A combined approach to improving large-scale production of tobacco etch virus protease

Tobacco etch virus NIa proteinase (TEV protease) is an important tool for the removal of fusion tags from recombinant proteins. Production of TEV protease in Escherichia coli has been hampered by insolubility and addressed by many different strategies. However, the best previous results and newer approaches for protein expression have not been combined to test whether further improvements are possible. Here, we use a quantitative, high-throughput assay for TEV protease activity in cell lysates to evaluate the efficacy of combining several previous modifications with new expression hosts and induction methods. Small-scale screening, purification and mass spectral analysis showed that TEV protease with a C-terminal poly-Arg tag was proteolysed in the cell to remove four of the five arginine residues. The truncated form was active and soluble but in contrast, the tagged version was also active but considerably less soluble. An engineered TEV protease lacking the C-terminal residues 238-242 was then used for further expression optimization. From this work, expression of TEV protease at high levels and with high solubility was obtained by using auto-induction medium at 37 degrees C. In combination with the expression work, an automated two-step purification protocol was developed that yielded His-tagged TEV protease with >99% purity, high catalytic activity and purified yields of approximately 400 mg/L of expression culture (approximately 15 mg pure TEV protease per gram of E. coli cell paste). Methods for producing glutathione-S-transferase-tagged TEV with similar yields (approximately 12 mg pure protease fusion per gram of E. coli cell paste) are also reported.     

A photographic approach to the possible mechanism of retrogradation of sweet potato starch

Although the subject of starch retrogradation has been studied for about 20 years, the mechanism of starch retrogradation seems not yet to be completely established. In this paper, the possible retrogradation mechanism of sweet potato starch was postulated from four optical micrographs at the stages of melting of the starch granules, autoclaving treatment and aging. The possible process of retrogradation consists of three stages. Firstly, starch granules was swelled and melted with loss of X-ray crystallinity and formation of both crystalline and amorphous lamellae; secondly, in crystalline lamellae, amylopectin began to form nucleation when they were autoclaved; finally, the nucleus grew up to great rod-like crystals as the result of congregating of amylose on plates which were composed of and prolongated by amylopectin.     

A note on a possible mathematical approach to the theory of individual freedom

As suggested in previous publications, freedom may be defined quantitatively as a restriction upon the choice of a number of activities. If the choice is determined by maximizing the satisfaction function, it is suggested that freedom may be defined in terms of the satisfaction function. If an individual is isolated and no physical restrictions limit his choice of activities, he is free to choose any activity in an amount which maximizes his satisfaction. This isolated state may be considered therefore as that of maximum freedom. If the individual interacts with another, he will choose different amounts of his object of satisfaction depending on whether he behaves egoistically or altruistically. But in either case the value chosen will not maximize his satisfaction function considered alone. A simple analytical expression is suggested as a measure of freedom in this case, and some problems which arise from this suggestion are mentioned.     

A vector projection approach to predicting HIV protease cleavage sites in proteins

A vector projection method is proposed to predict the cleavability of oligopeptides by extended-specificity site proteases. For an enzyme with eight specificity subsites the substrate octapeptide can be uniquely expressed as a vector in an 8-dimensional space, whose eight bases correspond to the amino acids at the eight subsites, P₁, P_1′, P_2′, P_3′ and P_4′, respectively. The component of such a characteristic vector on each of the eight bases is defined as the frequency of an amino acid occurring at a given site. These frequencies were derived from a set of octapeptides known to be cleaved by HIV protease. The cleavability of an octapeptide can then be estimated from the projection of its characteristic vector on an idealized, optimally cleavable vector. The high ratio of correct prediction vs. total prediction for the data in both the training and the testing sets indicates that the new method is self-consistent and efficient. It provides a rapid and accurate algorithm for analyzing the specificity of any multisubsite enzyme for which there is no coupling between subsites. In particular, it is useful for predicting the cleavability of an oligopeptide by either HIV-1 or HIV-2 protease, and hence offers a supplementary means for finding effective inhibitors of HIV protease as potential drugs against AIDS. © Wiley-Liss, Inc.     

A possible approach to the investigation of reacting sites of ozone in rat lung

As edematogenic agents, thiocarbamides and ozone share several pharmacological and toxicological features in common. In view of these striking similarities, an attempt was made to find out whether or not thiocarbamides and ozone interact with the same cellular constituents of the lungs. This was accomplished by incubating first, a constant amount of ¹⁴C-thiourea with lung slices of O₃-tolerant and control rats followed by subcellular fractionation and radio-activity determination. The results of this study reveal a substantial and significant reduction in binding of ¹⁴C-thiourea to all sub-cellular fractions of lungs of O₃-tolerant rats as compared to the rats exposed to ambient air. The data suggest that repeated exposure to a progressively increasing concentration of ozone inhibits ¹⁴C-thiourea binding in the lung by reducing binding sites by directly destroying binding sites or via an effect on cell population.     

