cis-Inhibition of proteasomal degradation by viral repeats: impact of length and amino acid composition

The Gly–Ala repeat (GAr) of the Epstein–Barr virus nuclear antigen 1 is a cis acting inhibitor of ubiquitin–proteasome proteolysis. We have investigated the capacity of various repeats to inhibit the turnover of the proteasomal substrate IκBα. Inhibition of TNFα-induced degradation was achieved by insertion of octamers containing three alanines or valines, interspersed by no more then three consecutive glycines. The inhibitory activity was abolished by increasing the length of the spacer, by eliminating the spacers, or by substitution of a single hydrophobic residue with a polar or charged residue. A serine containing octamer was inactive but inhibition was partially restored by insertion of three consecutive repeats. These findings suggest a model where inhibition requires the interaction of at least three alanine residues of the GAr in a β-strand conformation with adjacent hydrophobic binding pockets of a putative receptor.