Publication date: Dec 04, 2024

The main protease (M) is an attractive drug target for inhibiting the coronavirus. Lots of research has focused on the static viewpoint of the M, such as the X-ray crystal structure, inhibitors design, and the transition between monomer and dimer. However, the attention to the dynamical features of M is limited, which is essential for a deeper determination of the properties of the target protein. In our research, we constructed three single-tryptophan mutants (W31IN, W207IN, and W218IN) of M from SARS-CoV-2 and SARS-CoV to monitor the motion of M at the nano-second timescale using the time-resolved fluorescence assay. We found that the temperature-dependent Stokes shift results show various behaviors among the three single-tryptophan mutants: the microenvironment around the Trp207 residue is more temperature-sensitive compared to that in residues Trp31 and Trp218. The molecular dynamic simulation results further support that M is more flexible than that of M. This difference is directly related to the distinct perturbations of residues Phe185 to Gln192, a loop that connects domain II and domain III. For the first time, we were able to reveal the different motions between M and M, although the static structures of these two are not distinguished. The differences in dynamics would be an essential step towards understanding the evolving trend of coronavirus, providing a comprehensive view of the properties of M, and offering perspectives for designing inhibitors for further research.

Semantics

Original Article