A symmetry approach to electrocardiogram analysis

A qualitative characteristics of a symmetry of correlations in ECG parameters has been studied in experiments on rats with the adaptation syndrome and hypertonic patients (I-II stages). A geometrical model of cardiac cycle shaped as a rectangular triangle with temporal and amplitude ECG parameters as catheti. A total correlation between the ECG parameters is given: QT--QRS/QT--PQ.RR--PQ/RR--QRS = R--P/R--T = 1,309. In healthy individuals, the deviation from the ideal proportion constitutes less than 5%, and in patients with cardiovascular diseases, the deviations are substantial.     

A new approach to possible substrate binding mechanisms for nitrile hydratase

We combined normal mode analysis (NMA) with cavity calculations as a method to get more insight into static crystal structures. We used nitrile hydratase (NHase) as a case study, and the crystal structure of a complex of Pseudonocardia thermophila NHase (1UGP) with n-butyric acid was chosen as a reference structure. The reference structure was compared with the other available NHase crystal structures. Cavity calculations of the static structures showed the entrances to the active site and also a possible function of the N-terminal in the substrate selection of the Co-type NHase. When NMA was combined with cavity calculations, a closing-opening passage was observed. Analysis of low frequency modes combined with cavity calculations led us to propose "breathing" and "flip-flop" mechanisms which might be a key part of the substrate binding mechanism.     

A systematic approach to the analysis of protein phosphorylation

Reversible protein phosphorylation has been known for some time to control a wide range of biological functions and activities. Thus determination of the site(s) of protein phosphorylation has been an essential step in the analysis of the control of many biological systems. However, direct determination of individual phosphorylation sites occurring on phosphoproteins in vivo has been difficult to date, typically requiring the purification to homogeneity of the phosphoprotein of interest before analysis. Thus, there has been a substantial need for a more rapid and general method for the analysis of protein phosphorylation in complex protein mixtures. Here we describe such an approach to protein phosphorylation analysis. It consists of three steps: (1) selective phosphopeptide isolation from a peptide mixture via a sequence of chemical reactions, (2) phosphopeptide analysis by automated liquid chromatography-tandem mass spectrometry (LC-MS/MS), and (3) identification of the phosphoprotein and the phosphorylated residue(s) by correlation of tandem mass spectrometric data with sequence databases. By utilizing various phosphoprotein standards and a whole yeast cell lysate, we demonstrate that the method is equally applicable to serine-, threonine- and tyrosine-phosphorylated proteins, and is capable of selectively isolating and identifying phosphopeptides present in a highly complex peptide mixture.     

A tiered approach to estimate inventory data and impacts of chemical products and mixtures

Purpose

Mixtures of organic chemicals are a part of virtually all life cycles, but LCI data exist for only relatively few chemicals. Thus, estimation methods are required. However, these are often either very time-consuming or deliver results of low quality. This article compares existing and new methods in two scenarios and recommends a tiered approach of different methods for an efficient estimation of the production impacts of chemical mixtures.

Methods

Four approaches to estimate impacts of a large number of chemicals are compared in this article: extrapolation from existing data, substitution with generic datasets on chemicals, molecular structure-based models (MSMs, in this case the Finechem tool), and using process-based estimation methods. Two scenarios were analyzed as case studies: soft PVC plastic and a tobacco flavor, a mixture of 20 chemicals.

Results

Process models have the potential to deliver the best estimations, as existing information on production processes can be integrated. However, their estimation quality suffers when such data are not available and they are time-consuming to apply, which is problematic when estimating large numbers of chemicals. Extrapolation from known to unknown components and use of generic datasets are generally not recommended. In both case studies, these two approaches significantly underestimated the impacts of the chemicals compared to the process models. MSMs were generally able to estimate impacts on the same level as the more complex process models. A tiered approach using MSMs to determine the relevance of individual components in mixtures and applying process models to the most relevant components offered a simpler and faster estimation process while delivering results on the level of most process models.

Conclusions

The application of the tiered combination of MSMs and process models allows LCA practitioners a relatively fast and simple estimation of the LCIA results of chemicals, even for mixtures with a large number of components. Such mixtures previously presented a problem, as the application of process models for all components was very time-consuming, while the existing, simple approaches were shown to be inadequate in this study. We recommend the tiered approach as a significant improvement over previous approaches for estimating LCA results of chemical mixtures.