Abstract
The CTD (carboxy-terminal repeat domain) of the largest subunit of RNA Polymerase II in most eukaryotes consists of from 26 to 52 seven amino acid repeats, the consensus sequence of which is YSPTSPS. Even though this consensus repeat does not contain residues that are normally protonated under the conditions used for positive ion electrospray mass spectrometry, we find that the CTD acquires about one proton per repeat when analyzed by this procedure. We have termed this phenomenon superprotonation. Superprotonation is apparently a property of the consensus sequence as the repeat peptide, (YSPTSPS)4, is superprotonated whereas other proteins and the repeat peptides (YSPTSPK)4, (YSPTSPR)4and (YSPTAPR)4are not. The highly conserved nature of the contiguous consensus repeats in organisms ranging from yeast to mammals implies that the functionally significant behavior of the domain is easily perturbed. We propose that CTD superprotonation is a manifestation of a unique biophysical property that will influence and could be the basis for consensus repeat functionin vivo.
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