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1. The Dynamics of Viruslike Capsid Assembly and Disassembly

   https://doi.org/10.1021/jacs.2c04074  

   Timmermans, Suzanne B. P. E.; Ramezani, Alireza; Montalvo, Toni; Nguyen, Mark; van der Schoot, Paul; van Hest, Jan C. M.; Zandi, Roya (July 2022, Journal of the American Chemical Society)
2. Predicting the capsid architecture of phages from metagenomic data

   https://doi.org/10.1016/j.csbj.2021.12.032  

   Lee, Diana Y.; Bartels, Caitlin; McNair, Katelyn; Edwards, Robert A.; Swairjo, Manal A.; Luque, Antoni (January 2022, Computational and Structural Biotechnology Journal)
3. The Missing Tailed Phages: Prediction of Small Capsid Candidates

   https://doi.org/10.3390/microorganisms8121944  

   Luque, Antoni; Benler, Sean; Lee, Diana Y.; Brown, Colin; White, Simon (December 2020, Microorganisms)

   null (Ed.)

   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 3348 isolated tailed phage genomes and 1496 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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4. Neck and capsid architecture of the robust Agrobacterium phage Milano

   https://doi.org/10.1038/s42003-023-05292-1  

   Sonani, Ravi R; Esteves, Nathaniel C; Horton, Abigail A; Kelly, Rebecca J; Sebastian, Amanda L; Wang, Fengbin; Kreutzberger, Mark_A B; Leiman, Petr G; Scharf, Birgit E; Egelman, Edward H (December 2023, Communications Biology)

   Abstract Large gaps exist in our understanding of how bacteriophages, the most abundant biological entities on Earth, assemble and function. The structure of the “neck” region, where the DNA-filled capsid is connected to the host-recognizing tail remains poorly understood. We describe cryo-EM structures of the neck, the neck-capsid and neck-tail junctions, and capsid of theAgrobacteriumphage Milano. The Milano neck 1 protein connects the 12-fold symmetrical neck to a 5-fold vertex of the icosahedral capsid. Comparison of Milano neck 1 homologs leads to four proposed classes, likely evolved from the simplest one in siphophages to more complex ones in myo- and podophages. Milano neck is surrounded by the atypical collar, which covalently crosslinks the tail sheath to neck 1. The Milano capsid is decorated with three types of proteins, a minor capsid protein (mCP) and two linking proteins crosslinking the mCP to the major capsid protein. The extensive network of disulfide bonds within and between neck, collar, capsid and tail provides an exceptional structural stability to Milano. 

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5. The Structure of Spiroplasma Virus 4: Exploring the Capsid Diversity of the Microviridae

   https://doi.org/10.3390/v16071103  

   Mietzsch, Mario; Kailasan, Shweta; Bennett, Antonette; Chipman, Paul; Fane, Bentley; Huiskonen, Juha T; Clarke, Ian N; McKenna, Robert (July 2024, Viruses)

   Spiroplasma virus 4 (SpV4) is a bacteriophage of the Microviridae, which packages circular ssDNA within non-enveloped T = 1 icosahedral capsids. It infects spiroplasmas, which are known pathogens of honeybees. Here, the structure of the SpV4 virion is determined using cryo-electron microscopy to a resolution of 2.5 Å. A striking feature of the SpV4 capsid is the mushroom-like protrusions at the 3-fold axes, which is common among all members of the subfamily Gokushovirinae. While the function of the protrusion is currently unknown, this feature varies widely in this subfamily and is therefore possibly an adaptation for host recognition. Furthermore, on the interior of the SpV4 capsid, the location of DNA-binding protein VP8 was identified and shown to have low structural conservation to the capsids of other viruses in the family. The structural characterization of SpV4 will aid future studies analyzing the virus–host interaction, to understand disease mechanisms at a molecular level. Furthermore, the structural comparisons in this study, including a low-resolution structure of the chlamydia phage 2, provide an overview of the structural repertoire of the viruses in this family that infect various bacterial hosts, which in turn infect a wide range of animals and plants. 

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