DFI profiles of asymmetric dimer and fully assembled capsid. (a) DFI profile for each of the coat protein monomers in the unbound asymmetric dimer (dashed lines) and the bound asymmetric dimer (solid lines). One of the flexible FG-loops has now become rigid, with little to no change upon binding of RNA. (b) Color-coded DFI profile of the fully assembled T = 3 capsid in the absence of RNA. A closeup is shown of an asymmetric dimer, a symmetric dimer, and the threefold/fivefold axes. Even in the fully assembled capsid, the ordered FG-loop A/C retains its flexibility while the disordered FG-loop B remains rigid.

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... DFI profile for the asymmetric dimer is shown in Fig. 2(a). Remarkably, following the conformational change, the FG-loop B undergoes a significant reduction in flexibility, even in the absence of RNA. This can be attributed to the higher number of close contacts experienced by FG-loop B. To gauge the universality of this flexibility change across dimers, we extended our analysis to encompass a ...

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... change, the FG-loop B undergoes a significant reduction in flexibility, even in the absence of RNA. This can be attributed to the higher number of close contacts experienced by FG-loop B. To gauge the universality of this flexibility change across dimers, we extended our analysis to encompass a fully assembled MS2 capsid, as depicted in Fig. 2(b). Intriguingly, while the FG-loops of symmetric dimers maintain their high flexibility, one of the FG-loops in each asymmetric dimer remains rigid. This observation underscores that the dynamic characteristics of individual dimers persist even within the context of higher-order structures. Based on the flexibility profiles of the whole ...

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... further investigate how the RNA-induced conformational change facilitates successful capsid assembly, we examined the DCI profiles of the wildtype unbound symmetric dimer and the wildtype bound asymmetric dimer, as shown in Fig. 3 (see Fig. S2 for DCI analysis of the mutant dimer). In the unbound symmetric dimer [ Fig. 3(a)], the FGloops and the binding interface are strongly coupled to each other. Conversely, in the bound asymmetric dimer [ Fig. 3(b)], while FG-loops A/B are still highly coupled to the binding interface, only FG-loop A (in the flexible conformation) is ...

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... (see Fig. S1), lacks the capability for capsid assembly [31,32]. This presents a challenge in comprehending why a mutant with similar biophysical properties to the wildtype dimer cannot undergo a cooperative capsid assembly process. Interestingly, the asymmetry in dynamic coupling of the two FG-loops is not observed in the W82R mutant dimer (see Fig. S2), particularly having a negligible effect on the dynamic coupling between FG-loops. These observations may align with a prior study suggesting that the W82R mutation restricts the conformational and free-energy landscape of the symmetric dimer [32,33], possibly due to the replacement of a large hydrophobic amino acid (Trp) with a ...