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1. Fine structure of viral dsDNA encapsidation

   https://doi.org/10.1103/PhysRevE.101.022703  

   Walker, S; Arsuaga, J; Hiltner, L; Calderer, C: Vazquez (February 2020, Physical review)

   null (Ed.)

   Unraveling the mechanisms of packing of DNA inside viral capsids is of fundamental importance to understanding the spread of viruses. It could also help develop new applications to targeted drug delivery devices for a large range of therapies. In this article, we present a robust, predictive mathematical model and its numerical implementation to aid the study and design of bacteriophage viruses for application purposes. Exploiting the analogies between the columnar hexagonal chromonic phases of encapsidated viral DNA and chromonic aggregates formed by plank-shaped molecular compounds, we develop a first-principles effective mechanical model of DNA packing in a viral capsid. The proposed expression of the packing energy, which combines relevant aspects of the liquid crystal theory, is developed from the model of hexagonal columnar phases, together with that describing configurations of polymeric liquid crystals. The method also outlines a parameter selection strategy that uses available data for a collection of viruses, aimed at applications to viral design. The outcome of the work is a mathematical model and its numerical algorithm, based on the method of finite elements, and computer simulations to identify and label the ordered and disordered regions of the capsid and calculate the inner pressure. It also presents the tools for the local reconstruction of the DNA “scaffolding” and the center curve of the filament within the capsid. 

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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. Structure and dynamics of tail-free discotic liquid crystals: Simulations of fluorinated triphenylene

   https://doi.org/10.1063/5.0106722  

   Powers, M.; Twieg, R. J.; Portman, J.; Ellman, B. (October 2022, The Journal of Chemical Physics)

   Recently, a large family of at least 14 discotic liquid crystals was discovered that are exceptions to the conventional paradigm that discotic mesogens tend to feature long, flexible tails on their periphery. To understand why these materials are liquid crystals, as well as the structural determinants of discotic phase behavior, we studied a group of closely related small tail-free disk-like molecules, including both mesogenic and non-mesogenic compounds differing only in the position of a single fluorine substituent. The rigidity and structural simplicity of these molecules make them well suited to for study by large, fully all-atom simulations. Using a combination of static and dynamic metrics, we were able to identify several key features of the columnar mesophase and, thereby, conclusively identify a columnar liquid crystalline mesophase present in a subset of our systems. Our simulations feature molecules hopping between columns in the columnar mesophase and distinctive molecular rotations in 60° steps about the columnar axis. The ability to create and characterize columnar mesophases in silico provides a potent tool for untangling the structural determinants of liquid crystalline behavior in these and other tail-free discotic liquid crystals. 

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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. Structures of a large prolate virus capsid in unexpanded and expanded states generate insights into the icosahedral virus assembly

   https://doi.org/10.1073/pnas.2203272119  

   Fang, Qianglin; Tang, Wei-Chun; Fokine, Andrei; Mahalingam, Marthandan; Shao, Qianqian; Rossmann, Michael G.; Rao, Venigalla B. (October 2022, Proceedings of the National Academy of Sciences)

   Many icosahedral viruses assemble proteinaceous precursors called proheads or procapsids. Proheads are metastable structures that undergo a profound structural transition known as expansion that transforms an immature unexpanded head into a mature genome-packaging head. Bacteriophage T4 is a model virus, well studied genetically and biochemically, but its structure determination has been challenging because of its large size and unusually prolate-shaped, ∼1,200-Å-long and ∼860-Å-wide capsid. Here, we report the cryogenic electron microscopy (cryo-EM) structures of T4 capsid in both of its major conformational states: unexpanded at a resolution of 5.1 Å and expanded at a resolution of 3.4 Å. These are among the largest structures deposited in Protein Data Bank to date and provide insights into virus assembly, head length determination, and shell expansion. First, the structures illustrate major domain movements and ∼70% additional gain in inner capsid volume, an essential transformation to contain the entire viral genome. Second, intricate intracapsomer interactions involving a unique insertion domain dramatically change, allowing the capsid subunits to rotate and twist while the capsomers remain fastened at quasi-threefold axes. Third, high-affinity binding sites emerge for a capsid decoration protein that clamps adjacent capsomers, imparting extraordinary structural stability. Fourth, subtle conformational changes at capsomers’ periphery modulate intercapsomer angles between capsomer planes that control capsid length. Finally, conformational changes were observed at the symmetry-mismatched portal vertex, which might be involved in triggering head expansion. These analyses illustrate how small changes in local capsid subunit interactions lead to profound shifts in viral capsid morphology, stability, and volume. 

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