sodium-dodecyl-sulfate and formic-acid

We report an improved shotgun method for analyzing proteomic samples containing sodium dodecyl sulfate (SDS). This method is based on the use of strong-cation exchange (SCX) liquid chromatography (LC) for SDS removal that can be integrated with peptide separation as the first dimension of the two-dimensional LC tandem mass spectrometry workflow. To optimize the performance of SDS removal, various experimental conditions, including the concentrations of chemical reagents and salts in the sample, the SDS concentration, and the SCX mobile phase composition, were investigated. It was found that a peptide recovery rate of about 90% could be achieved while removing SDS efficiently. One key finding was that, by increasing the SDS concentration to a certain level (0.5%) in the digested peptide sample, the sample recovery rate could be increased. The peptide recovery rate of BSA digests was found to be 90.6 ± 1.0% (n = 3), and SDS in the SCX fractions collected was not detectable by pyrolysis GC-MS, i.e., below the detection limit of 0.00006% for the undesalted SCX fractions. The peptide recovery rates were found to be 90.9% ± 2.7 (n = 3) and 89.5% ± 0.5% (n = 3) for the digests of the membrane-protein-enriched fractions of E. coli cell lysates and the MCF-7 breast cancer cell line, respectively. Compared to the methods that use acid-labile surfactants, such as RapiGest and PPS, for the MCF-7 membrane fraction sample, the SDS method identified, on average (n = 3), more peptides (∼5%) and proteins (∼16%) than the RapiGest method, while the RapiGest method identified more peptides (∼21%) and proteins (∼7%) from the E. coli membrane fraction than the SDS method. In both cases, the two methods identified more peptides and proteins than the PPS method. Since SCX is widely used as the first dimension of 2D-LC MS/MS, integration of SDS removal with peptide separation in SCX does not add any extra steps to the sample handling process. We demonstrated the application of this method for 2D-LC MS/MS profiling of the MCF-7 membrane protein fraction and identified 6889 unique peptides, corresponding to 2258 unique proteins or protein groups from two replicate experiments with a false peptide discovery rate of ∼0.8%, compared to 5172 unique peptides and 1847 unique proteins identified by the RapiGest method.

Topics: Cations; Cell Line, Tumor; Chromatography, Ion Exchange; Databases, Protein; Escherichia coli; Formates; Humans; Limit of Detection; Membrane Proteins; Peptide Fragments; Peptide Mapping; Proteomics; Sodium Dodecyl Sulfate; Surface-Active Agents; Tandem Mass Spectrometry

Curli are amyloid-like fibers on the surface of some strains of Escherichia coli and Salmonella enteritidis. We tested the use of horizontal sodium dodecyl sulfate (SDS)-agarose gel electrophoresis to detect, isolate, and quantitate curli. Cell extracts fractionated in SDS-agarose gels and stained with Coomassie blue exhibited a soluble fraction that entered the gel and an insoluble fraction that remained in the well. Much more insoluble material was observed with curli-proficient strains than with strains that do not make curli. Both highly purified curli and the insoluble material isolated from an SDS-agarose gel could be dissociated into monomers when treated with formic acid. For quantitation, we immobilized samples in SDS-agarose prior to electrophoresis. This avoids losses during the staining of the gel. Our methods provide a rapid and simple fractionation of curli using equipment that is readily available.

Topics: Bacterial Proteins; Electrophoresis, Agar Gel; Escherichia coli; Formates; Immobilized Proteins; Rosaniline Dyes; Salmonella enteritidis; Sodium Dodecyl Sulfate

