Deamidation (revision 6)

Deamidation is the conversion of an asparagine or glutamine side-chain amide to a carboxylic acid, with loss of ammonia. It is among the most common chemical degradation routes in peptides and proteins, and it proceeds spontaneously in aqueous solution without any external agent.^[1]

The mass change is +0.984 Da, which is small enough that unit-resolution mass spectrometry cannot distinguish a deamidated peptide from its parent. The charge change is more consequential: an uncharged amide becomes a negatively charged carboxylate, which alters chromatographic behaviour and, in a receptor-binding peptide, may alter activity.^[2]

Rate depends strongly on sequence context. Asparagine followed by glycine deamidates orders of magnitude faster than most other contexts, because the small following residue permits formation of the cyclic succinimide intermediate through which the reaction proceeds.^[1]

At neutral and alkaline pH the dominant pathway is intramolecular: the backbone nitrogen of the following residue attacks the asparagine side-chain carbonyl, forming a five-membered succinimide with loss of ammonia. The succinimide then hydrolyses to give aspartate or isoaspartate, typically in roughly a one-to-three ratio.^[1]

Isoaspartate formation is the more damaging outcome, because it inserts an extra methylene into the backbone and changes the local conformation. It is isobaric with aspartate and is not distinguishable by intact mass; detection requires a specific enzymatic or chromatographic method.