Rules governing selective protein carbonylation.
BACKGROUND
Carbonyl derivatives are mainly formed by direct metal-catalysed oxidation (MCO) attacks on the amino-acid side chains of proline, arginine, lysine and threonine residues. For reasons unknown, only some proteins are prone to carbonylation.


RESULTS
we used mass spectrometry analysis to identify carbonylated sites in: BSA that had undergone in vitro MCO, and 23 carbonylated proteins in Escherichia coli. The presence of a carbonylated site rendered the neighbouring carbonylatable site more prone to carbonylation. Most carbonylated sites were present within hot spots of carbonylation. These observations led us to suggest rules for identifying sites more prone to carbonylation. We used these rules to design an in silico model (available at http://www.lcb.cnrs-mrs.fr/CSPD/), allowing an effective and accurate prediction of sites and of proteins more prone to carbonylation in the E. coli proteome.


CONCLUSIONS
We observed that proteins evolve to either selectively maintain or lose predicted hot spots of carbonylation depending on their biological function. As our predictive model also allows efficient detection of carbonylated proteins in Bacillus subtilis, we believe that our model may be extended to direct MCO attacks in all organisms.
Laboratoire de Chimie Bactérienne - Aix Marseille Université - UPR 9043-CNRS, 31, Chemin Joseph Aiguier, Marseille, France.
Etienne
E
Maisonneuve
Adrien
A
Ducret
Pierre
P
Khoueiry
Sabrina
S
Lignon
Sonia
S
Longhi
Emmanuel
E
Talla
Sam
S
Dukan
D000595:Amino Acid Sequence; D001120:Arginine / Q000737:chemistry; D001412:Bacillus subtilis / Q000378:metabolism*; D001671:Biochemistry / Q000379:methods*; D002244:Carbon / Q000737:chemistry; D002384:Catalysis; D004926:Escherichia coli / Q000378:metabolism; D006801:Humans; D008239:Lysine / Q000737:chemistry; D013058:Mass Spectrometry / Q000379:methods; D008670:Metals / Q000737:chemistry*; D008969:Molecular Sequence Data; D010100:Oxygen / Q000737:chemistry*; D011392:Proline / Q000737:chemistry; D050050:Protein Carbonylation; D011506:Proteins / Q000737:chemistry; D012709:Serum Albumin / Q000737:chemistry; D013912:Threonine / Q000737:chemistry
D008670:Metals; D011506:Proteins; D012709:Serum Albumin; D013912:Threonine; D002244:Carbon; D001120:Arginine; D011392:Proline; D008239:Lysine; D010100:Oxygen