Contribution of the C-terminal amino acid to the stability of Bacillus subtilis neutral protease

The role of the C-terminal Leu300 in maintaining thermal stabilityof the neutral protease of Bacillus subtilis was investigated.From model building studies based on the three dimensional structureof thermolysin, the neutral protease of B.thermoproteolyticus,it was conduded that this residue is located in a hydrophobicpocket composed of residues located in the C-terminal and themiddle domain. To test the hypothesis that Leu300, by contributingto a stabilizing interaction between these domains, is importantfor enzyme stability, several neutral protease mutants wereconstructed and characterized. The thermostability of the enzymewas lowered by deleting Leu300 or by replacing this residueby a smaller (Ala), a polar (Asn) or a sterically unfavourable(He) amino acid. Thermostabiity was increased upon replacingLeu300 by Phe. These results are in agreement with model-buildingstudies. The effects on thermostability observed after mutatingthe corresponding Val318 in the thermostable neutral proteaseof B.stearothermophilus were less pronounced.     

Untangling decision tree and real options analyses: a public infrastructure case study dealing with political decisions,structural integrity and price uncertainty

Managerial flexibility in infrastructure investment and replacement decisions adds value. Real options analysis (ROA) captures this value under uncertain market prices. The concept of ROA is that future unfavourable payoffs can be deferred as soon as more information about market prices becomes available. The popularity of ROA is seen in a growing number of case studies on real assets. Despite its increasing popularity, ROA has not gained a foothold in public infrastructure decision making. One of the difficulties in the application of ROA is the required estimation of market variables. To avoid this, a simplified but not correct version of ROA is easily applied, referred to as a Decision Tree Approach (DTA) to ROA. Another difficulty is that infrastructure assets are subject to other types of uncertainties, defined here as asset uncertainties. This study investigates the value of managerial flexibility in a public infrastructure replacement decision. The uncertainty drivers are the strength of a bridge, political decisions regarding traffic flow and the price development of construction costs. Three valuation approaches are compared: DTA, ROA and the DT approach to ROA. Although it is complex, ROA certainly adds value in public infrastructure decision making when market price uncertainty is prevalent. However, in the absence of reasonable estimates of market variables, the DT approach to ROA is the best alternative. In the absence of market price uncertainties, ROA should be avoided DTA is to be preferred.     

Native Liquid Chromatography and Mass Spectrometry to Structurally and Functionally Characterize Endo-Xylanase Proteoforms

Xylanases are of great value in various industries, including paper, food, and biorefinery. Due to their biotechnological production, these enzymes can contain a variety of post-translational modifications, which may have a profound effect on protein function. Understanding the structure–function relationship can guide the development of products with optimal performance. We have developed a workflow for the structural and functional characterization of an endo-1,4-β-xylanase (ENDO-I) produced by Aspergillus niger with and without applying thermal stress. This workflow relies on orthogonal native separation techniques to resolve proteoforms. Mass spectrometry and activity assays of separated proteoforms permitted the establishment of structure–function relationships. The separation conditions were focus on balancing efficient separation and protein functionality. We employed size exclusion chromatography (SEC) to separate ENDO-I from other co-expressed proteins. Charge variants were investigated with ion exchange chromatography (IEX) and revealed the presence of low abundant glycated variants in the temperature-stressed material. To obtain better insights into the effect on glycation on function, we enriched for these species using boronate affinity chromatography (BAC). The activity measurements showed lower activity of glycated species compared to the non-modified enzyme. Altogether, this workflow allowed in-depth structural and functional characterization of ENDO-I proteoforms.     

