Structure-based identification and clustering of protein families and superfamilies

Summary We describe an approach to protein structure comparison designed to detect distantly related proteins of similar fold, where the procedure must be sufficiently flexible to take into account the elasticity of protein folds without losing specificity. Protein structures are represented as a series of secondary structure elements, where for each element a local environment describes its relations with the elements that surround it. Secondary structures are then aligned by comparing their features and local environments. The procedure is illustrated with searches of a database of 468 protein structures in order to identify proteins of similar topology to porcine pepsin, porphobilinogen deaminase and serum amyloid P-component. In all cases the searches correctly identify protein structures of similar fold as the search proteins. Multiple cross-comparisons of protein structures allow the clustering of proteins of similar fold. This is exemplified with a clustering of /- and -class protein structures. We discuss applications of the comparison and clustering of three-dimensional protein structures to comparative modelling and structure-based protein design.     

Comparative assessment of solid-phase extraction clean-up procedures, GC columns and perfluoroacylation reagents for determination of type B trichothecenes in wheat by GC-ECD

Various solid-phase extraction (SPE) procedures for clean-up, two perfluoroacylation reagents (pentafluoropropionic anhydride (PFPA) and heptafluorobutyric anhydride (HFBA)) and two chromatographic columns (HP-1701 and HP-5) have been assessed comparatively to achieve the determination of type B trichothecenes (deoxynivalenol (DON), nivalenol (NIV), 3- and 15-acetyldeoxynivalenol (3- and 15-ADON)) in wheat grain by gas chromatography (GC)-electron-capture detection (ECD). Spiked wheat samples were extracted with acetonitrile-water (84:16, v/v). Tested SPE procedures were MycoSep 225 column, Florisil and different cartridges prepared in the laboratory with mixtures of various sorbents like alumina, Celite 545, C18, silica and charcoal. We propose MycoSep 225 column, and cartridges made with alumina-charcoal-silica and alumina-charcoal-C18 silica mixtures as clean-up procedures on the basis of recovery values (89.6, 87.3 and 86.1% for deoxynivalenol, respectively, at 1.0 mg/kg spiking level). The two last procedures are less expensive. Pentafluoropropionic anhydride was more stable against moisture and less expensive, while recoveries were similar to those obtained with heptafluorobutyric anhydride. HP-1701 column can separate 3- and 15-acetyldeoxynivalenol derivatives while HP-5 cannot, although this last column provided lower bleed and better sensitivity.     

Replacing Synthetic with Microbial Surfactants as Collectors in the Treatment of Aqueous Effluent Produced by Acid Mine Drainage,Using the Dissolved Air Flotation Technique

Dissolved air flotation (DAF) is a well-established separation process employing micro bubbles as a carrier phase. The application of this technique in the treatment of acid mine drainage, using three yeast biosurfactants as alternative collectors, is hereby analyzed. Batch studies were carried out in a 50-cm high acrylic column with an external diameter of 2.5 cm. High percentages (above 94%) of heavy metals Fe(III) and Mn(II) were removed by the biosurfactants isolated from Candida lipolytica and Candida sphaerica and the values were found to be similar to those obtained with the use of the synthetic sodium oleate surfactant. The DAF operation with both surfactant and biosurfactants, achieved acceptable turbidity values, in accordance with Brazilian standard limits. The best ones were obtained by the biosurfactant from C. lipolytica, which reached 4.8 NTU. The results obtained with a laboratory synthetic effluent were also satisfactory. The biosurfactants removed almost the same percentages of iron, while the removal percentages of manganese were slightly higher compared with those obtained in the acid mine drainage effluent. They showed that the use of low-cost biosurfactants as collectors in the DAF process is a promising technology for the mining industries.     

Archaeometrical study of paleometallurgical materials from the archaeological site “Cerro de las Balsas — Chinchorro” (La Albufereta, Alacant, Spain)

An Iberian archaeological site located in the east of Spain is one of the most important cupellation centers found in the 4th century b.c. Different metallurgical materials were found in the archaeological site as minerals, cast slags, forged slags, metallic lead, cupella fragments and bronzes. Also was found reverbs remains used for cupper-based materials and cupellation procedure, and hearth forge remains for obtained iron material. The recuperated samples were studied by comparing samples of the same type of material by macroanalysis and microanalysis. The microanalysis and quantitation of the different archaeological materials was carried out by SEM/EDX. The information provides about the knowledge of a metallurgic process such as that of silver production by lead cupellation. The microanalysis results reflect the variety of elements that constitute the slags and other materials, and that come from the forge of the worked metallic materials. Also, the process cupellation was confirmed by the identification of lead and silver. The presence of forge slag corroborates the use of the great amount of recovered heart forges in the excavation like metallurgical structures for the iron work.     

Identification by GC-FID and GC-MS of amino acids, fatty and bile acids in binding media used in works of art

GC-FID was used as single methodology for the identification and differentiation of proteins, lipids and ox bile from binders used in artistic paintings. The samples were hydrolyzed by HCl. Subsequently, the simultaneous formation of volatile derivatives of the amino, fatty and bile acids with ethyl chloroformate was performed quickly and safely in an aqueous medium. The derivatives were separated by capillary GC and characterized by GC-MS. The ageing of drying oils was studied, identifying pelargonic acid among other degradation products. Proteinaceous and lipoid binding media were characterized by means of the quotients between the areas of the peaks for each amino or fatty acid with respect to the area of the peak for alanine or palmitic acid. Fatty acids from ox bile were easily identified by their retention times characteristic for eicosanoic, docosanoic and pentadecanoic acids. The suggested method was applied to the analysis of binders in baroque paintings by Palomino in Valencia (Spain). Animal gelatine and linseed oil were found. Received: 27 September 2000 / Revised: 16 January 2001 / Accepted: 17 January 2001     

Analytical study of proteinaceous binding media in works of art by gas chromatography using alkyl chloroformates as derivatising agents

In this work, we present the results obtained in an analytical study of the different types of proteinaceous binding media most commonly used in paintings, using GC-FID as the technique of analysis and GC-MS as a confirmatory technique. The application of this methodology requires prior hydrolysis of the proteins in the binding media to obtain free amino acids and then volatile derivatives, in this case by reaction with chloroformates due to advantages of speed, safety and the aqueous medium in which the reaction occurs. The method proposed for the proteinaceous binding media study is to calculate the proportions of the different amino acids with respect to alanine. This method provided good characterisation of different binding media, such as pork gelatine, beef gelatine, albumin, egg white and casein. The proposed method is used for the identification of binding media (including mixtures of binders) present in real samples from paintings in the city of Valencia, Spain.     

Analysis of the common characteristics of the Hartmann,Ronchi, and Shack–Hartmann tests

An overview of the settings of the planes for the filters and observed patterns in the Hartmann and Ronchi tests is presented. Also a new set of filters for both test were developed. In a similar way, it is easy to extend this analysis to the Shack–Hartmann test, and to propose a new Null Shack–Hartmann filter.