The accumulation of amyloid beta protein (Abeta) in the Tg2576 mouse model of Alzheimer's disease (AD) was evaluated by ELISA, immunoblotting, and immunocytochemistry. Changes in Abeta begin at 6-7 months as SDS-insoluble forms of Abeta42 and Abeta40 that require formic acid for solubilization appear. From 6 to 10 months, these insoluble forms increase exponentially. As insoluble Abeta appears, SDS-soluble Abeta decreases slightly, suggesting that it may be converting to an insoluble form. Our data indicate that it is full-length unmodified Abeta that accumulates initially in Tg2576 brain. SDS-resistant Abeta oligomers and most Abeta species that are N-terminally truncated or modified develop only in older Tg2576 mice, in which they are present at levels far lower than in human AD brain. Between 6 and 10 months, when SDS-insoluble Abeta42 and Abeta40 are easily detected in every animal, histopathology is minimal because only isolated Abeta cores can be identified. By 12 months, diffuse plaques are evident. From 12 to 23 months, diffuse plaques, neuritic plaques with amyloid cores, and biochemically extracted Abeta42 and Abeta40 increase to levels like those observed in AD brains. Coincident with the marked deposition of Abeta in brain, there is a decrease in CSF Abeta and a substantial, highly significant decrease in plasma Abeta. If a similar decline occurs in human plasma, it is possible that measurement of plasma Abeta may be useful as a premorbid biomarker for AD.

Topics: Aging; Alzheimer Disease; Amyloid beta-Peptides; Amyloid beta-Protein Precursor; Animals; Biomarkers; Brain; Brain Chemistry; Disease Models, Animal; Enzyme-Linked Immunosorbent Assay; Female; Formates; Humans; Immunoblotting; Immunohistochemistry; Male; Mice; Mice, Inbred C57BL; Mice, Transgenic; Organ Specificity; Plaque, Amyloid; Sodium Dodecyl Sulfate

The effect of ethanol and formate radicals on the major proteins of human erythrocyte membranes has been investigated.. Human erythrocyte ghosts and of erythrocyte ghosts stripped of peripheric proteins were irradiated in phosphate buffer with 100 mmol dm(-3) ethanol or 100 mmol dm(-3) formate under N2 or N2O. The alterations of the proteins were investigated by SDS-polyacrylamide gel electrophoresis and high-performance gel permeation chromatography.. In contrast to previous results on ribonuclease and on serum albumin the ethanol radicals were found to have a higher efficiency to damage erythrocyte membrane proteins than the formate radicals. Spectrin (Bands 1 and 2) and capnophorin (Band 3) showed the highest radiation-induced loss of all membrane proteins. When cysteamine or dithiothreitol were added to the erythrocyte ghosts with a similar OH-scavenging capacity as ethanol or formate, no degradation or aggregation of the membrane proteins could be observed even after a dose as high as 1800 Gy.. The results of this study confirm the high radiosensitivity of spectrin and capnophorin to primary radicals. Similarly to soluble proteins, membrane-associated proteins are more significantly damaged by ethanol radicals than by formate radicals.

Topics: Adult; Blood Proteins; Chromatography, High Pressure Liquid; Electrophoresis, Polyacrylamide Gel; Erythrocyte Membrane; Ethanol; Formates; Free Radicals; Humans; Sodium Dodecyl Sulfate

The hypothesis to be tested in this study was that toothpastes containing sodium lauryl sulfate (SLS) is unsuitable vehicles for xylitol. The bacteriostatic (and cariostatic) effect of xylitol is assumed to be caused by intracellular accumulation of xylitol-5-P in plaque bacteria. Experiments were designed to investigate whether presence of SLS would affect the uptake of xylitol by interacting with the bacterial membranes and thus inhibit xylitol-5-P formation. It was shown in an in vitro study that even very low concentrations of the strong anionic detergent SLS inhibited uptake of xylitol and xylitol-5-phosphate formation by dental plaque totally. The mild nonionic detergent ethoxylated stearyl alcohol (30x EO) had no such effect. In vivo experiments with toothpastes containing xylitol and either the strong or the mild detergent, showed that xylitol in toothpaste with SLS was not available for the plaque bacteria and gave no adaptation to xylitol, whereas in the presence of 30x EO it was available, and a xylitol adaptation was observed. Glucose metabolism, which was also studied for the plaque samples, was not significantly affected by presence of any of the 2 detergents, indicating that the amounts of xylitol in toothpastes were presumably too low to give clinical significant effects, even when mild detergents are used.

