The N-end rule is a rule that governs the rate of protein degradation through recognition of the N-terminal residue of proteins. The rule states that the N-terminal amino acid of a protein determines its half-life (likelihood of being degraded). The rule applies to both eukaryotic and prokaryotic organisms, but with different strength, rules, and outcome. In eukaryotic cells, these N-terminal residues are recognized by N-degrons that are targeted by ubiquitin ligases, mediating ubiquitination thereby marking the protein for degradation. The rule was initially discovered by Alexander Varshavsky and co-workers in 1986. However, only rough estimations of protein half-life can be deduced from this 'rule', as N-terminal amino acid modification can lead to variability and anomalies, whilst amino acid impact can also change from organism to organism. Other degradation signals, known as degrons, can also be found in sequence.
Rules in different organisms
The rule may operate differently in different organisms.
- Met, Gly, Ala, Ser, Thr, Val, Pro - > 20 hrs (stabilizing)
- Ile, Glu - approx. 30 min (stabilizing)
- Tyr, Gln - approx. 10 min (destabilizing)
- Leu, Phe, Asp, Lys - approx. 3 min (destabilizing)
- Arg - approx. 2 min (destabilizing)
"N"-terminal residues - approximate half-life of proteins in mammalian systems 
- Val -> 100h
- Met, Gly -> 30h
- Pro -> 20h
- Ile -> 20h
- Thr -> 7.2h
- Leu -> 5.5h
- Ala -> 4.4h
- His -> 3.5h
- Trp -> 2.8h
- Tyr -> 2.8h
- Ser -> 1.9h
- Asn -> 1.4h
- Lys -> 1.3h
- Cys -> 1.2h
- Asp -> 1.1h
- Phe -> 1.1h
- Glu -> 1.0h
- Arg -> 1.0h
- Gln -> 0.8h
In Escherichia coli, positively-charged and some aliphatic and aromatic residues on the N-terminus, such as arginine, lysine, leucine, phenylalanine, tyrosine, and tryptophan, have short half-lives of around 2-minutes and are rapidly degraded. Other amino acids on the other hand may have half-lives of more than 10 hours when added to the N-terminal of the same protein. However, a complicating issue is that the first residue of bacterial proteins is normally expressed with an N-terminal formylmethionine (f-Met). The formyl group of this methionine is quickly removed, and the methionine itself is then removed by methionyl aminopeptidase. The removal of the methionine is more efficient when the second residue is small and uncharged (for example alanine), but inefficient when it is bulky and charged such as arginine. Once the f-Met is removed, the second residue becomes the N-terminal residue and are subject to the N-end rule. Residues with middle sized side-chains such as leucine as the second residue therefore may have a short half-life.
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