Integration of Cypoviruses into polyhedrin matrix

Abstract

Unlike in other viruses, in Cypoviruses the genome is doubly protected since their icosahedral capsids are embedded into a perfect polyhedrin crystal. Current experimental methods cannot resolve the resulting interface structure and we propose a symmetry-based approach to predict it. We reveal a remarkable match between the surfaces of Cypovirus and the outer polyhedrin matrix. The match arises due to the preservation of the common tetragonal symmetry, allowing perfect contacts of polyhedrin trimers with VP1 and VP5 capsid proteins. We highlight a crucial role of the VP5 proteins in embedding the Cypovirus into the polyhedrin matrix and discuss the relationship between the nucleoside triphosphatase activity of the proteins and their role in the superstructure formation. Additionally, we propose an electrostatic mechanism that drives the viral superstructure disassembly occurring in the alkaline environment of the insect intestines. Our study may underpin novel strategies for engineering proteinaceous nanocontainers in diverse biotechnological and chemical applications.

Fig. 1. Structures of polyhedrin crystal and Cypovirus capsid. (a) Two polyhedrin tetrahedrons with the centers at the nodes of body centered cubic lattice. (b) Cypovirus capsid and its asymmetric structural unit consisting of five structural proteins. Sixty such units form the entire shell.

Fig. 2. Embedding of the Cypovirus capsid into the polyhedrin crystal matrix. (a) Polyhedrin trimer shown in different orientations. (b) Primitive cubic cell of the polyhedrin crystal containing eight trimers. More convex frontal sides of four green trimers are facing the cell center; four yellow trimers are facing outward. (c) Icosahedron inscribed into a cube and superimposed with a smaller cube. Edges of the cubes are related as 2 : 3. Common rotational axes of the groups T and I are shown in red and yellow. (d) A fragment of the polyhedrin crystal formed by 4 × 4 × 4 primitive cells. Eight trimers (shown in red) in the vertices of the fragment are the only ones located outside of the virus capsid and potentially not excluded upon virus embedding. (e and f) Two variants of the capsid embedding into the polyhedrin cage (see the main text). All trimers of the 3 × 6 × 6 cluster that are not excluded upon virus embedding, are shown in green. Remaining trimers (shown in red) belong to the 4 × 4 × 4 fragment and occupy 3-fold axes of the superstructure. Triplets of the closest neighbors of the red trimers are shown in yellow. The insert in panel e shows the cavity behind the trimers facing the virus in the depicted embedding variant. VP1 and VP5 proteins are shown in light purple and purple, respectively, while 5-fold turrets assembled from VP3 are shown grey. (g) The viral surface and trimers contacting it in the second embedding variant showing the trimers that have contact area exceeding 260 Ų. Blue trimers are in contact with VP3; green trimers are in contact with VP5.

Fig. 3. Arrangement of the Cypovirus superstructure in the vicinity of the 3-fold axes. (a and b) Contact regions (highlighted in yellow) between trimers occupying 3-fold axes and capsid proteins. (c and d) Localization of NTP molecules in the vicinity of VP5 proteins. In panels (a and c), trimer faces the virus (also see ESI Movie 2†) and in panels (b and d), trimer faces the opposite direction. ATP in the middle of panel (c), located far from VP5 proteins, is in contact with them in the opposite trimer orientation shown in panel (d). The same applies for GTP in panel (d).

Fig. 4. Electrostatic effects associated with Cypovirus superstructure disassembly. (a) Charges of CPV1 capsid (3JAY) proteins and polyhedrin (5GQL) trimers occupying positions at 3-fold axes of the capsid expressed in the elementary charge units e₀ as a function of the pH level. Data for the proteins in the vicinity of the trimers facing virus capsid (labeled “front”) is shown with solid lines and data for the proteins in the vicinity of the trimers facing the opposite direction (labeled “back”) are shown with dotted lines. (b) Effective electrostatic energy of polyhedrin crystal normalized per trimer as a function of pH (green) and electrostatic interaction energy between Cypovirus capsid and polyhedrin trimers, both in the units of k_BT.