Distinct Structural Flexibility within SARS-CoV-2 Spike Protein Reveals Potential Therapeutic Targets

Serena H. Chen; M. Todd Young; John Gounley; Christopher Stanley; Debsindhu Bhowmik

To locate the different structural features between the protomer and trimer in their 3-D structures, we compared the difference between the distance matrices of the representative protomer and trimer structures selected from the clusters in the latent dimensions (Fig. 4 A) . Most differences between the distance matrices result from interdomain arrangement. However, there are some disparities within the S2 domain (Fig. 4 B) . One region of difference corresponds to residue numbers 784 to 810 in the PDB. In the 3-D structure, this region forms a beta sheet in the trimer while the structure is lost in the protomer (Fig. 4 C) . Further investigation into this region reveals that the beta sheet in the trimer is stabilized by another beta sheet constituted by residues 700 to 710 of another chain (Fig. 4 D) . Without the presence of other chains, this stability is lost; not only do residues 784 to 810 in the S2 domain lose the beta sheet structure, but residues 700 to 710 in the hinge region connecting the two subunits become an extended loop (Fig. 4 E) . Oligomeric proteins are often stabilized by oligomerization and hold highly flexible regions in the protomer state [18] . The transition between the structured and unstructured form of these flexible regions is sometime reversible, but due to the size of the S protein protomer and the timescale applied in this study, we did not observe reversible behavior of the two loop regions in the protomer state. Interestingly, a fragment between residues 784 and 810 was identified previously as an immunodominant site in SARS-CoV-1 S protein [19] . Complementary antibodies acting on this site provided the dominant immune response for patients who recovered from the SARS-CoV 1 infection. Our results provide structural comprehension on the previous experimental observation and posit that targeting these residues might not only interfere with S protein trimerization and the subsequent viral activity but also aid antibody immune response. Our findings provide insights into therapeutic design targeting the S protein beyond the oft-targeted RBD domain.