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Review
. 2017 Jun;25(6):438-446.
doi: 10.1016/j.tim.2016.12.007. Epub 2017 Jan 13.

AChiralPentagonalPolyhedralFramework forCharacterizingVirusCapsidStructures

Affiliations
Review

AChiralPentagonalPolyhedralFramework forCharacterizingVirusCapsidStructures

Aditya Raguram et al. Trends Microbiol. 2017 Jun.

Abstract

Recent developments of rational strategies for the design of antiviral therapies, including monoclonal antibodies (mAbs), have naturally relied extensively on available viral structural information. As new strategies continue to be developed, it is equally important to continue to refine our understanding and interpretation of viral structural data. There are known limitations to the traditional (Caspar-Klug) theory for describing virus capsid structures that involves subdividing a capsid into triangular subunits. In this context, we describe a more general polyhedral framework for describing virus capsid structures that is able to account for many of these limitations, including a more thorough characterization of intersubunit interfaces. Additionally, our use of pentagonal subunits instead of triangular ones accounts for the intrinsic chirality observed in all capsids. In conjunction with the existing theory, the framework presented here provides a more complete picture of a capsid's structure and therefore can help contribute to the development of more effective antiviral strategies.

Keywords: pentagon; polyhedral; structure; virus.

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Figures

Figure 1
Figure 1. The Chiral Nature of the L-A Virus Capsid
A visualization of the actual crystal structure data is shown on the right (PDB ID: 1M1C). An artificial mirror image (“enantiomorph”) is shown on the left. The orientation of the two units outlined in red shows that the capsid assembly scaffold (indicated by the green colored subunits) possesses a definite handedness.
Figure 2
Figure 2. Pentagonal vs. Triangular Tilings
Both images show projections of the L-A virus crystal structure viewed along a three-fold symmetry axis. The appropriate right-handed pentagonal tiling is shown on the left outlined in red, with the dashed line connecting the adjacent five-fold axes. A triangular tiling subdivided into deltoids is shown on the right, which does not capture the chiral twist of the viral subunits about the three-fold axis. The pentagonal tiling also places the two-fold axes along edges instead of at vertices, which affects the orientation of the interface at that position. The calculated dimensions of the appropriate pentagons are given in Supp. Figure 5.
Key Figure, Figure 3
Key Figure, Figure 3. Chiral Pentagonal Frameworks Describe the L-A Virus and Polyomavirus Capsids
The top images show how the pentagonal hexecontahedron is able to accurately capture the geometry of the L-A virus capsid (PDB ID: 1M1C) by superimposing two appropriate pentagons (outlined in red) around a two-fold axis of the assembly. Similarly, the bottom images show two units of the asymmetric pentagonal hexecontahedron superimposed on the polyomavirus capsid (PDB ID: 1SIE). In both cases, the pentagons capture the chirality and outline key viral protein subunit interfaces, thereby providing a more fitting description than triangles. The calculated dimensions of the appropriate pentagons are given in Supp. Figures 5 and 8.
Figure 4
Figure 4. An Asymmetric Pentagon Describes the Polyomavirus Capsid
(a) A pentagonal asymmetric unit with dots representing the locations of monomer viral protein units. Vertices are labeled O, A, B, C, and D to distinguish the different types of decorations observed (one, two, or zero monomer units). (b) The asymmetric pentagonal assembly superimposed on the 7d icosahedral lattice (adapted from Rayment et. al. [31]) along with polyomavirus capsomers (not to scale) in the appropriate orientations. The white pentamers fall on the true five-fold axes, while the colored ones fall on the pseudo five-fold axes. Other symmetry axes are denoted by orange symbols. The calculated dimensions of the appropriate pentagons are given in Supp. Figure 8.

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