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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. Sculpting the shapes of giant unilamellar vesicles using isotropic–nematic–isotropic phase cycles

   https://doi.org/10.1039/D1SM00910A  

   Jani, Purvil ; Nayani, Karthik ; Abbott, Nicholas L. ( October 2021 , Soft Matter)

   Understanding how soft matter deforms in response to mechanical interactions is central to the design of functional synthetic materials as well as elucidation of the behaviors of biological assemblies. Here we explore how cycles of thermally induced transitions between nematic (N) and isotropic (I) phases can be used to exert cyclical elastic stresses on dispersions of giant unilamellar vesicles (GUVs) and thereby evolve GUV shape and properties. The measurements were enabled by the finding that I–N–I phase transitions of the lyotropic chromonic liquid crystal disodium cromoglycate, when conducted via an intermediate columnar (M) phase, minimized transport of GUVs on phase fronts to confining surfaces. Whereas I to N phase transitions strained spherical GUVs into spindle-like shapes, with an efflux of GUV internal volume, subsequent N to I transitions generated a range of complex GUV shapes, including stomatocyte, pear- and dumbbell-like shapes that depended on the extent of strain in the N phase. The highest strained GUVs were observed to form buds (daughter vesicles) that we show, via a cycle of I–N–I–N phase transitions, are connected via a neck to the parent vesicle. Additional experiments established that changes in elasticity of the phase surrounding the GUVs and not thermal expansion of membranes were responsible for the shape transitions, and that I–N–I transformations that generate stomatocytes can be understood from the Bilayer-Coupling model of GUV shapes. Overall, these observations advance our understanding of how LC elastic stresses can be regulated to evolve the shapes of soft biological assemblies as well as provide new approaches for engineering synthetic soft matter. 

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4. Highly Basic Clusters in the Herpes Simplex Virus 1 Nuclear Egress Complex Drive Membrane Budding by Inducing Lipid Ordering

   https://doi.org/10.1128/mBio.01548-21  

   Thorsen, Michael K. ; Lai, Alex ; Lee, Michelle W. ; Hoogerheide, David P. ; Wong, Gerard C. ; Freed, Jack H. ; Heldwein, Ekaterina E. ( August 2021 , mBio)

   Shenk, Thomas (Ed.)

   ABSTRACT During replication of herpesviruses, capsids escape from the nucleus into the cytoplasm by budding at the inner nuclear membrane. This unusual process is mediated by the viral nuclear egress complex (NEC) that deforms the membrane around the capsid by oligomerizing into a hexagonal, membrane-bound scaffold. Here, we found that highly basic membrane-proximal regions (MPRs) of the NEC alter lipid order by inserting into the lipid headgroups and promote negative Gaussian curvature. We also find that the electrostatic interactions between the MPRs and the membranes are essential for membrane deformation. One of the MPRs is phosphorylated by a viral kinase during infection, and the corresponding phosphomimicking mutations block capsid nuclear egress. We show that the same phosphomimicking mutations disrupt the NEC-membrane interactions and inhibit NEC-mediated budding in vitro , providing a biophysical explanation for the in vivo phenomenon. Our data suggest that the NEC generates negative membrane curvature by both lipid ordering and protein scaffolding and that phosphorylation acts as an off switch that inhibits the membrane-budding activity of the NEC to prevent capsid-less budding. IMPORTANCE Herpesviruses are large viruses that infect nearly all vertebrates and some invertebrates and cause lifelong infections in most of the world’s population. During replication, herpesviruses export their capsids from the nucleus into the cytoplasm by an unusual mechanism in which the viral nuclear egress complex (NEC) deforms the nuclear membrane around the capsid. However, how membrane deformation is achieved is unclear. Here, we show that the NEC from herpes simplex virus 1, a prototypical herpesvirus, uses clusters of positive charges to bind membranes and order membrane lipids. Reducing the positive charge or introducing negative charges weakens the membrane deforming ability of the NEC. We propose that the virus employs electrostatics to deform nuclear membrane around the capsid and can control this process by changing the NEC charge through phosphorylation. Blocking NEC-membrane interactions could be exploited as a therapeutic strategy. 

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5. Controlling the surface charge of simple viruses

   https://doi.org/10.1371/journal.pone.0255820  

   Duran-Meza, A. L. ; Villagrana-Escareño, M. V. ; Ruiz-García, J. ; Knobler, C. M. ; Gelbart, W. M. ( September 2021 , PLOS ONE)

   Rao, A. L. (Ed.)

   The vast majority of plant viruses are unenveloped, i . e ., they lack a lipid bilayer that is characteristic of most animal viruses. The interactions between plant viruses, and between viruses and surfaces, properties that are essential for understanding their infectivity and to their use as bionanomaterials, are largely controlled by their surface charge, which depends on pH and ionic strength. They may also depend on the charge of their contents, i.e., of their genes or–in the instance of virus-like particles–encapsidated cargo such as nucleic acid molecules, nanoparticles or drugs. In the case of enveloped viruses, the surface charge of the capsid is equally important for controlling its interaction with the lipid bilayer that it acquires and loses upon leaving and entering host cells. We have previously investigated the charge on the unenveloped plant virus Cowpea Chlorotic Mottle Virus (CCMV) by measurements of its electrophoretic mobility. Here we examine the electrophoretic properties of a structurally and genetically closely related bromovirus, Brome Mosaic Virus (BMV), of its capsid protein, and of its empty viral shells, as functions of pH and ionic strength, and compare them with those of CCMV. From measurements of both solution and gel electrophoretic mobilities (EMs) we find that the isoelectric point (pI) of BMV (5.2) is significantly higher than that of CCMV (3.7), that virion EMs are essentially the same as those of the corresponding empty capsids, and that the same is true for the pIs of the virions and of their cleaved protein subunits. We discuss these results in terms of current theories of charged colloidal particles and relate them to biological processes and the role of surface charge in the design of new classes of drug and gene delivery systems. 

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