Deamidation: difference between revisions
Diff·revision 4 → 5·01:03, 21 Nov 2024
Difference between revision 4 and revision 5 of Deamidation. 2 lines changed; the page grew by 287 bytes.
| Revision 4 — 10:30, 12 Nov 2024 ResolutionRoo (talk) give the limit of quantitation with the signal-to-noise ratio it assumes 2,020 bytes ±0 | Revision 5 — 01:03, 21 Nov 2024 Retention_Time_Rae (talk) correct the water-content figure — the source reports it on a dry basis 2,307 bytes +287 | ||
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| 11 | The mass change is +0.984 Da, which is small enough that unit-resolution [[Mass spectrometry|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.{{r|usp1503}} | 11 | The mass change is +0.984 Da, which is small enough that unit-resolution [[Mass spectrometry|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.{{r|usp1503}} |
| 12 | 12 | ||
| + | 13 | 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.{{r|robinson2001}} | |
| + | 14 | ||
| 13 | == Mechanism and rate == | 15 | == Mechanism and rate == |
| 14 | 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.{{r|robinson2001}} | 16 | 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.{{r|robinson2001}} |