Structural and dynamic asymmetry in icosahedrally symmetric virus capsids

Abstract

A common characteristic of virus capsids is icosahedral symmetry, yet these highly symmetric structures can display asymmetric features within their virions and undergo asymmetric dynamics. The fields of structural and computational biology have entered a new realm in the investigation of virus infection mechanisms, with the ability to observe symmetry-breaking features. This review will cover important studies on icosahedral virus structure and dynamics, covering both symmetric and asymmetric conformational changes. However, the main emphasis of the review will be towards recent studies employing cryo-electron microscopy or molecular dynamics simulations, which can uncover asymmetric aspects of these systems relevant to understanding viral physical-chemical properties and their biological impact.

Figure 1.

Structural dynamics of viruses. A) The prohead II structure of bacteriophage HK97 (PDB ID: 3e8k) [15]. B) The head II structure of of HK97 (PDB ID: 1OHG) [16]. C) The icosahedrally averaged X-ray structure of FHV (PDB ID: 4FTB). D) EM map of heat treated (“puffed”) particle of FHV (EMD-9732) [38]. The red density on the right is believed to be RNA extruded from the capsid.

Figure 2.

Asymmetric features in icosahedral virus capsids. A) The icosahedrally averaged X-ray structure of MS2. (PDB ID:2MS2) [49]. B) The EM map of the MS2 internal RNA density (EMD-3404) [52]. The protruding blue density on the right is the A-protein. C) The FCV capsid (PDB ID: 6GSH) [58] with capsid proteins colored red, blue and grey. On the right side of the capsid, the portal is observed (PDB ID:6GSI) with receptor proteins colored yellow and the portal forming VP2 proteins in green. D) Top down view of the FCV portal complex (PDB ID:6GSI) [58].

Figure 3.

Dynamics of HBV capsid. A) Local dynamics from root-mean-squared fluctuations (RMSF) of atomic positions, stars indication 5-fold symmetry axis. B). Measurement of opposing pentameric displacements from capsid center reveal dynamic asymmetric distortions in the capsid shape. Figure is modified from [70].