Catalytically active Dengue virus NS3 protease forms aggregates that are separable by size exclusion chromatography

An active form of the Dengue virus protease NS3 (CF40.Gly.NS3pro) was expressed in Escherichia coli. This construct consists of a critical 40 amino acid cofactor domain from NS2B fused to the N-terminal 184 amino acid protease domain of NS3 via a flexible, covalent linker (Gly(4)SerGly(4)). The recombinantly produced protein is soluble and has a hexa-histidine tag engineered at the N-terminus for ease of purification using metal affinity chromatography. However, the presence of lower molecular weight impurities after affinity chromatography indicated the need for additional purification steps. The consistent appearance of these impurities suggested that they may be the products of proteolysis and/or auto-proteolysis. The latter possibility was subsequently excluded by the observation of the same impurities in a purified, catalytically inactive form of the recombinant protease (CF40.Gly.NS3pro.SA). Further analysis indicated that these impurities may represent premature translation termination products. Regardless of their origin, they were shown to form various sized aggregates with full-length CF40.Gly.NS3pro that can be separated by size exclusion chromatography, yielding fractions of active protease of sufficient purity for crystallisation trials. The ultimate goal of these studies is to obtain a crystal structure of a catalytically active form of the Dengue virus NS3 protease for structure-based drug design. (C) 2002 Elsevier Science (USA). All rights reserved.

Allowance for thermodynamic non-ideality in the characterization of protein self-association by frontal exclusion chromatography: hemoglobin revisited

This investigation re-examines theoretical aspects of the allowance for effects of thermodynamic non-ideality on the characterization of protein self-association by frontal exclusion chromatography, and thereby provides methods of analysis with greater thermodynamic rigor than those used previously. Their application is illustrated by reappraisal of published exclusion chromatography data for hemoglobin on the controlled-pore-glass matrix CPG-120. The equilibrium constant of 100/M that is obtained for dimerization of the (02 species by this means is also deduced from re-examination of published studies of concentrated hemoglobin solutions by osmotic pressure and sedimentation equilibrium methods. (C) 2003 Elsevier Science B.V. All rights reserved.

Analytical exclusion chromatography

This review summarizes the development of exclusion chromatography, also termed gel filtration, molecular-sieve chromatography and gel permeation chromatography, for the quantitative characterization of solutes and solute interactions. As well as affording a means of determining molecular mass and molecular mass distribution, the technique offers a convenient way of characterizing solute selfassociation and solute-ligand interactions in terms of reaction stoichiometry and equilibrium constant. The availability of molecular-sieve media with different selective porosities ensures that very little restriction is imposed on the size of solute amenable to study. Furthermore, access to a diverse array of assay procedures for monitoring the column eluate endows analytical exclusion chromatography with far greater flexibility than other techniques from the viewpoint of solute concentration range that can be examined. In addition to its widely recognized prowess as a means of solute separation and purification, exclusion chromatography thus also possesses considerable potential for investigating the functional roles of the purified solutes. (C) 2003 Elsevier Science B.V. All rights reserved.

Addressing trypsin bias in large scale (phospho)proteome analysis by size exclusion chromatography and secondary digestion of large post-trypsin peptides.

In the vast majority of bottom-up proteomics studies, protein digestion is performed using only mammalian trypsin. Although it is clearly the best enzyme available, the sole use of trypsin rarely leads to complete sequence coverage, even for abundant proteins. It is commonly assumed that this is because many tryptic peptides are either too short or too long to be identified by RPLC-MS/MS. We show through in silico analysis that 20-30% of the total sequence of three proteomes (Schizosaccharomyces pombe, Saccharomyces cerevisiae, and Homo sapiens) is expected to be covered by Large post-Trypsin Peptides (LpTPs) with M(r) above 3000 Da. We then established size exclusion chromatography to fractionate complex yeast tryptic digests into pools of peptides based on size. We found that secondary digestion of LpTPs followed by LC-MS/MS analysis leads to a significant increase in identified proteins and a 32-50% relative increase in average sequence coverage compared to trypsin digestion alone. Application of the developed strategy to analyze the phosphoproteomes of S. pombe and of a human cell line identified a significant fraction of novel phosphosites. Overall our data indicate that specific targeting of LpTPs can complement standard bottom-up workflows to reveal a largely neglected portion of the proteome.

