3.1. Structural Analysis of MD Simulations
Molecular dynamics (MD) simulations were performed for the Nsp1 of SARS-COV-2 and SARS-CoV-1. The RMSD plot indicates that both proteins reached equilibrium after 100 ns and that the SARS-CoV-1 Nsp1 deviation is less than the SARS-CoV-2 Nsp1. We also found that the Nsp1 F157S variant has less stability than the wild type Nsp1 (Figure 1a). The Nsp1 SARS-CoV-1 exhibited a lower Rg values compared to the SARS-CoV-2 Nsp1. The difference between Rg of these two proteins is ~ 0.12, which indicates functional movements of SARS-CoV-2 Nsp1 due to the lesser compactness of the structure. In general, the Rg for both sequences showed a determined pattern: SARS-CoV-2 Nsp1 > SARS-CoV-1 Nsp1, as shown in Figure 1b. The RMS plot was constructed from the 100 ns data in order to understand the deviation of each Nsp1. The RMSF of the backbone for the SARS-CoV-2 Nsp1 displayed more flexible 164 to 170 residues (Lys, His, Ser, Ser, Gly, Val, and Ter), as compared to the SARS-CoV-1 Nsp1 (Figure 1c). This region corresponds to the C-terminal of the Nsp1 related to the protein interaction with the ribosome through CT, meaning that its flexibility could be related to its function.
In order to analyze H-bond interactions during the 100 ns simulation time, intermolecular H-bond plots were constructed for the Nsp1 of SARS-CoV-2 and SARS-CoV-1 (Figure 1d). We found that the SARS-CoV-2 Nsp1 has an approximately similar number of intermolecular H-bonds as the SARS-CoV-1 Nsp1. In addition, the SASA analysis showed that the amino acid residues of both structures approximately exhibit a similar behavior of the hydrophilic and hydrophobic residues (Figure 1e). In order to understand the total motion of Nsp1 structures in the phase space, the first two eigenvectors were projected onto it. The results indicate that the motion features characterized by the two eigenvectors are different in the SARS-CoV-2 and SARS-CoV-1 Nsp1 proteins. As shown in Figure 2a, SARS-CoV-2 Nsp1 show a wider motions than SARS-CoV-1 Nsp1, indicating more conformational changes.
The plots in Figure 2b-c represent a comparative view of the Free Energy Surface (FES) landscape as a function of RMSD and Rg for Nsp1. The general trend applying to both Nsp1 proteins is that the higher the value of the two parameters (RMSD and Rg), the lower the free energy surface. We found that the Rg of SARS-CoV-2 Nsp1 is higher than SARS-CoV-1 Nsp1, suggesting that SARS-CoV-2 Nsp1 has less energy and more stability in compared with SARS-CoV-1 Nsp1.