Are kuravirus capsid diameters quantized? The first all-atom genome tracing method for double-stranded DNA viruses

TL;DR

This paper introduces a new method to model DNA in virus capsids, suggesting that kuravirus capsid diameters may be quantized based on DNA winding patterns.

Contribution

The paper presents the first all-atom genome tracing method for double-stranded DNA viruses.

Findings

A new method was developed to model DNA in icosahedral capsids using spiral winding patterns.

The method successfully explained most of the density in the kuravirus SU10 capsid.

The results suggest discrete capsid inner diameters determined by DNA turns in the end caps.

Abstract

The revolution in cryo-electron microscopy has resulted in unprecedented power to resolve large macromolecular complexes including viruses. Many methods exist to explain density corresponding to proteins and thus entire protein capsids have been solved at the all-atom level. However methods for nucleic acids lag behind, and no all-atom viral double-stranded DNA genomes have been published at all. We here present a method which exploits the spiral winding patterns of DNA in icosahedral capsids. The method quickly generates shells of DNA wound in user-specified, idealized spherical or cylindrical spirals. For transition regions, the method allows guided semiflexible fitting. For the kuravirus SU10, our method explains most of the density in a semiautomated fashion. The results suggest rules for DNA turns in the end caps under which two discrete parameters determine the capsid inner diameter. We suggest that other kuraviruses viruses may follow the same winding scheme, producing a discrete rather than continuous spectrum of capsid inner diameters. Our software may be used to explain the published density maps of other double-stranded DNA viruses and uncover their genome packaging principles.

Graphical Abstract

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