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, ) with a 6-fold molar excess of REG? (BostonBiochem, USA) or REG???(41) at 37° C for 30 min in 20 mM HEPES, Reconstitution of 20S-PA28 complexes and degradation of short fluorogenic substrates, of MP-45 polypeptide and of KH-52 polypeptide were performed according methods already described, vol.40, p.41

, REG?-h20Sc or REG??-h20Sc (20 nM), for 8 hr at 37° C in 20 mM HEPES, pH 7.6, 2 mM NaCl. To assay peptides generated during protein degradation, we measured the appearance of new amino groups using fluorescamine as described (40), For kinetics analysis and generation of peptide products for MS/MS studies, KH-52 (50 µM) was incubated with h20Sc

, The acetonitrile was allowed to evaporate in a Speed-Vac and then the samples were resuspended in 6µl eluent A (see the composition below) for nLC-MS/MS analysis. 2µl of each sample were injected as technical replicate on a nLC-ESI-MS/MS quadrupole Orbitrap QExactive-HF mass spectrometer (Thermo Fisher Scientific). Peptides separation was achieved on a linear gradient from 95% solvent A (2% ACN, 0.1% formic acid) to 50% solvent B, 40 ?l 80% acetonitrile in 0.1% formic acid

. Inc and M. A. Woburn, MS data were acquired using a data-dependent top 15 method for HCD fragmentation. Survey full scan MS spectra (300-1750 Th) were acquired in the Orbitrap with 60000 resolution, AGC target 1 e6 , IT 120 ms. For HCD spectra, Thermo Scientific) connected to a 25-cm fused-silica emitter of 75 µm inner diameter (New Objective

. Nce-28%, Data processing and analysis For quantitative proteomic Raw data were processed with MaxQuant (ver. 1.5.2.8) searching against a database containing only the sequence of KH-52 Intron SIINFEKL, no enzyme specificity was selected and no difference between I and L. Mass deviation for MS-MS peaks was set at 20 ppm and peptides false discovery rates (FDR) at 0.01; the minimal length required for a peptide identification was eight amino acids. The list of identified peptides was filtered to eliminate reverse hits. Statistical analysis was done with Perseus (ver. 1.5.1.6) considering peptides intensity; normalization with Z-score and imputation were applied

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