Rapid, quantitative determination of polar compounds in fats and oils by solid-phase extraction and size-exclusion chromatography using monostearin as internal standard

A rapid and simple method was developed for quantitation of polar compounds in fats and oils using monostearin as internal standard. Starting from 50 mg of oil sample, polar compounds were obtained by solid-phase extraction (silica cartridges) and subsequently separated by high-performance size-exclusion chromatography into triglyceride polymers, triglyceride dimers, oxidized triglyceride monomers, diglycerides, internal standard and fatty acids. Quantitation of total polar compounds was achieved through the internal standard method and then amounts of each group of compounds could be calculated. A pool of polar compounds was used to check linearity, precision and accuracy of the method, as well as the solid-phase extraction recovery. The procedure was applied to samples with different content of polar compounds and good quantitative results were obtained, especially for samples of low alteration level.

Inverse size exclusion chromatography (ISEC)

In this work, an improved protocol for inverse size-exclusion chromatography (ISEC) was established to assess important pore structural data of porous silicas as stationary phases in packed chromatographic columns. After the validity of the values generated by ISEC was checked by comparison with data obtained from traditional methods like nitrogen sorption at 77 K (Study A), the method could be successfully employed as valuable tool at the development of bonded poly(methacrylate)-coated silicas, while traditional methods generate partially incorrect pore structural information (Study B). Study A: Different mesoporous silicas were converted by a pseudomorphical transition into ordered MCM-41-type silica while maintaining the particle-size and -shape. The essential parameters like specific surface area, average pore diameter and specific pore volume, the pore connectivity from ISEC remained nearly the same which was reflected by the same course of the theoretical plate height vs. linear velocity curves. Study B: In the development of bonded poly(methacrylate)-coated silicas for the reversed phase separation of biopolymers, ISEC was the only method to generate valid pore structural information of the polymer-coated materials. Synthesis procedures were developed to obtain reproducibly covalently bonded poly(methacrylate) coatings with good thermal stability on different base materials, employing as well particulate and monolithic materials.

The development of chromatography for the characterization of protein interactions: a personal perspective

This article reviews the progress of a personal endeavour to develop chromatography as a quantitative procedure for the determination of reaction stoichiometries and equilibrium constants governing protein interactions. As well as affording insight into an aspect of chromatography with which many protein chemists are unfamiliar, it shows the way in which minor adaptations of conventional chromatographic practices have rendered the technique one of the most powerful methods available for the characterization of interactions. That pathway towards quantification is followed from the introduction of frontal gel filtration for the study of protein self-association to the characterization of ligand binding by the biosensor variant of quantitative affinity chromatography.

Monodisperse lignin fractions as standards in size-exclusion analysis Comparison with polystyrene standards

The difficulty of preparing monodisperse lignin fractions on a large scale is a limiting factor in many applications. The present paper addresses this problem by examining the properties and size-exclusion behavior of lignin isolated by the acetosolv pulping process from post-extraction crushed sugarcane bagasse. The isolated lignin was subjected to a solvent pretreatment, followed by preparative gel permeation chromatography fractionation. The fractions were analyzed by high-performance size-exclusion chromatography (HPSEC) and these samples showed a great decrease in polydispersity, compared to the original acetosolv lignin. Several fractions of very low polydispersity, close to unity, were employed as calibration curve standards in HPSEC analysis. This original analytical approach allowed calibration with these lignin fractions to be compared with the polystyrene standards that are universally employed for lignin molecular mass determination. This led to a noteworthy result, namely that the lignin fractions and polystyrene standards showed very similar behavior over a large range of molecular masses in a typical HPSEC analysis of acetosolv lignin. (C) 2009 Elsevier B.V. All rights reserved.

