title: Unexpected trypsin cleavage at ubiquitinated lysines.
abstract: Unexpected tryptic cleavage has been characterized at modified K48 residues in polyubiquitins. In particular, the tryptic products of all seven of the lysine-linked dimers of ubiquitin and of three trimers-linear Ub-(48)Ub-(48)Ub, linear Ub-(63)Ub-(63)Ub, and the branched trimer [Ub]2-(6,48)Ub-have been analyzed. In addition to the peptide products expected under commonly used tryptic conditions, we observe that peptides are formed with an unexpected ε-glycinylglycinyl-Lys carboxyl terminus when the site of linkage is Lys48. Trypsin from three different commercial sources exhibited this aberration. Initial cleavage at R74 is proposed in a distal ubiquitin to produce a glycinylglycinyl-lysine residue which is bound by trypsin.
authors.forename: Meghan C
authors.initials: MC
authors.lastname: Burke
authors.forename: Yan
authors.initials: Y
authors.lastname: Wang
authors.forename: Amanda E
authors.initials: AE
authors.lastname: Lee
authors.forename: Emma Kimm
authors.initials: EK
authors.lastname: Dixon
authors.forename: Carlos A
authors.initials: CA
authors.lastname: Castaneda
authors.forename: David
authors.initials: D
authors.lastname: Fushman
authors.forename: Catherine
authors.initials: C
authors.lastname: Fenselau
mesh_terms: D000595:Amino Acid Sequence; D019295:Computational Biology; D008239:Lysine / Q000737:chemistry*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D014357:Trypsin / Q000378:metabolism*; D025801:Ubiquitin / Q000378:metabolism*; D054875:Ubiquitination
chemical_list: D025801:Ubiquitin; D014357:Trypsin; D008239:Lysine