Foldon unfolding mediates the interconversion between Mpro-C monomer and 3D domain-swapped dimer

The C-terminal domain (M-pro-C) of SARS-CoV main protease adopts two different fold topologies, a monomer and a 3D domain-swapped dimer. Here, we report that M-pro-C can reversibly interconvert between these two topological states under physiological conditions. Although the swapped alpha(1)-helix is fully buried inside the protein hydrophobic core, the interconversion of M-pro-C is carried out without the hydrophobic core being exposed to solvent. The 3D domain swapping of M-pro-C is activated by an order-to-disorder transition of its C-terminal alpha(5)-helix foldon. Unfolding of this foldon promotes self-association of M-pro-C monomers and functions to mediate the 3D domain swapping, without which M-pro-C can no longer form the domain-swapped dimer. Taken together, we propose that there exists a special dimeric intermediate enabling the protein core to unpack and the alpha(1)-helices to swap in a hydrophobic environment, which minimizes the energy cost of the 3D domain-swapping process.