Dissecting protein-protein interactions in proteasome assembly: Implication to its self-assembly

The 26S proteasome is a multi-catalytic ATP-dependent protease complex that recognizes and cleaves damaged or misfolded proteins to maintain cellular homeostasis. The 26S subunit consists of 20S core and 19S regulatory particles. 20S core particle consists of a stack of heptameric alpha and beta subunits. To elucidate the structure-function relationship, we have dissected protein-protein interfaces of 20S core particle and analyzed structural and physiochemical properties of intra-alpha, intra-beta, inter-beta, and alpha-beta interfaces. Furthermore, we have studied the evolutionary conservation of 20S core particle. We find the size of intra-alpha interfaces is significantly larger and is more hydrophobic compared with other interfaces. Inter-beta interfaces are well packed, more polar, and have higher salt-bridge density than other interfaces. In proteasome assembly, residues in beta subunits are better conserved than alpha subunits, while multi-interface residues are the most conserved. Among all the residues at the interfaces of both alpha and beta subunits, Gly is highly conserved. The largest size of intra-alpha interfaces complies with the hypothesis that large interfaces form first during the 20S assembly. The tight packing of inter-beta interfaces makes the core particle impenetrable from outer wall of the cylinder. Comparing the three domains, eukaryotes have large and well-packed interfaces followed by archaea and bacteria. Our findings provide a structural basis of assembly of 20S core particle in all the three domains of life.