Abstract
Many larger and more complex viruses deviate from the capsid layouts predicted in the seminal Caspar–Klug theory of icosahedral viruses. Instead of being built from one type of capsid protein (CP), they code for multiple distinct structural proteins that either break the local symmetry of the CP building blocks (capsomers) in specific positions or exhibit auxiliary proteins that stabilize the capsid shell. We investigate here the hypothesis that this occurs as a response to mechanical stress. For this, we construct a coarse-grained model of a viral capsid, derived from the experimentally determined atomistic positions of the CPs, that represents the basic features of protein organization in the viral capsid as described in Caspar–Klug theory. We focus here on viruses in the PRD1-adenovirus lineage. For T = 28 viruses in this lineage, which have capsids formed from two distinct structural proteins, we show that the tangential shear stress in the viral capsid concentrates at the sites of local symmetry breaking. In the T = 21, 25 and 27 capsids, we show that stabilizing proteins decrease the tangential stress. These results suggest that mechanical properties can act as selective pressures on the evolution of capsid components, offsetting the coding cost imposed by the need for such additional protein components.
Highlights
Viral capsids are protein containers that encapsulate and protect the genomic material between rounds of infection
We show that local symmetry breaking and the occurrence of additional protein components can be correlated with the mechanical properties and curvature of these capsid shells
For viruses in the second class, the situation is less definite, in that in some cases the loci of stress concentration do not coincide with the sites at which reinforcing proteins are located. This could be the result of us using coarse-grained models that are built from the atomic positions of the capsid protein (CP), and they implicitly contain contributions from any auxiliary proteins at the inner capsid surface that are not captured by a simple model of the capsid shell
Summary
Viral capsids are protein containers that encapsulate and protect the genomic material between rounds of infection. We focus on the distribution of the residual shear stress in medium-sized capsids in the PRD1-adenovirus lineage (figure 1), spanning T = 21 to T = 28 architecture in size, because they exhibit a wide spectrum of different deviations from Caspar–Klug theory and are ideal to test our hypothesis The capsids of these viruses fall into two classes: either they have a different organization of the major coat proteins at some of the hexameric positions at and around the twofold axes or they have ancillary cementing proteins that reinforce the shell, again near the twofold axes. For viruses in the second class, the situation is less definite, in that in some cases the loci of stress concentration do not coincide with the sites at which reinforcing proteins are located This could be the result of us using coarse-grained models that are built from the atomic positions of the CPs, and they implicitly contain contributions from any auxiliary proteins at the inner capsid surface that are not captured by a simple model of the capsid shell. Our analysis demonstrates that non-quasi-equivalent components in a complex viral capsid, in the form of either local symmetry breaking of the hexamers or the occurrence of additional protein components at the inner capsid shell, can be rationalized, at least in part, as a consequence of mechanical stress
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