Structure of the top a-t component of alfalfa mosaic virus a non-icosahedral virion

Cusack, Stephen; Oostergetel, Gert T.; Krijgsman, P.C.J.; Mellema, J.E.; Klug, A

doi:10.1016/s0022-2836(83)80350-7

Cited by 21 publications

(16 citation statements)

References 22 publications

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“…Oblate capsules have been seen in T=1 alfalfa mosaic virus 34. The transition between icosahedral capsids and tubular capsules has also been experimentally observed in cowpea chlorotic mottle virus32 and theoretically predicted to occur by Bruinsma et al 14 Twisted capsules, to our knowledge, are reported here for the first time; however, we suspect that they are often mistakenly identified as either tubular capsules or enlarged icosahedral capsids because of their similar size and shape.…”

Section: Resultssupporting

confidence: 71%

Generalized Structural Polymorphism in Self-Assembled Viral Particles

Nguyen

Brooks

2008

Nano Lett.

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The protein shells, called capsids, of nearly all spherical viruses adopt icosahedral symmetry; however, self-assembly of such empty structures often occurs with multiple mis-assembly steps resulting in the formation of aberrant structures. Using simple models that represent the coat proteins pre-assembled in the two different predetermined species that are common motifs of viral capsids (i.e., pentameric and hexameric capsomers), we perform molecular dynamics simulations of the spontaneous self-assembly of viral capsids of different sizes containing 1, 3, 4 to 19 proteins in their icosahedral repeating unit (T=1, 3, 4 to 19, respectively). We observe, in addition to icosahedral capsids, a variety of non-icosahedral yet highly ordered and enclosed capsules. Such structural polymorphism is demonstrated to be an inherent property of the coat proteins, independent of the capsid complexity and the elementary kinetic mechanisms. Moreover, there exist two distinctive classes of polymorphic structures: aberrant capsules that are larger than their respective icosahedral capsids, in T=1-7 systems; and capsules that are smaller than their respective icosahedral capsids when T=7-19. Different kinetic mechanisms responsible for self-assembly of those classes of aberrant structures are deciphered, providing insights into the control of the self-assembly of icosahedral capsids.

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Section: Resultssupporting

confidence: 71%

Generalized Structural Polymorphism in Self-Assembled Viral Particles

Nguyen

Brooks

2008

Nano Lett.

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“…According to ref. 42, this particle is elongated but slightly flattened. This structure could be a prolate centered on a 2-fold axis, which due to the distribution of pentamers in the caps, might adopt a more flattened shape (Fig.…”

Section: Resultsmentioning

confidence: 89%

Optimal architectures of elongated viruses

Luque

Zandi

Reguera

2010

Proc. Natl. Acad. Sci. U.S.A.

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Many viruses protect their genetic material by a closed elongated protein shell. Unlike spherical viruses, the structure of these prolates is not yet well understood, and only a few of them have been fully characterized. We present the results of a simple phenomenological model, which describes the remarkable structures of prolate or bacilliform viral shells. Surprisingly, we find that the special well-defined geometry of these elongated viruses arises just as a consequence of free-energy minimization of a generic interaction between the structural units of the capsid. Hemispherical T -number caps centered along the 5-, 3-, and 2-fold axes with hexagonally ordered cylindrical bodies are found to be local energy minima, thus justifying their occurrence as optimal viral structures. Moreover, closed elongated viruses show a sequence of magic numbers for the end-caps, leading to strict selection rules for the length and structure of the body as well as for the number of capsomers and proteins of the capsid. The model reproduces the architecture of spherical and bacilliform viruses, both in vivo and in vitro, and constitutes an important step towards understanding viral assembly and its potential control for biological and nanotechnological applications.assembly | polymorphism | prolate or bacilliform shells | simulation | viral capsids

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“…It is worth noting that the right-handed structure at N ϭ 72 can be compared with the polyoma virus (49), a well known non-quasi-equivalent virus capsid structure that contains 72 identical pentamers and consists of 360 total subunits in a T ϭ 7d configuration, which does not fit the CK framework but is predicted by the tiling theory of Twarock and coworkers (39). Additionally, the cluster structure found for N ϭ 27 may correspond to several nonicosahedral spherical viruses, such as the middle component of the pea enation mosaic virus, the top component of the tobacco streak virus, and the Tulare apple mosaic virus, which consist of Ϸ150 subunits or 27 capsomers (12 pentamers and 15 hexamers) and violate CK quasi-equivalence theory, as suggested by Cusack (50). To our knowledge, this is the first theoretical or computational prediction of this experimentally proposed structure.…”

Section: Self-assembly Of Cones and Spherical Particles (Moderate To mentioning

confidence: 88%

A precise packing sequence for self-assembled convex structures

Chen¹,

Zhang²,

Glotzer

2007

Proc. Natl. Acad. Sci. U.S.A.

117

111

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Molecular simulations of the self-assembly of cone-shaped particles with specific, attractive interactions are performed. Upon cooling from random initial conditions, we find that the cones self-assemble into clusters and that clusters comprised of particular numbers of cones (e.g., 4 -17, 20, 27, 32, and 42) have a unique and precisely packed structure that is robust over a range of cone angles. These precise clusters form a sequence of structures at specific cluster sizes (a ''precise packing sequence'') that for small sizes is identical to that observed in evaporation-driven assembly of colloidal spheres. We further show that this sequence is reproduced and extended in simulations of two simple models of spheres self-assembling from random initial conditions subject to convexity constraints, including an initial spherical convexity constraint for moderate-and large-sized clusters. This sequence contains six of the most common virus capsid structures obtained in vivo, including large chiral clusters and a cluster that may correspond to several nonicosahedral, spherical virus capsids obtained in vivo. Our findings suggest that this precise packing sequence results from free energy minimization subject to convexity constraints and is applicable to a broad range of assembly processes.colloids ͉ self-assembly ͉ simulation ͉ virus assembly T he recent fabrication by means of evaporation-driven selfassembly of colloidal clusters containing micrometer-sized plastic spheres arranged in perfect polyhedra (1) has generated much excitement in the materials community. Precise structures such as these are rare in materials self-assembly problems (2, 3), with some notable, recent exceptions (e.g., refs. 4-6). In biology, however, precise structures are commonplace. A classic example is that of viruses, in which protein subunits, or small groups of protein subunits called capsomers, self-organize into precisely structured shells with icosahedral and other symmetries (7). Although obtained via wholly different processes, the precise packing of colloidal clusters [often referred to as colloidal ''molecules'' (8)] and virus capsids motivates us to investigate, in this article, the minimum set of organizing principles required for the self-assembly of precise structures such as these.One interesting building block shape that self-organizes into precise structures is the cone. Certain amphiphilic nanoparticles (9), molecules (4, 10, 11), and some virus capsomers (12, 13) that self-assemble into precise structures can, to first approximation, be modeled as cone-shaped particles associating via weak attractive interactions. What are the rules that govern the selfassembly of finite numbers of cones into precise clusters? Tsonchev et al. (14) presented a geometric packing analysis to explain the spherical shape resulting from the self-assembly of N cone-shaped amphiphilic nanoparticles in the limit of very large N, in which local hexagonal packing of hard cones is assumed. For clusters of smaller numbers of particles, however, the f...

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Structure of the top a-t component of alfalfa mosaic virus a non-icosahedral virion

Cited by 21 publications

References 22 publications

Generalized Structural Polymorphism in Self-Assembled Viral Particles

Generalized Structural Polymorphism in Self-Assembled Viral Particles

Optimal architectures of elongated viruses

A precise packing sequence for self-assembled convex structures

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