Structural prediction of chimeric immunogen candidates to elicit targeted antibodies against betacoronaviruses
Fig 5
Structural stability of simulated chimeras.
Molecular dynamics simulations were computed for predicted structures and root-mean-squared deviation (RMSD) from a reference structure is plotted versus time. Plots are given for (a-b) the eight chimeras in the low-sequence-similarity cluster with the highest predicted relative stability(c-d) five low-stability controls. SARS-Cov-2 is plotted in both panels as an additional control. Panels (a,c) plot RMSD from the starting structure, whereas panels (b,d) plot RMSD from the ending structure. As expected, the low-stability controls showed the greatest RMSD, with one showing gross structural changes. The eight predicted-stable chimeras and SARS-CoV-2 all showed an initial increase in RMSD followed by a stabilization over the course of the 100-ns simulation. This can also be seen in RMSD plots relative to the end of the simulation (S6 Fig).