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1. Chromonic liquid crystals and packing configurations of bacteriophage viruses

   https://doi.org/10.1098/rsta.2020.0111  

   Hiltner, Lindsey; Carme Calderer, M.; Arsuaga, Javier; Vázquez, Mariel (July 2021, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences)

   null (Ed.)

   We study equilibrium configurations of hexagonal columnar liquid crystals in the context of characterizing packing structures of bacteriophage viruses in a protein capsid. These are viruses that infect bacteria and are currently the focus of intense research efforts, with the goal of finding new therapies for bacteria-resistant antibiotics. The energy that we propose consists of the Oseen–Frank free energy of nematic liquid crystals that penalizes bending of the columnar directions, in addition to the cross-sectional elastic energy accounting for distortions of the transverse hexagonal structure; we also consider the isotropic contribution of the core and the energy of the unknown interface between the outer ordered region of the capsid and the inner disordered core. The problem becomes of free boundary type, with constraints. We show that the concentric, azimuthal, spool-like configuration is the absolute minimizer. Moreover, we present examples of toroidal structures formed by DNA in free solution and compare them with the analogous ones occurring in experiments with other types of lyotropic liquid crystals, such as food dyes and additives. This article is part of the theme issue ‘Topics in mathematical design of complex materials’. 

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2. Helical organization of DNA-like liquid crystal filaments in cylindrical viral capsids

   https://doi.org/10.1098/rspa.2022.0047  

   Liu, Pei; Arsuaga, Javier; Calderer, M. Carme; Golovaty, Dmitry; Vazquez, Mariel; Walker, Shawn (October 2022, Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences)

   We study equilibrium configurations of double-stranded DNA in a cylindrical viral capsid. The state of the encapsidated DNA consists of a disordered inner core enclosed by an ordered outer region, next to the capsid wall. The DNA configuration is described by a unit helical vector field, tangent to an associated centre curve, passing through properly selected locations. We postulate an expression for the energy of the encapsulated DNA based on that of columnar chromonic liquid crystals. A thorough analysis of the Euler–Lagrange equations yields multiple solutions. We demonstrate that there is a trivial, non-helical solution, together with two solutions with non-zero helicity of opposite sign. Using bifurcation analysis, we derive the conditions for local stability and determine when the preferred coiling state is helical. The bifurcation parameters are the ratio of the twist versus the bend moduli of DNA and the ratio between the sizes of the ordered and the disordered regions. 

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3. A computational spatial whole-Cell model for hepatitis B viral infection and drug interactions

   https://doi.org/10.1038/s41598-023-45998-0  

   Ghaemi, Zhaleh; Nafiu, Oluwadara; Tajkhorshid, Emad; Gruebele, Martin; Hu, Jianming (December 2023, Scientific Reports)

   Abstract Despite a vaccine, hepatitis B virus (HBV) remains a world-wide source of infections and deaths. We develop a whole-cell computational platform combining spatial and kinetic models describing the infection cycle of HBV in a hepatocyte host. We simulate key parts of the infection cycle with this whole-cell platform for 10 min of biological time, to predict infection progression, map out virus-host and virus-drug interactions. We find that starting from an established infection, decreasing the copy number of the viral envelope proteins shifts the dominant infection pathway from capsid secretion to re-importing the capsids into the nucleus, resulting in more nuclear-localized viral covalently closed circular DNA (cccDNA) and boosting transcription. This scenario can mimic the consequence of drugs designed to manipulate viral gene expression. Mutating capsid proteins facilitates capsid destabilization and disassembly at nuclear pore complexes, resulting in an increase in cccDNA copy number. However, excessive destabilization leads to premature cytoplasmic disassembly and does not increase the cccDNA counts. Finally, our simulations can predict the best drug dosage and its administration timing to reduce the cccDNA counts. Our adaptable computational platform can be parameterized to study other viruses and identify the most central viral pathways that can be targeted by drugs. 

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4. Near-atomic, non-icosahedrally averaged structure of giant virus Paramecium bursaria chlorella virus 1

   https://doi.org/10.1038/s41467-022-34218-4  

   Shao, Qianqian; Agarkova, Irina V.; Noel, Eric A.; Dunigan, David D.; Liu, Yunshu; Wang, Aohan; Guo, Mingcheng; Xie, Linlin; Zhao, Xinyue; Rossmann, Michael G.; et al (October 2022, Nature Communications)

   Abstract Giant viruses are a large group of viruses that infect many eukaryotes. Although components that do not obey the overall icosahedral symmetry of their capsids have been observed and found to play critical roles in the viral life cycles, identities and high-resolution structures of these components remain unknown. Here, by determining a near-atomic-resolution, five-fold averaged structure of Paramecium bursaria chlorella virus 1, we unexpectedly found the viral capsid possesses up to five major capsid protein variants and a penton protein variant. These variants create varied capsid microenvironments for the associations of fibers, a vesicle, and previously unresolved minor capsid proteins. Our structure reveals the identities and atomic models of the capsid components that do not obey the overall icosahedral symmetry and leads to a model for how these components are assembled and initiate capsid assembly, and this model might be applicable to many other giant viruses. 

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5. Large, double‐stranded DNA viruses tend to suppress phytoplankton populations more effectively than small viruses of diverse genome type

   https://doi.org/10.1002/lol2.70035  

   Edwards, Kyle_F; McBeain, Kelsey_A; Schvarcz, Christopher_R; Steward, Grieg_F (June 2025, Limnology and Oceanography Letters)

   Abstract Viruses infecting aquatic microbes vary immensely in size, but the ecological consequences of virus size are poorly understood. Here we used a unique suite of diverse phytoplankton strains and their viruses, all isolated from waters around Hawai'i, to assess whether virus size affects the suppression of host populations. We found that small viruses of diverse genome type (3–24 kb genome size, 23–70 nm capsid diameter) have very similar effects on host populations, suppressing hosts less strongly and for a shorter period of time compared to large double‐stranded DNA viruses (214–1380 kb, 112–386 nm). Suppressive effects of larger viruses were more heterogeneous, but most isolates reduced host populations by many orders of magnitude, without recovery over the ~ 25‐d experiments. Our results suggest that disparate lineages of viruses may have ecological consequences that are predictable in part based on size, and that ecosystem impacts of viral infection may vary with the size structure of the viral community. 

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