Lysine deacetylases exhibit distinct changes in activity profiles due to fluorophore conjugation of substrates
Open accessAbstract
Lysine deacetylases (KDACs) are enzymes that reverse the post-translational modification of lysine acetylation. Thousands of potential substrates, acetylated protein sequences, have been identified in mammalian cells. Properly regulated acetylation and deacetylation have been linked to many biological processes, while aberrant KDAC activity has also been linked to numerous diseases. Commercially available peptide substrates that are conjugated to fluorescent dye molecules, such as 7-amino-4-methylcoumarin (AMC), are commonly used to monitor deacetylation in studies addressing both substrate specificity and small molecule modulators of activity. Here, we have compared the activity of several KDACs, representing all major classes of KDACs, with substrates in the presence and absence of AMC as well as peptides for which tryptophan has been substituted for AMC. Our results unequivocally demonstrate that AMC has a significant effect on activity for all KDACs tested. Furthermore, in neither the nature of the effect nor the magnitude is consistent across KDACs, making it impossible to predict the effect of AMC on a particular enzyme-substrate pair. AMC did not affect acetyllysine preference in a multiply acetylated substrate. In contrast, AMC significantly enhanced KDAC6 substrate affinity, greatly reduced Sirt1 activity, eliminated the substrate sequence specificity of KDAC4, and had no consistent effect with KDAC8 substrates. These results indicate that profiling of KDAC activity with labeled peptides is unlikely to produce biologically relevant data.
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Fluorophore-coupled substrates have been questioned in several contexts.
“Finally, because fluorophore-coupled substrates have been questioned in several contexts (Kaeberlein et al., 2005; Toro et al., 2017), we validated the preference for demyristoylation over deacetylation using non-fluorogenic peptides ( 7 -9 ) in an LC-MS-based assay (Fig. 2B).”
From Histone deacetylase 11 is an ε-N-Myristoyllysine hydrolase (2018) · cites this paper as Toro et al., 2017
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- Authors
- Toro, T. B., Bryant, J. R., & Watt, T. J.
- Affiliations
- Xavier University of Louisiana (US)
- Corresponding author
- Watt, Terry J.
- ORCID
- Watt, Terry J.
- Venue
- Biochemistry
- Publisher
- American Chemical Society (ACS)
- Published
- 2017-08-16
- Volume
- 56
- Issue
- 34
- Pages
- 4549-4558
- ISSN
- 0006-2960 (ISSN-L)
- 1520-4995
- PMC
- PMC5937523
- OpenAlex
- W2741419889
- Cited by
- 11
- References
- 59
- Citations by year
- 2023: 3 · 2021: 1 · 2020: 1 · 2019: 2 · 2018: 2 · 2017: 2
- FWCI
- 0.78
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Biochemistry (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Division of Chemistry (1625993)
- National Center on Minority Health and Health Disparities (5G12MD007595)
- Army Research Office (W911NF1310129)
- Army Research Laboratory
- National Institute of General Medical Sciences (TL4GM118968, UL1GM118967)
- Louisiana Cancer Research Consortium
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Histone Deacetylase Inhibitors Research
- Health Sciences › Medicine › Geriatrics and Gerontology › Sirtuins and Resveratrol in Medicine
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Ubiquitin and proteasome pathways
- Keywords
- lysine deacetylases, lysine acetylation, 7-amino-4-methylcoumarin, fluorophore conjugation, fluorescent peptide substrate, SIRT1, substrate specificity, enzyme activity profiling, tryptophan substitution
- MeSH terms
- Coumarins, Histone Deacetylases, Humans, Substrate Specificity
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