Electrophoretic mobility of Alzheimer’s amyloid-β peptides in urea–sodium dodecyl sulfate–polyacrylamide gel electrophoresis

Abstract The 43-amino acid Alzheimer’s amyloid-β peptide (Aβ peptide) retains a predominantly α-helix and β-strand structure in sodium dodecyl sulfate (SDS) solution. This conformer has a high tendency to aggregate during conventional SDS–polyacrylamide gel electrophoresis (PAGE). Both the secondary structure and the proclivity for aggregation are obviated by the use of urea–SDS–PAGE: In 8 M urea—with or without SDS—the Aβ peptide becomes 100% random coil and remains monomeric. However, during electrophoresis in this medium, the peptide and its truncated variants do not obey the law of mass/mobility relationship that most proteins—including Aβ peptides—follow in conventional SDS–PAGE. Rather, the smaller carboxy-terminally truncated peptides migrate slower than the larger full-length peptide, while the amino terminally truncated peptide does migrate faster than the full-length Aβ peptide. Thus, despite their small size (2–4 kDa) and minor differences between their lengths, the Aβ peptides display a wide separation in this low-porosity (12% acrylamide) gel. We found that this unusual electrophoretic mobility in 8 M urea is due to the fact that the quantity of [ 35 S]SDS bound to the Aβ peptides, instead of being proportional to the total number of amino acids, is rather proportional to the sum of the hydrophobicity consensus indices of the constituent amino acids. It is then their hydrophobicity and, hence, the net negative charges contributed by the peptide-bound SDS that plays a major role in determining the mobility of Aβ peptides in 8 M urea–SDS–PAGE. The high selectivity of the 8 M urea–SDS–PAGE method allowed us to detect the presence of hitherto unknown Aβ peptide variants that were secreted in the conditioned medium by cultured HeLa cells.