Dephosphorylation of intact glycoprotein to greatly improve digestion efficiency coupled with matrix-assisted laser desorption/ionization–Fourier transform ion cyclotron resonance mass spectrometric analysis

Sialylation is essential for a variety of cellular functions. Herein, we used bovine fetuin with three potential N-linked glycosylation sites containing complex-type glycan structures, four potential O-linked glycosylation sites and six potential phosphorylation sites as a model compound to develop a highly-efficient digestion strategy for sialylated glycoproteins and efficient enrichment strategy for sialylated glycopeptides using titanium dioxide. The former according to the process of alkaline phosphatase digestion followed by tryptic digestion and then proteinase K digestion could greatly improve the enzymatic efficiency on fetuin, and the latter could obviously enhance the enrichment efficiency for multisialylated glycopeptides using phosphoric acid solution as elution buffer. The mass spectra of the enriched glycopeptides derived from fetuin reveal that several series of the ion clusters with mass difference of 291 Da correspond to the presence of multisialylated glycopeptides. In addition, the approach was applied to characterize the sialylated status of α2-macroglobulin and transferrin, respectively, from the sera of healthy subjects and sex- and age-matched patients with thyroid cancer, and their spectra indicate that the change in the amount of the glycoforms containing different number of sialic acid (SA) residues from one glycosylation site may be used to differentiate between healthy subjects and cancer cases.     

Highly selective artificial gel antibodies for detection and quantification of biomarkers in clinical samples. I. Spectrophotometric approach to design the calibration curve for the quantification

High selectivity of a biomarker is a basic requirement when it is used for diagnosis, prognosis and treatment of a disease. The artificial gel antibodies, which we synthesise by a molecular imprinting method, have this property not only for proteins, but also for bioparticles, such as viruses and bacteria. However, diagnosis of a disease requires not only that the biomarker can be “fished out” from a body fluid with high selectivity, but also that its concentration in the sample can rapidly be determined and preferably by a simple technique. This paper deals primarily with the development of a spectrophotometric method, which is so simple and fast that it can be used with advantage in a Doctor's Office. The development of this method was not straight‐forward. However, by modifications of the performance of these measurements we can now design standard curves in the form of a straight line, when we plot the true (not the recorded “apparent” absorption) against known protein concentrations. In an additional publication (see the following paper in this issue of JSS) we show an application of such a plot: determination of the concentration of albumin in serum and cerebrospinal fluid from patients with neurological disorders to investigate whether albumin is a biomarker for these diseases.     

Composition, structure and solution properties of polysaccharides extracted from leaves of Mesembryanthenum crystallinum

Water and Chelator-soluble polymers were independently isolated from the alcoholic-insoluble substance (AIS) of Mesembryanthenum crystallinum leaves. After precipitation in ethanol and ultrafiltration (40 kD cut-off) of recovered solids dissolved in water, the yield relative of the so-call Lw and LCh polymers to the AIS dry matter was 2.5 ± 0.2 and 7 ± 0.5%. The galacturonic acid contents were 67 ± 3% and 63 ± 5%. The degrees of methylesterification of ca. 45 ± 3% and 50 ± 3%, showed that Lw and LCh belonged to the fairly methylesterified pectin class. From sugar analysis, LCh was shown to contain at least two types of pectic blocks, homogalacturonan (HG: 58%) and rhamnogalacturonan-I (RG-I: 34%). Their structure were deduced after saponification, polygalacturonase treatments, size exclusion chromatography (SEC) onto Sephacryl S-200 and then sugar composition of the collected fractions. The main polymers were methylesterified HG (32%), some of them being linked to non-methylesterified HG (10%), and to polygalacturonase-resistant HG (17%). In addition, there were (1) a highly soluble RG-I with long galactan side chains (RG-I-gal accounting for 9%) and (2) a RG-I with short arabino-galactan side chains (25%), named RG-I-ara/gal that was almost totally lost during SEC analysis, due to its low solubility at room temperature and in absence of chelators.SEC coupled with differential refractive index and light scattering showed that highly methylesterified HG chains exhibited aggregate structures in solution due to intermolecular hydrophobic interactions. These interactions formed hydrophobic clusters, which have been characterized by surface tension measurements and with a polarity probe, the Coomassie Brilliant Blue dye. After alkaline treatment of LCh, the self-assembly of HG disappeared.     

