Designing 26s Proteasome Activating Peptides

Background and aim: the 26s proteasomes maintain protein homeostasis through the degradation of damaged proteins which are tagged by polyubiquitination. therefore, enhancing proteasome activity has been identified as a novel method to protect against proteotoxic diseases. usp14 is a subunit of the 26s proteasome, which can rescue substrates from degradation by the elimination of the ubiquitin. thus, the design of an inhibitor for usp14 could enhance protein degradation. usp14 includes a ubl domain, which is a critical regulator of proteasomal activity. recently it has been demonstrated that the ubl domain stimulates the degradation of peptides, non-ubiquitinated, and ubiquitinated proteins. considering the importance of the functional ubl domain, structural investigation of usp14 interaction with the proteasome would be helpful in drug design. methods: in order to design proteasome activating peptides, first, the interaction of the ubl domain of usp14 (pdb id: 1wgg) and rpn1 subunit of the proteasome (pdb id: 4cr2) was investigated using haddock 2.2. then, a core peptide inhibitor was designed using peptiderive from the rosetta package, and a library of peptides was created based on the interaction pattern. finally, the binding energy of each peptide with the binding site was calculated using autodock software. results: based on the docking results, the core peptide has the binding energy of -4.45 kcal/mol and the binding energy ranges for the peptide library were from -5.36 to 1.12 kcal/mol. therefore, among ten amino acid sequences in the peptide library, sqparqk, with binding energy of -5.36 kal/mol was selected as a suitable peptide to inhibit usp14 activity because of its high binding affinity relative to the core peptide. conclusion: according to these studies, the proposed peptide may be able to prevent the binding of usp14 to the proteasome by inhibiting its effective interaction at the rpn1 site, and therefore increasing the activity of the proteasome.