Discussion
The COVID-19 epidemic is spreading as an unsolvable problem worldwide. Despite the efforts of researchers, many details on SARS-CoV-2 biology remain unknown. Our study focused on the Nsp1 structure and stability by using different computational tools. We found that SARS-CoV-2 Nsp1 has a reduced compactness in comparison with SARS-CoV-1 Nsp1, with an increase in structural movements, suggesting this protein can more easily approach the active site of the ribosome compared to SARS-CoV-1 Nsp1. In addition, we found that the C-terminal of the SARS-CoV-2 Nsp1, in particular residues 164 to 170, are more flexible than other regions of SARS-CoV-2 Nsp1 and SARS-CoV-1 Nsp1, confirming the role of this region in the interaction with the 40S subunit.
Interestingly, a previous study suggested that when SARS-CoV-2 5′-UTR bind to Nsp1 N-terminal, the covalently linked Nsp1 C-terminal is not able to bind the 40S subunit [38]. The authors suggest that this may be due to a steric factor in which Nsp1 C-terminal is unable to approach the 40S subunit to form the Nsp1-ribosome complex. We found that mutation R24C had the highest frequency among all protein substitution mutations identified by us. Therefore, the occurrence of this mutation in the Nsp1 N-terminal may change the affinity of Nsp1 binding to the 5′-UTR of SARS-CoV-2, perhaps making it more effective in using the host ribosome for translation of viral proteins.
The Nps1 C-terminal was identified as being intrinsically disordered. In addition, E155, F157, D156, Q158, V169, T170, L173, F172, M174, and N178 emerged from the RIN analysis of betweenness and stress as 10 key residues governing the stability and affinity of the Nsp1 for interaction with ribosome. We also found that 11 mutations at HTH motif, which affect the Nsp1 structure, stability and binding affinity. Structural studies revealed that IDRs influence viral genome (RNA) adaptive capacity, host-virus interactions, virus-host range, cross-species transmission, and host tropism[39–43]. In antigen selection, IDRs may induce an undesirable immune response, such as weak or even completely non-immune responses [44]. Thus, these results indicated that IDRs may affect the interaction between the Nsp1 and the ribosome. If Nsp1 is used as an antigen, it may lead to an inappropriate immune response due to the presence of CT IDRs.