Structural puzzles in virology solved with an overarching icosahedral design principle

Twarock, Reidun; Luque, Antoni

doi:10.1038/s41467-019-12367-3

Cited by 92 publications

(111 citation statements)

References 61 publications

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“…Patience shows pseudo T = 7 laevo capsid organization, as is common among many dsDNA bacteriophages. Regarding the newly proposed framework to describe capsid organization, it appears to have T t (2,1) = 28/3 (~9.33, which means it has a surface area close to the classic Caspar and Klug T = 9) organization [36] and has a minor coat protein that surrounds the major capsid protein hexamer (Figure 4). Patience also has a decoration protein that links the minor coat proteins together and makes no contact with the major capsid protein ( Figure 5).…”

Section: Capsid Morphologies and Accessory Proteinsmentioning

confidence: 99%

Structures of Three Actinobacteriophage Capsids: Roles of Symmetry and Accessory Proteins

Calabrese

Alexandrescu

et al. 2020

Viruses

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Here, we describe the structure of three actinobacteriophage capsids that infect Mycobacterium smegmatis. The capsid structures were resolved to approximately six angstroms, which allowed confirmation that each bacteriophage uses the HK97-fold to form their capsid. One bacteriophage, Rosebush, may have a novel variation of the HK97-fold. Four novel accessory proteins that form the capsid head along with the major capsid protein were identified. Two of the accessory proteins were minor capsid proteins and showed some homology, based on bioinformatic analysis, to the TW1 bacteriophage. The remaining two accessory proteins are decoration proteins that are located on the outside of the capsid and do not resemble any previously described bacteriophage decoration protein. SDS-PAGE and mass spectrometry was used to identify the accessory proteins and bioinformatic analysis of the accessory proteins suggest they are used in many actinobacteriophage capsids.

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Section: Capsid Morphologies and Accessory Proteinsmentioning

confidence: 99%

Structures of Three Actinobacteriophage Capsids: Roles of Symmetry and Accessory Proteins

Calabrese

Alexandrescu

et al. 2020

Viruses

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“…Icosahedral capsids are characterized by the triangulation number T, which determines the number of quasi-equivalent proteins (complexity) and the total number of proteins forming the capsid [18,19]. As illustrated in Figure 2, icosahedral capsids can organize their proteins in four different lattices, accommodating different stoichiometries of major and minor capsid proteins [19].…”

Section: Introductionmentioning

confidence: 99%

The Missing Tailed Phages: Prediction of Small Capsid Candidates

Luque

Benler

Lee

et al. 2020

Preprint

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Tailed phages are the most abundant and diverse group of viruses on the planet. Yet, the smallest tailed phages display relatively complex capsids and large genomes compared to other viruses. The lack of tailed phages forming the common icosahedral capsid architectures T = 1 and T = 3 is puzzling. Here, we extracted geometrical features from high-resolution tailed phage capsid reconstructions and built a statistical model based on physical principles to predict the capsid diameter and genome length of the missing small tailed phage capsids. We applied the model to 3,348 isolated tailed phage genomes and 1,496 gut metagenome-assembled tailed phage genomes. Four isolated tailed phages were predicted to form T = 3 icosahedral capsids, and twenty-one metagenome-assembled tailed phages were predicted to form T < 3 capsids. The smallest capsid predicted was a T = 4/3 ≈ 1.33 architecture. No tailed phages were predicted to form the smallest icosahedral architecture, T = 1. We discuss the feasibility of the missing T = 1 tailed phage capsids and the implications of isolating and characterizing small tailed phages for viral evolution and phage therapy.

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“…Recently, a new classification scheme for virus structure has been introduced [28]. This models capsid architecture via a wider range of surface lattices, and contains the capsid geometries of Caspar-Klug theory as special cases.…”

Section: Discussionmentioning

confidence: 99%

Surface stresses in complex viral capsids and non-quasi-equivalent viral architectures

Indelicato

Cermelli

Twarock

2020

J. R. Soc. Interface.

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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.

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Structural puzzles in virology solved with an overarching icosahedral design principle

Cited by 92 publications

References 61 publications

Structures of Three Actinobacteriophage Capsids: Roles of Symmetry and Accessory Proteins

Structures of Three Actinobacteriophage Capsids: Roles of Symmetry and Accessory Proteins

The Missing Tailed Phages: Prediction of Small Capsid Candidates

Surface stresses in complex viral capsids and non-quasi-equivalent viral architectures

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