Purification and partial characterization of cathepsin D from porcine (Sus scrofa) liver using affinity chromatography

Cathepsin D, a lysosomal aspartic protease, has been purified from porcine liver using a combination of pepstatin-A agarose and Affi-Gel Blue affinity chromatography, followed by size-exclusion chromatography. The purified protein consists of two polypeptide chains of 15 and 30 kDa, and has an isoelectric point of 6.8. Porcine liver cathepsin D has maximum activity at pH 2.5-3.0 as determined by its activity against hemoglobin, with a K-cat of 14.3 s(-1) and a k(cat)/K-M of 2.70 x 10(6) s(-1) M-1 as determined by the hydrolysis of a fluorogenic peptide substrate.

Size exclusion chromatogram of the Tannermoor 2009 sample after saltout experiments

Samples from a pristine raised peat bog runoff in Austria, the Tannermoor creek, were analysed for their iron linked to natural organic matter (NOM) content. Dissolved organic carbon < 0.45 µm (DOC) was 41 to 64 mg/L, iron 4.4 to 5.5 mg/L. Samples were analysed applying asymmetric field flow fractionation (AsFlFFF) coupled to UV-Vis absorption, fluorescence and inductively coupled plasma mass spectrometry (ICP-MS). The samples showed an iron peak associated with the NOM peak, one sample exhibiting a second peak of iron independent from the NOM peak. As highland peat bogs with similar climatic conditions and vegetation to the Tanner Moor are found throughout the world, including areas adjacent to the sea, we examined the behaviour of NOM and iron in samples brought to euhaline (35 per mil) conditions with artificial sea salt. The enhanced ionic strength reduced NOM by 53% and iron by 82%. Size exclusion chromatography (SEC) of the samples at sea-like salinity revealed two major fractions of NOM associated with different iron concentrations. The larger one, eluting sharply after the upper exclusion limits of 4000-5000 g/mol, seems to be most important for iron chelating. The results outline the global importance of sub-mountainous and mountainous raised peat bogs as a source of iron chelators to the marine environment at sites where such peat bogs release their run-offs into the sea.

Otimização das condições de produção de ésteres etílicos a partir de óleo de peixe com elevado teor de ácidos graxos ômega-3

The production of ethyl esters by alcoholysis is an alternative for splitting triacylglycerols due to the possibility of using low temperatures, which results in oxidative protection of the polyunsaturated fatty acids. Ethyl esters produced under mild conditions of temperature could be used as substrate for obtaining structured lipids. The reaction parameters of production of ethyl esters from fish oil with high content of omega-3 fatty acids by alcoholysis were optimized using response surface methodology. An experimental design (2³) (with levels +1 and -1, six axial points with levels -alpha and +alpha and three central points) was applied. The variables investigated were concentration of catalyst, amount of ethyl alcohol and temperature. Ethyl ester conversion was monitored by high performance size exclusion chromatography (HPSEC) and the best result obtained was 95% conversion rate. The optimal conditions were 40 °C, 1% of NaOH and 36% of ethanol.

Dextranas em açúcares do estado de São Paulo

The characterization of dextran in sugars by size exclusion chromatography (SEC) has been carried out according to the number-average molecular weight (Mn), the weight-average molecular weight (Mw), the Z-average molecular weight (Mz), and the polydispersity (Mw/Mn). The results suggest that all the analyzed thirty sugar samples from São Paulo state were contaminated with two or three different dextran polymers. The collected data clearly point out that the total dextran content together with the mass distribution parameters Mw, Mn, Mz, and Mw/Mn should be considered during the evaluation of the quality of the sugar used for the cachaça sweeting process.