Reinvestigation of the antioxidant properties of conjugated linoleic acid

Despite repeated suggestions that antioxidant activity of conjugated linoleic acid (CLA), a collective of conjugated dienoic isomers of linoleic acid, underlies its reported anticarcinogenic and antiatherosclerotic effects, the antioxidant properties of CLA remain ill-defined. Therefore, this study was undertaken to gain more insight into the mechanism of potential CLA antioxidant activity. It was tested whether CLA could protect membranes composed of 1-palmitoyl-2-linoleoyl phosphatidylcholine (PLPC) from oxidative modification under conditions of metal ion-dependent or-independent oxidative stress. Progress of oxidation was determined by direct spectrophotometric measurement of conjugated diene formation and by gas chromatographic/mass spectrometric analysis of fatty acids. The oxidative susceptibility of CLA was higher than that of linoleic acid, and comparable to arachidonic acid. When oxidation of PLPC (1.0 mM) was initiated using the lipid-soluble 2,2′-azobis(2,4-dimethylvaleronitrile) or the water-soluble 2,2′-azobis(2-amidinopropane) hydrochloride, the radical scavengers vitamin E and butylated hydroxytoluene (BHT) at 0.75 μM efficiently inhibited PLPC oxidation, as evident from a clear lagphase. In contrast, 0.75 μM CLA did not have any significant effect on PLPC oxidation. Inhibition of PLPC oxidation by higher concentrations of CLA appeared due to competition, not to an antioxidant effect. When oxidation of PLPC was initiated by hydrogen peroxide/Fe²⁺ (500 μM/0.05–20 μM), both vitamin E (1 μM) and ethylene glycol-bis(aminoethyl ether) tetraacetic acid (50 μM) efficiently inhibited PLPC oxidation. However, CLA (1–50 μM) did not show a clear protective effect under any of the conditions tested. We conclude that CLA, under these test conditions, does not act as an efficient radical scavenger in any way comparable to vitamin E or BHT. CLA also does not appear to be converted into a metal chelator under metal-ion dependent oxidative stress, as had previously been suggested. On the basis of our observations, a role for CLA as an antioxidant does not seem plausible.     

Microstructural analysis of MTR fuel plates damaged by a coolant flow blockage

In 1975, as a result of a blockage of the coolant inlet flow, two plates of a fuel element of the BR2 reactor of the Belgian Nuclear Research Centre (SCK•CEN) were partially melted. The fuel element consisted of Al-clad plates with 90% ²³⁵U enriched UAl_x fuel dispersed in an Al matrix. The element had accumulated a burn up of 21% ²³⁵U before it was removed from the reactor. Recently, the damaged fuel plates were sent to the hot laboratory for detailed PIE.Microstructural changes and associated temperature markers were used to identify several stages in the progression to fuel melting. It was found that the temperature in the center of the fuel plate had increased above 900-950 °C before the reactor was scrammed. In view of the limited availability of such datasets, the results of this microstructural analysis provide valuable input in the analysis of accident scenarios for research reactors.     

The actin content of different muscles from beef and pork

In the literature 3-methylhistidine (3-MeHis) is mentioned as a parameter for the determination of meat content. Because of the variable molar ratio of 3-MeHis in the myofibrillar protein myosin, this indicator cannot be used without some restriction. However, the content of 3-MeHis in the myofibrillar protein actin is constant. Moreover, actin is relatively heat-stable in comparison with other muscle proteins. These facts made actin an interesting parameter for determination of the meat (protein) content of heated and raw meat products.

Fast protein liquid chromatography (FPLC) was used to separate from a meat extract an actin-containing fraction without myosin. The actin content of the meat was calculated from its content in the fraction. The latter was determined by means of a 3-MeHis method.

Several muscles of the beef and pig carcass were examined for their actin contents. Generally, the actin values were comparable with the data reported in the literature.

The influence of heat treatment was also studied on one type of beef muscle. The determined actin content was not affected up to a temperature of 85°C.     