Topics: Acetates; Adult; Bacteria; Cariostatic Agents; Cell Membrane; Dental Plaque; Detergents; Drug Interactions; Fatty Alcohols; Female; Formates; Glucose; Humans; Male; Pharmaceutical Vehicles; Propionates; Sodium Dodecyl Sulfate; Sorbitol; Surface-Active Agents; Toothpastes; Xylitol

In this study, we evaluate the ability of several solvents to solubilize insoluble paired helical filaments (PHF) of Alzheimer disease. Specifically, we use protein extraction and reduction in the volume of insoluble material as quantitative assays to establish solvents of PHF. Using sequential categories of protein solvent to analyze insoluble PHF, only alkali or exhaustive proteolysis are effective in completely solubilizing PHF, while a variety of denaturants are ineffective. Alkali does not affect the phosphorylation state of PHF and complete dephosphorylation of PHF with hydrofluoric acid does not affect PHF solubility. These findings suggest that the 'hyperphosphorylation' of PHF proteins is not responsible for PHF insolubility. However the in vitro glycation of tau generates PHF that are insoluble in SDS and soluble in alkali. These findings suggest that protein crosslinks, including advanced glycation endproduct-derived crosslinks which were recently described in Alzheimer disease, play a major role in effecting PHF insolubility in vivo.

Topics: Adolescent; Adult; Aged; Aged, 80 and over; Alkalies; Alzheimer Disease; Cell Fractionation; Cross-Linking Reagents; Densitometry; Endopeptidases; Formates; Glycation End Products, Advanced; Guanidine; Guanidines; Hemostatics; Humans; Immunoblotting; Microscopy, Electron; Middle Aged; Neurofilament Proteins; Phosphorylation; Protein Denaturation; Sodium Dodecyl Sulfate; Solubility; Urea

A procedure for examining possible sequence homology in the triplet neurofilament proteins using a sodium dodecyl sulfate-polyacrylamide gel electrophoresis system is described. Five different chemical reagents (cyanogen bromide, BNPS-skatole, hydroxylamine, formic acid, and nitrothiocyanobenzoic acid) have been used for peptide mapping studies. Potential applications of this technique are discussed.

Topics: Amino Acid Sequence; Animals; Cattle; Cyanogen Bromide; Electrophoresis, Polyacrylamide Gel; Formates; Hydroxylamine; Hydroxylamines; Intermediate Filament Proteins; Neurofilament Proteins; Peptide Fragments; Skatole; Sodium Dodecyl Sulfate; Thiocyanates

A vegetalizing factor which induces the formation of endodermal and mesodermal organs in amphibian gastrula ectoderm was purified from chicken embryos. Preparative sodium dodecyl sulfate polyacrylamide electrophoresis and gel permeation chromatography on sephadex with different eluants were employed. In buffer containing 6 M urea the molecular weight of the factor was estimated to about 28 000-30 000. In buffer containing sodium dodecyl sulfate (SDS) the factor partially dissociates to smaller polypeptide chains. Because an equilibrium between molecules of different size is established, SDS-containing buffers are not suitable for preparative purposes. In 50%-70% formic acid the factor completely dissociates into smaller peptide chains (Mr about 13 000-15 000). Furthermore, very little absorption of the factor to the gel matrices or glass surfaces is observed in formic acid. The final purification can be achieved by high-performance gel permeation chromatography with glycerolpropyl-treated silica gel as column packing and 50% formic acid as eluant.

Topics: Animals; Chemical Phenomena; Chemistry; Chick Embryo; Chromatography, Gel; Electrophoresis, Polyacrylamide Gel; Endoderm; Formates; Growth Substances; Mesoderm; Molecular Weight; Proteins; Sodium Dodecyl Sulfate; Triturus