CGMD simulations of CA dimer assembly in the presence of IP6. (a) Time-series plot of assembled lattice size as a function of CG time step. CA assemble into a conical capsid in the presence of IP6 (CA hexamer NTDs are green, pentamer NTDs are red and all CTDs are gray). Simulation snapshots taken at

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... ( Fig. S1) reflects the ability of our CA model to assemble spontaneously into both helical tubes and cones with a preference for tubular structures in the absence of IP6. These results are reproducible in additional simulations albeit with a statistical spread. We further analyzed the intrinsic curvature of individual hexamers in the CA tube (Fig. S3c). In agreement with high resolution cryo-EM structures, hexamers adopt curved geometries to accommodate capsid curvature ...

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... examine the effects of IP6 during self-assembly, simulations were performed with 4mM CA and 600 IP6 molecules using the aforementioned assembly conditions, including the concentration of inert crowders and the CA conformational switching rate described earlier. Figure 3 presents different stages of IP6 mediated capsid assembly. A small and curled hexameric lattice formed initially with small curvature since the dihedral angle between adjacent hexamer-hexamer planes was close to 180°. ...

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... copyright holder for this preprint this version posted October 17, 2022. ; https://doi.org/10.1101/2022.05.03.490470 doi: bioRxiv preprint Interestingly, the narrow end of the cone formed last in our simulations where five proximal pentamers emerged, leading to the high-curvature cap shown in Figure 3 and movie S2. For comparison, our prior CG model (37) in the absence of IP6 tended to form the narrow high curvature cap first. ...

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... hexamers and exactly 12 pentamers. In this case, both pentamer and hexamers adopted intrinsic curvature. CA hexamers exerted a homogenous distribution of curvature ( Fig. S3b) while pentamers adopted a wide range of curvatures to accommodate geometrical limitations of conical shapes (Fig. ...

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... hexamers and exactly 12 pentamers. In this case, both pentamer and hexamers adopted intrinsic curvature. CA hexamers exerted a homogenous distribution of curvature ( Fig. S3b) while pentamers adopted a wide range of curvatures to accommodate geometrical limitations of conical shapes (Fig. ...

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... observed that curvature generation in capsid intermediates was always dictated by stabilization of pentameric defects by IP6. Unusually early incorporation of these pentameric defects resulted in smaller cores (Figure 3 and 7b), whereas more timely pentamer incorporation into the forming extended hexagonal lattice sheet led to appropriate curvature generation for relatively larger mature core formation as shown in Figure 7a,c,e. Although rarer than the regular conical capsid, a pill-shaped core (Fig. 7d), capped by the introduction of six pentameric defects at both ends, was also observed during our simulations. ...

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... simulations in the presence of IP6 (CA color scheme as in Figure 3). IP6 molecules stabilize lattice curvature inducing the formation of kinetically trapped structural outcomes. ...