Fluorescence assay of SIRT protein deacetylases using an acetylated peptide substrate and a secondary trypsin reaction

• Published in: Analytical biochemistry 2004-09, Vol.332 (1), p.90-99
• Main Authors: Marcotte, Patrick A., Richardson, Paul R., Guo, Jun, Barrett, Leo W., Xu, Nan, Gunasekera, Angelo, Glaser, Keith B.
• Format: Article
• Language: English
• Subjects: Chromatography, High Pressure Liquid; Fluorescence assays; Fluorescent Dyes - metabolism; FRET assays; HDAC; Histone deacetylase; Histone Deacetylase Inhibitors; Histone Deacetylases - analysis; Histone Deacetylases - metabolism; Humans; Kinetics; NAD - metabolism; Niacinamide - analogs & derivatives; Niacinamide - metabolism; Peptide Fragments - metabolism; Sirtuin 1; Sirtuin 2; Sirtuin deacetylase; Sirtuins - analysis; Sirtuins - antagonists & inhibitors; Sirtuins - metabolism; Trypsin - metabolism
• ISSN: 0003-2697; 1096-0309
• DOI: 10.1016/j.ab.2004.05.039

A novel fluorescent substrate was devised for the sirtuin (SIRT) class of human protein deacetylases comprised of a peptide sequence containing a single acetyl-lysine residue, with a fluorescent group (tetramethylrhodamine-6-carboxylic acid, 6-TAMRA) near the carboxyl terminus and a nonfluorescent quenching group (QSY-7) near the amino terminus. The peptide sequence is modeled after the p53 acetylation site but is unreactive toward trypsin because all other lysine and arginine residues have been replaced by serine. However, the SIRT-deacetylated peptide is readily cleaved by trypsin, resulting in a maximal 30-fold enhancement of the 6-TAMRA fluorescence. Nicotinamide at millimolar concentrations stops the deacetylation but does not inhibit trypsin, and a microtiter plate assay of the SIRTs has been devised using the fluorescent substrate and these reagents. Using this method, the kinetics of the reaction of the cosubstrate nicotinamide adenine dinucleotide and the competitive inhibitor nicotinamide with SIRT1 and SIRT2 has been analyzed. Several nicotinamide analogs have also been tested as inhibitors and found to have much lower affinity for these enzymes than does the parent compound.