Substrate Binding to the Catalytic Domains of Lysine Deacetylase 6

Abstract

Thousands of acetylated protein sequences have been identified in humans. Lysine deacetylases (KDACs or HDACs) are enzymes known to reverse acetylation by catalyzing hydrolysis of acetyllysine residues. Proper regulation of acetylation levels by KDACs and the opposing lysine acetyltransferases plays a role in many biological processes. Irregular activities of KDACs have been associated with a variety of diseases including various cancers. KDAC6 is the only known human KDAC to have two catalytic domains (CDs). The individual contributions of the catalytic domains to the overall activity of the enzyme and interaction with substrates are not well understood. Additionally, there are not many known substrates for the enzyme. We hypothesized that each CD has independent deacetylase activity and different substrate selectivity. To test this hypothesis, the activity of each domain was determined with a variety of peptides, many derived from acetylated proteins that are putative substrates of KDAC6. The second catalytic domain appears to be responsible for the majority of catalysis. To determine why peptides were active with one domain and not the other, we used molecular dynamics simulations to model the interaction between the CDs and the peptides. We identified residues relevant in interactions between each catalytic domain and peptide pair. Activity data and apparent substrate affinity were used to validate molecular dynamics results as explanatory for differences in substrate affinity for each CD.Support or Funding InformationNIH TL4GM118968, UL1GM118967, 5G12MD007595, and R15GM129682; NSF CHE 1625993 and MCB 1817358; U. S. Army Research Laboratory and the U. S. Army Research Office W911NF1810450; and the Louisiana Cancer Research Consortium.