The NS1 protein of the tick-borne encephalitis virus potentially has three glycosylation sites. When processing the PNGase F protein on SDS-PAGE, I observe three bands - a fully glycosylated 52 kDa protein and two fractions of a partially deglycosylated protein. Why I don't see band of completely deglycosylated protein about 42 kDa?
The amount of the enzyme, as well as the reaction time, were followed by the manufacturer's protocol.
Oligosaccharides with a fucose α(1→3)-linked to the asparagine-linked N-acetylglucosamine (GlcNAc) are commonly found in glycoproteins from sources like plants and parasitic worms and are resistant to PNGase F. In these cases, PNGase A is required. However, PNGase A is ineffective if sialic acid is present on the N-linked oligosaccharide. Additionally, glycoproteins may have buried or inaccessible glycoconjugates. To address this, consider sequential deglycosylation using sialidases and exoglycosidases.
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