BackgroundTo date, the complexity of the plasma proteome exceeds the analytical capacity of conventional approaches to isolate lower abundance proteins that may prove to be informative biomarkers. Only complex multistep separation strategies have been able to detect a substantial number of low abundance proteins (<100 ng/ml). The first step of these protocols is generally the depletion of high abundance proteins by the use of immunoaffinity columns or, alternatively, the enrichment of by the use of solid phase hexapeptides ligand libraries.Methodology/Principal FindingsHere we present a direct comparison of these two approaches. Following either approach, the plasma sample was further fractionated by SCX chromatography and analyzed by RP-LC-MS/MS with a Q-TOF mass spectrometer. The depletion of the 20 most abundant plasma proteins allowed the identification of about 25% more proteins than those detectable following low abundance proteins enrichment. The two datasets are partially overlapping and the identified proteins belong to the same order of magnitude in terms of plasma concentration.Conclusions/SignificanceOur results show that the two approaches give complementary results. However, the enrichment of low abundance proteins has the great advantage of obtaining much larger amount of material that can be used for further fractionations and analyses and emerges also as a cheaper and technically simpler approach. Collectively, these data indicate that the enrichment approach seems more suitable as the first stage of a complex multi-step fractionation protocol.

The complexes formed by partially folded human and bovine α‐lactalbumin with oleic acid (OA) have been reported to display selective apoptotic activity against tumor cells. These complexes were named human (HAMLET) or bovine (BAMLET) alpha‐lactalbumin made lethal to tumor cells. Here, we analyzed the OA complexes formed by fragments of bovine α‐lactalbumin obtained by limited proteolysis of the protein. Specifically, the fragments investigated were 53–103 and the two‐chain fragment species 1–40/53–123 and 1–40/104–123, these last being the N‐terminal fragment 1–40 covalently linked via disulfide bridges to the C‐terminal fragment 53–123 or 104–123. The OA complexes were obtained by mixing the fatty acid and the fragments in solution (10‐fold and 15‐fold molar excess of OA over protein fragment) or by chromatography of the fragments loaded onto an OA‐conditioned anion exchange column and salt‐induced elution of the OA complexes. Upon binding to OA, all fragments acquire an enhanced content of α‐helical secondary structure. All OA complexes of the fragment species showed apoptotic activity for Jurkat tumor cells comparable to that displayed by the OA complex of the intact protein. We conclude that the entire sequence of the protein is not required to form an apoptotic OA complex, and we suggest that the apoptotic activity of a protein–OA complex does not imply specific binding of the protein.

The aggregation process of wild-type human lysozyme at pH 3.0 and 60°C has been analyzed by characterizing a series of distinct species formed on the aggregation pathway, specifically the amyloidogenic monomeric precursor protein, the oligomeric soluble prefibrillar aggregates, and the mature fibrils. Particular attention has been focused on the analysis of the structural properties of the oligomeric species, since recent studies have shown that the oligomers formed by lysozyme prior to the appearance of mature amyloid fibrils are toxic to cells. Here, soluble oligomers of human lysozyme have been analyzed by a range of techniques including binding to fluorescent probes such as thioflavin T and 1-anilino-naphthalene-8-sulfonate, Fourier transform infrared spectroscopy, and controlled proteolysis. Oligomers were isolated after 5 days of incubation of the protein and appear as spherical particles with a diameter of 8-17 nm when observed by transmission electron microscopy. Unlike the monomeric protein, oligomers have solventexposed hydrophobic patches able to bind the fluorescent probe 1-anilinonaphthalene-8-sulfonate. Fourier transform infrared spectroscopy spectra of oligomers are indicative of misfolded species when compared to monomeric lysozyme, with a prevalence of random structure but with significant elements of the β-sheet structure that is characteristic of the mature fibrils. Moreover, the oligomeric lysozyme aggregates were found to be more susceptible to proteolysis with pepsin than both the monomeric protein and the mature fibrils, indicating further their less organized structure. In summary, this study shows that the soluble lysozyme oligomers are locally unfolded species that are present at low concentration during the initial phases of aggregation. The nonnative conformational features of the lysozyme molecules of which they are composed are likely to be the factors that confer on them the ability to interact inappropriately with a variety of cellular components including membranes.

Background and Aims: Grape proteins are responsible for the appearance of haziness in white wines during storage after bottling. However, only a few studies have approached the analysis of the fate of must proteins throughout the alcoholic fermentation. This study aimed to systematically investigate the daily variations in protein type and content during the fermentation in order to understand its influence on hazing potential and to attain some basic information to improve the practical management of grape proteins involved in the hazing of white wines. Methods and Results: The evolution of total soluble protein and individual protein fractions was studied in samples taken before, during and after alcoholic fermentation of a white grape must. The results were then related to variations in protein instability as measured by the heat test. Both the quantity of soluble protein and the protein instability increased during fermentation and then decreased after 1-month storage of the wine. Protein composition did not vary during fermentation as assessed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and anion exchange chromatography (AEC). However, variations in the relative proportions of the six protein fractions obtainable by AEC were noted in the different samples. The contribution of each AEC protein fraction to wine instability was determined by considering both the intrinsic instability and the relative quantity of each of the individual protein fractions in the wine. It was demonstrated that the grape thaumatin-like protein VVTL1, as identified by mass spectrometry, showed the largest increase during fermentation and accounted for almost 40% of the heat-induced haze of the final wine. Moreover, the decreased protein instability noted after one month storage of the wine could be attributed to the stabilizing effect of polysaccharides released by the yeast cells. Conclusions: The quantity and relative proportion of soluble proteins vary during and after the alcoholic fermentation, as does their heat instability in wine. Grape VVTL1, constituting a large proportion of the total proteins in wine, seems to play a major role in protein haze formation. The release of yeast polysaccharides is related to an increased heat stability of total wine protein, despite the increase in the relative proportion of their most unstable component VVTL1. Therefore, the hazing potential of a white wine seems to be affected by variations in the relative proportions of its macromolecular components occurring in the early stages of winemaking. Significance of the Study: This study addressed for the first time the issue of the protein changing during the fermentation of white wine. The results obtained here offer useful information to aid understanding of the contribution of individual proteins to white wine instability, which can be applied for the improvement of the winemaking process. AbbreviationsAEC anion-exchange chromatography; KDS potassium dodecyl sulfate; MS mass spectrometry; MW molecular weight, PAS periodic aci...