to those experienced by a full catalyst brick when attached to a vehicle. Due to the novel micro-structure, no washcoat was required for the initial testing and 13 g/ft3 of Pd was deposited directly throughout the substrate structure in the absence of a washcoat.<br/><br/>Initial results for CO oxidation indicate that the advanced micro-structure leads to enhanced conversion efficiency. Despite an 79% reduction in metal loading and the absence of a washcoat, the novel substrate sample performs well, with a light-off temperature (LOT) only 15 °C higher than the commercial 400 cpsi sample.<br/><br/>To test the effects of catalyst ageing on light-off temperature, each sample was aged statically at a temperature of 1000 °C, based on the Bench Ageing Time (BAT) equation. The novel substrate performed impressively when compared to the commercial samples, with a variation in light-off temperature of only 3% after 80 equivalent hours of ageing, compared to 12% and 25% for the 400 cpsi and 900 cpsi monoliths, respectively.

THE SURFACE-STRUCTURE OF A C(2 X-2) POTASSIUM OVERLAYER ON CO(1010)

<p>The surface structure of the clean Co{1010BAR} surface and a c(2 x 2) potassium overlayer have been determined by quantitative low energy electron diffraction. The Co{1010BAR} sample has been shown to be laterally unreconstructed with the surface being uniquely terminated by an outermost closely packed double layer (dz12 = 0.68 angstrom). A damped oscillatory relaxation of the outermost three atomic layers occurs, with relaxations DELTA-dz12 = -6.5 +/- 2% and DELTA-dz23 = +1.0 +/- 2%.</p><p>The c(2 x 2) overlayer formed at a coverage of 0.5 ML was subjected to a full I-V analysis. A range of adsorption sites were tested including fourfold hollow, on-top, and both long and short bridge sites in combination with both "long" and "short" cobalt interlayer terminations. A clear preference was found for adsorption in the maximal coordination fourfold hollow site. No switching of surface termination occurs. The potassium adatoms reside in the [1210BAR] surface channels directly above second layer cobalt atoms with a potassium to outermost cobalt interlayer separation of 2.44 +/- 0.05 angstrom. Potassium-cobalt bond lengths of 3.40 +/- 0.05 and 3.12 +/- 0.05 angstrom between the four (one) outermost (second) layer nearest-neighbour substrate atoms suggests a potassium effective radius of 1.87 +/- 0.05 angstrom, somewhat smaller than the Pauling covalent radius and considerably larger than the ionic radius (1.38 angstrom). The alkali-surface bonding is thus predominantly "covalent"/"metallic".</p>

¹⁴C as a tool to trace terrestrial carbon in a complex lake system: implications for foodweb structure and carbon cycling

Carbon and nitrogen stable isotope analysis (SIA) has identified the terrestrial subsidy of freshwater food-webs but relies on different 13C fractionation in aquatic and terrestrial primary producers. However dissolved inorganic carbon (DIC) is partly comprised of 13C depleted respiration of terrestrial C and ‘old’ C derived from weathering of catchment geology. SIA thus fails to differentiate between the contribution of old and recently fixed terrestrial C. DIC in alkaline lakes is partially derived from weathering of 14C-free carbonaceous bedrock This<br/>yields an artificial age offset leading samples to appear significantly older than their actual age. As such, 14C can be used as a biomarker to identify the proportion of autochthonous C in the food-web. With terrestrial C inputs likely to increase, the origin and utilisation of ‘old’ or ‘recent’ allochthonous C in the food-web can also be determined. Stable isotopes and 14C were measured for biota, particulate organic matter (POM), DIC and dissolved organic carbon (DOC) from Lough Erne, Northern Ireland, a humic but alkaline lake. High winter δ15N values in calanoid zooplankton (δ15N =24‰) relative to phytoplankton and POM (δ15N =6‰ and 12‰ respectively) may reflect several microbial trophic levels between terrestrial C and calanoids. Furthermore winter calanoid 14C ages are consistent with DOC from inflowing rivers (87 and 75 years BP respectively) but not phytoplankton (355 years BP). Summer calanoid δ13N, δ15N and 14C (312 years BP) indicate greater reliance on phytoplankton. There is also temporal and spatial variation in DIC, DOC and POM C isotopes.