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. 2017 Nov 29;29(47):474003.
doi: 10.1088/1361-648X/aa9351.

Self-assembly of model proteins into virus capsids

Karol Wołek  1 , Marek Cieplak
Affiliations

Self-assembly of model proteins into virus capsids

Karol Wołek et al. J Phys Condens Matter. .

Abstract

We consider self-assembly of proteins into a virus capsid by the methods of molecular dynamics. The capsid corresponds either to SPMV or CCMV and is studied with and without the RNA molecule inside. The proteins are flexible and described by the structure-based coarse-grained model augmented by electrostatic interactions. Previous studies of the capsid self-assembly involved solid objects of a supramolecular scale, e.g. corresponding to capsomeres, with engineered couplings and stochastic movements. In our approach, a single capsid is dissociated by an application of a high temperature for a variable period and then the system is cooled down to allow for self-assembly. The restoration of the capsid proceeds to various extent, depending on the nature of the dissociated state, but is rarely complete because some proteins depart too far unless the process takes place in a confined space.

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Figures

Figure 1.
Figure 1.
Cross-sections of the SPMV (on the left) and CCMV (on the right) virus capsids in our model. The snapshots are shown after equilibration. The dark blue symbols represent the structured segments of the proteins whereas the light blue symbols represent the dangling ends. The RNA molecule is shown in gray.
Figure 2.
Figure 2.
The temperature dependence of the equilibrium parameters describing the SPMV capsid (empty capsid in the left panels and encompassing the RNA in the right panels). The top panels show the normalized specific heat (in blue), Q (in black), Qp (in black), and Qpp (in red). The dashed lines indicate the level of 12. The bottom panels show Rg and RMSD. The bottom left panel also shows the RMSD for a single protein when studied alone (the dotted line) or as a part of the capsid (the solid black line).
Figure 3.
Figure 3.
Similar to figure 2 but for CCMV, except that here no results for single proteins are shown.
Figure 4.
Figure 4.
Characterization of the RNA molecule in the model SPMV (the left panels) and CCMV (the right panels) capsids. The top panels represent the end-to-end distance. The bottom panels show the average radius of gyration and the vertical bars show the width of the distribution of the average distance from the center of mass.
Figure 5.
Figure 5.
Snapshots form one trajectory of dissociation of the model SPMV with RNA at Th written at the top. Under each snapshot, there is information about the corresponding values of Qpp, Qp, and the time of heating. The colors used to show proteins are arbitrary. The RNA is shown in gray.
Figure 6.
Figure 6.
Similar to figure 5 but for CCMV with RNA. Chains A, B, and C are marked in blue, red, and black respectively.
Figure 7.
Figure 7.
The top panels show the time dependence of Qpp during heating, on the left for SPMV and on the right for CCMV. The numbers indicate the values of Th in units of ϵ/kB. The bottom panels show the average dissociation times for various indicated levels of what is considered to be a successful dissociation.
Figure 8.
Figure 8.
Similar to figure 7 but for capsids with RNA.
Figure 9.
Figure 9.
Examples of the SPMV capsid assembly after thermal denaturation at the temperature indicted at the top. Each horizontal triplet of panels shows snapshots appearing after evolving from the leftmost structure. This starting structure has been obtained at Th applied for time th written underneath in the brackets. The values of Qpp and Qp are indicated. The colors of the proteins are arbitrary.
Figure 10.
Figure 10.
Similar to figure 9 but form SPMV with RNA. The RNA molecule is shown in gray.
Figure 11.
Figure 11.
Similar to figure 9 but for for CCMV. Chains A, B, and C are marked in blue, red, and black respectively.
Figure 12.
Figure 12.
Similar to figure 9 but for CCMV with RNA1. Chains A, B, and C are marked in blue, red, and black respectively.
Figure 13.
Figure 13.
The time dependence of Qpp during self-assembly at Tr for the systems indicted. The initial states were obtained by heating at Th with values written in the right bottom corners of the panels.
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References

    1. Ahnert S E, Marsh J A, Hernandez H, Robinson C V, Teichmann S A. Science. 2015;350:aaa2245. doi: 10.1126/science.aaa2245. - DOI - PubMed
    1. Berman H M, Westbrook J, Feng Z, Gilliland G, Bhat T N, Weissig H, Shindyalov I N, Bourne P E. Nucl. Acids Res. 2000;28:235–42. doi: 10.1093/nar/28.1.235. - DOI - PMC - PubMed
    1. Gething M-J, Sambrook J. Nature. 1992;355:33–45. doi: 10.1038/355033a0. - DOI - PubMed
    1. Harrison P M, Arosio P. Biochim. Biophys. Acta. 1996;1275:161–203. doi: 10.1016/0005-2728(96)00022-9. - DOI - PubMed
    1. Wu C, Shea J E. Curr. Opin. Struct. Biol. 2011;21:209–20. doi: 10.1016/j.sbi.2011.02.002. - DOI - PubMed

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