RAMA stain: A fast,sensitive and less protein‐modifying CBB R250 stain

SDS‐PAGE and CBB staining are two of the most popular methods used for protein analysis. Although many reports that describe such staining methods have been published, these conventional protocols require several hours or days for staining and de‐staining. In this study we describe a recently developed, fast and sensitive CBB staining method that utilizes the staining solution of RAMA that consists of the low‐cost reagents: CBB R250, acetic acid, methanol and ammonium sulfate, and the destaining solution of water. Our method dose dependently detects 12 nanograms protein within 60 min and with a wide protein spectrum. Although the features of the dose‐dependent relationship depend upon protein amounts and protein types, for most of the protein samples tested, a linear relationship was observed in the region from 12 to 330 ng. Moreover, through further washing, the detection sensitivity of protein is enhanced and reaches a maximum at 1.4 ng and then gradually decreases in the de‐staining process. It has been shown recently through MS analyses that the sensitive colloidal CBB staining methods frequently result in artifactual methylations due to the strong acid and long contact during staining and the destaining processes. Such artifacts were reported to be reduced by the replacement of strong inorganic acid with acetic acid and because RAMA utilizes acetic acid and is in contact with the proteins for a short time during staining and de‐staining, it is expected that in vitro artifacts will be reduced. Finally, MS analyses of RAMA‐stained protein bands were revealed not to have been methylated.     

Antibody-based surfaces: rapid characterization using two complementary colorimetric assays

Finding a general solution for optimizing the grafting of antibody on solid surfaces is difficult due to the variety of material, grafting principles and chemistries or surface formats available (beads, microplates, fibers, etc.). Pre-screening methods able to assess grafting efficiency (GE) and specific activity (SA) are required. In this context, we present here two colorimetric assays that can be used on a wide variety of surface format, chemistry, etc. The first one, ADECA (Amino Density Estimation by Colorimetric Assay) allows a rapid estimation of grafted antibodies and allows calculating the GE. The second one, A₂HRP (Antibody Anti-HorseRadish Peroxidase) provides a measure of the amount of active antibody, which, combined to ADECA, is used to determine the SA of grafted antibody. Analytical parameters (limit of detection, repeatability, linearity, etc.) of these two colorimetric assays are presented. Using two commercially available microplates, we demonstrated that, when used in parallel, these rapid and sensitive methods are well adapted to pre-screening of antibody grafting performances.     

An affine-scaling interior-point CBB method for box-constrained optimization

We develop an affine-scaling algorithm for box-constrained optimization which has the property that each iterate is a scaled cyclic Barzilai–Borwein (CBB) gradient iterate that lies in the interior of the feasible set. Global convergence is established for a nonmonotone line search, while there is local R-linear convergence at a nondegenerate local minimizer where the second-order sufficient optimality conditions are satisfied. Numerical experiments show that the convergence speed is insensitive to problem conditioning. The algorithm is particularly well suited for image restoration problems which arise in positron emission tomography where the cost function can be infinite on the boundary of the feasible set. This material is based upon work supported by the National Science Foundation under Grants 0203270, 0619080, and 0620286.     

Photocatalytic Activity of Radial Rutile Titanium(IV) Oxide Microspheres for Aerobic Oxidation of Organics

Radial rutile TiO₂ nanorod homomesocrystals (TiO₂-NR HOMCs) or the so-called “sea urchin-like TiO₂ microspheres” were synthesized by using a hydrothermal method. TiO₂-NR HOMCs show photocatalytic activity for aerobic oxidative degradation of 2-naphthol under irradiation of UV- and visible light. Furthermore, extremely small iron oxide clusters were formed on the surface of TiO₂-NR HOMCs (FeO_x/TiO₂-NR HOMCs) by the chemisorption-calcination technique to reduce the band gap. The FeO_x-surface modification gives rise to drastic enhancement of the UV- and visible-light activity. Reversed double-beam photoacoustic spectroscopy measurements were performed for TiO₂-NR HOMCs and FeO_x/TiO₂-NR HOMCs to obtain the ERDT (energy-resolved distribution of electron traps)/CBB (conduction-band bottom) patterns. The ERDT/CBB pattern of TiO₂-NR HOMCs consists of two components derived from rutile (C1) and amorphous TiO₂ (C2). In the pattern, the surface electron traps in C2 exist near the CBB to be removed by the FeO_x-surface modification. By taking this finding into consideration, the striking surface modification effect is ascribable to the electrocatalytic activity (or the action as an electron reservoir) of the FeO_x clusters for multiple ORR, the suppression of recombination, and the increase in the visible-light harvesting efficiency.