Monte Carlo uncertainty quantification of the effective delayed neutron fraction

The applicability of Monte Carlo techniques, namely the Monte Carlo sensitivity method and the random-sampling method, for uncertainty quantification of the effective delayed neutron fraction β_eff is investigated using the continuous-energy Monte Carlo transport code, MCNP, from the perspective of statistical convergence issues. This study focuses on the nuclear data as one of the major sources of β_eff uncertainty. For validation of the calculated β_eff, a critical configuration of the VENUS-F zero-power reactor was used. It is demonstrated that Chiba's modified k-ratio method is superior to Bretscher's prompt k-ratio method in terms of reducing the statistical uncertainty in calculating not only β_eff but also its sensitivities and the uncertainty due to nuclear data. From this result and a comparison of uncertainties obtained by the Monte Carlo sensitivity method and the random-sampling method, it is shown that the Monte Carlo sensitivity method using Chiba's modified k-ratio method is the most practical for uncertainty quantification of β_eff. Finally, total β_eff uncertainty due to nuclear data for the VENUS-F critical configuration is determined to be approximately 2.7% with JENDL-4.0u, which is dominated by the delayed neutron yield of ²³⁵U.     

UO2 dissolution in Boom Clay conditions

The solubility of uranium dioxide (UO₂) was measured in real and synthetic Boom Clay waters with varying concentrations of humic acids and carbonate under reducing conditions at 20 °C. Uranium concentrations in function of time suggest the reduction of U(VI) to U(IV) by the humic acids which is occurring faster in real clay water than in synthetic clay waters. Humic acids induce also a competition to complex U(VI) in carbonate-containing solution, but they are not able to control the uranium concentration at high bicarbonate concentration (0.02 mol dm⁻³). Nevertheless they may play a role at low carbonate concentration. In our experimental conditions, the geochemical calculations indicate that two uranium secondary phases (U₄O₉ and UO_2(c)) are susceptible to control the uranium concentration in solution. These calculations are in good agreement with results of the X-ray photoelectron spectroscopy. At the end of tests, uranium concentrations reach steady-state values between 3 × 10⁻⁸ and 5 × 10⁻⁸ mol dm⁻³ in the bicarbonate-rich solutions. Although these concentrations are considered as conservative, they are 10-100 times higher than in natural Boom Clay. The consequence is that spent fuel could slowly dissolve in the interstitial clay water undersaturated with respect to UO₂/UO_2+x of the fuel.     

Introduction of a stabilizing 10 residue {beta}-hairpin in Bacillus subtilis neutral protease

A 10 residue ß-hairpin, which is characteristic ofthermostable Bacillus neutral proteases, was engineered intothe thermolabile neutral protease of Bacillus subtilis. Therecipient enzyme remained fully active after introduction ofthe loop. However, the mutant protein exhibited autocatalyticnicking and a 0.4°C decrease in thermostability. Two additionalpoint mutations designed to improve the interactions betweenthe enzyme surface and the introduced ß-hairpin resultedin reduced nicking and increased thermostability. After theintroduction of both additional mutations in the loopcontainingmutant, nicking was largely prevented and an increase in thermostabilityof 1.1°C was achieved.     

The effect of cavity-filling mutations on the thermostability of Bacillus stearothermophilus neutral protease

Cavities in the hydrophobic core of the neutral protease ofBacillus stearothermophilus were analyzed using a threedimensionalmodel that was inferred from the crystal structure of thermolysin,the highly homologous neutral protease of B.thermoproteolyticus(85% sequence identity). Site–directed mutagenesis wasused to fill some of these cavities, thereby improving hydrophobicpacking in the protein interior. The mutations had small effectson the thermostability, even after drastic changes, such asLeu284Trp and Met168Trp. The effects on T50, the temperatureat which 50% of the enzyme is irreversibly inactivated in 30min, ranged from 0.0 to +0.4°C. These results can be explainedby assuming that the mutations have positive and negative structuraleffects of approximately the same magnitude. Alternatively,it could be envisaged that the local unfolding steps, whichrender the enzyme susceptible towards autolysis and which arerate limiting in the process of thermal inactivation, are onlyslightly affected by alterations in the hydrophobic core.