1. Screening ubiquitin specific protease activities using chemically synthesized ubiquitin and ubiquitinated peptides
- Author
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Gilles Ferry, Jean A. Boutin, Aude Kreiter, Karine Puget, Magali Jullian, Thibault Coursindel, Marine Bacchi, Olivier Nosjean, Benjamin Fould, and Amélie Maurras
- Subjects
0301 basic medicine ,Ubiquitin-Protein Ligases ,Lysine ,Biophysics ,Peptide ,Ubiquitin-conjugating enzyme ,Biochemistry ,Substrate Specificity ,Deubiquitinating enzyme ,03 medical and health sciences ,Ubiquitin ,Humans ,Molecular Biology ,chemistry.chemical_classification ,biology ,Circular Dichroism ,Ubiquitination ,Proto-Oncogene Proteins c-mdm2 ,Cell Biology ,Peptide Fragments ,Amino acid ,Ubiquitin ligase ,030104 developmental biology ,chemistry ,Proteolysis ,Chromatography, Gel ,biology.protein ,Mdm2 ,Ubiquitin-Specific Proteases ,Protein Processing, Post-Translational - Abstract
Ubiquitin, a 76 amino acid protein, is a key component that contributes to cellular protein homeostasis. The specificity of this modification is due to a series of enzymes: ligases, attaching the ubiquitin to a lysine, and deubiquitinases, which remove it. More than a hundred of such proteins are implicated in the regulation of protein turnover. Their specificities are only partially understood. We chemically synthesized ubiquitin, attached it to lysines belonging to the protein sequences known to be ubiquitinated. We chose the model protein “murine double minute 2” (mdm2), a ubiquitin ligase, itself ubiquitinated and deubiquitinated. We folded the ubiquitinated peptides and checked their tridimensional conformation. We assessed the use of these substrates with a series of fifteen deubiquitinases to show the potentiality of such an enzymological technique. By manipulating the sequence of the peptide on which ubiquitin is attached, we were able to detect differences in the enzyme/substrate recognition, and to determine that these differences are deubiquitinase-dependent. This approach could be used to understand the substrate/protein relationship between the protagonists of this reaction. The methodology could be customized for a given substrate and used to advance our understanding of the key amino acids responsible for the deubiquitinase specificities.
- Published
- 2017