Dipeptide synthesis in biphasic medium: evaluating the use of commercial porcine pancreatic lipase preparations and the involvement of contaminant proteases

Dipeptide syntheses starting from Ac-L-Tyr-OEt or Z-L-X-OMe (X: Asp, Tyr, Phe, Arg, Lys or Thr) and glycine amide in biphasic reaction media were achieved using two commercially available porcine pancreatic lipase (PPL) preparations (crude (cPPL) and purified PPL (pPPL)). Under the mild conditions employed, α-chymotrypsin, a pancreatic protease that also presents esterase activity, catalyzed Ac-L-Tyr-Gly-NH2 synthesis with high productivity. Product hydrolysis also occurred in most of the syntheses studied. Polyacrylamide gel electrophoresis, enzymatic assays employing specific chromogenic substrates and size-exclusion chromatography revealed that cPPL and pPPL contain contaminant proteases and, therefore, exhibit esterase and amidase activities. Overall, these data indicate that those contaminants may be the main catalysts of peptide bond synthesis when Nα-blocked-L-amino acid esters and the commercial PPL preparations are used. On the other hand, such data do not contest the possibility of using such enzyme preparations as an inexpensive source of catalysts for dipeptide synthesis under soft conditions.

In vivo bioavailability of selenium in enriched Pleurotus ostreatus mushrooms

The in vivo bioavailability of Se was investigated in enriched Pleurotus ostreatus mushrooms. A bioavailability study was performed using 64 Wistar male rats separated in 8 groups and fed with different diets: without Se, with mushrooms without Se, with enriched mushrooms containing 0.15, 0.30 or 0.45 mg kg(-1) Se and a normal diet containing 0.15 mg kg(-1) of Se using sodium selenate. The experiment was performed in two periods: depletion (14 days) and repletion (21 days), according to the Association of Official Analytical Chemists. After five weeks, the rats were sacrificed under carbon dioxide, and blood was drawn by heart puncture. Blood plasma was separated by centrifugation. The total Se concentration in the plasma of rats fed with enriched mushrooms was higher than in rats fed with a normal diet containing sodium selenate. The plasma protein profiles were obtained using size exclusion chromatography (SEC) and UV detectors. Aliquots of effluents (0.5 mL per minute) were collected throughout in the end of the chomatographic column. However, Se was determined by graphite furnace atomic absorption spectrometry (GF AAS) only in the aliquots where proteins were detected by SEC-UV. The plasma protein pro. le of rats fed with different diets was similar. The highest Se concentration was observed in a peptide presenting 8 kDa. Furthermore, the higher Se concentration in this peptide was obtained for rats fed with a diet using enriched mushrooms (7 mu g L(-1) Se) compared to other diets (2-5 mu g L(-1) Se). These results showed that Se-enriched mushrooms can be considered as an alternative Se food source for humans, due to their high bioavailability.

CHEMICAL AND PHYSICO-CHEMICAL CHARACTERIZATION OF LIGNINS OBTAINED FROM ETHANOL-WATER FRACTIONATION OF BAGASSE

Organosolv lignins can replace petroleum chemicals such as phenol either partially or totally in various applications. Eight lignins, seven of which corresponded to the ethanol-water fractionation of bagasse and the other to a reference lignin (Alcell (R)) were analyzed with the aim to evaluate their chemical and physicochemical characteristics. The purity of the lignin fractions was determined by high pressure liquid chromatography (HPLC) and by ash content. Fourier Transform-Infrared Spectroscopy (FTIR) techniques and differential UV spectroscopy were applied to identify the chemical groups in the lignin samples. The molecular weight distribution was determined by size exclusion chromatography (HPSEC). Thermogravimetric analysis (TGA) and differential scanning calorimetry (DSC) techniques were used to determine the mass loss due to the high temperature treatment. The lignins studied showed the presence of p-hydroxyphenyl (H unit) and a greater proportion of guaiacyl (G unit) moieties, lower purity, similar or greater amount of phenolic hydroxyl groups, and higher degradation temperatures, than the Alcell (R) lignin.