3.2. Structural analysis of Nsp1-ribosome complex and Residue interaction networks (RINs)
The complex structure of the SARS-CoV-2 Nsp1 protein and human ribosomal 40S subunit were analyzed. The binding site of Nsp1 to the ribosome contains 26 residues at Nsp1 C-terminal (Supplementary Table S1). Among these residues, 17 residues form a helix-turn-helix (HTH) motif and lead to form Nsp1-ribosome complex. As shown in Table 1, HTH interacts simultaneously with different regions of the ribosome called “head region” including uS3 and “body region” including eS30 and uS5 (Figure 3). HTH interacts with uS3 by D152, E155, D156, E159, Q158, and N160 residues, as well as this motif involved in interaction with uS5 by Y154, F157, Q158, W161, T170, L173, L177, N178 residues. R175, E176, and G179 residues of HTH motif play a key role in forming Nsp1-ribosome (eS30) complex. We calculated the binding energy (ΔGBinding) for these interactions, which showed that the interaction between the Nsp1 and uS3 is stronger than the other interactions (Table 2).
In addition, the key residues for Nsp1 binding the ribosome were determined by using stress and betweenness as the two main parameters of the local metrics. The analysis of Nsp1 (HTH motif) network revealed crucial residues including D156, F157, V169, T170, E172, L173, and M174 (Figure 4a). Moreover, the investigating betweenness and stress parameters for SARS-CoV-2 Nsp1 (HTH) binding the ribosome indicated E155, Q158, L173, M174, and N178 as residues of interest (Figure 4b). The high betweenness and stress values suggest that the node is a mediator of interactions with other nodes and that is probably a key structural residue. Therefore, we reported these amino acids as critical residues at the interface between the SARS-CoV-2 Nsp1 and ribosome, which may play a vital role in forming the complex.