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The C-terminal domain (Mpro -C) of SARS-CoV main protease adopts two different fold topologies, a monomer and a 3D domain-swapped dimer. Here, we report that Mpro -C can reversibly interconvert between these two topological states under physiological conditions. Although the swapped α1 -helix is fully buried inside the protein hydrophobic core, the interconversion of Mpro -C is carried out without the hydrophobic core being exposed to solvent. The 3D domain swapping of Mpro -C is activated by an order-to-disorder transition of its C-terminal α5 -helix foldon. Unfolding of this foldon promotes self-association of Mpro -C monomers and functions to mediate the 3D domain swapping, without which Mpro -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 α1 -helices to swap in a hydrophobic environment, which minimizes the energy cost of the 3D domain-swapping process.

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

Foldon unfolding mediates the interconversion between M ^pro -C monomer and 3D domain-swapped dimer