Self-assembly of polyhedral shells: A molecular dynamics study

Rapaport, D. C.

doi:10.1103/physreve.70.051905

Cited by 155 publications

(200 citation statements)

References 20 publications

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“…The simplest models represent the capsomers as isotropic bodies, but they require additional geometrical constraints such as a template of the virus capsid [14][15][16][17][18][19] . In other more complex models each capsomer is represented as a discrete set of either isotropic 17,[20][21][22][23][24] or anisotropic interaction centres [25][26][27] , or as a continuous body of interaction points plus some extra discrete centres 28 .…”

Section: Introductionmentioning

confidence: 99%

A minimal representation of the self-assembly of virus capsids

2014

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Viruses are biological nanosystems with a capsid of protein-made capsomer units that encloses and protects the genetic material responsible for their replication. Here we show how the geometrical constraints of the capsomer-capsomer interaction in icosahedral capsids fix the form of the shortest and universal truncated multipolar expansion of the two-body interaction between capsomers. The structures of many of the icosahedral and related virus capsids are located as single lowest energy states of this potential energy surface. Our approach unveils relevant features of the natural design of the capsids and can be of interest in fields of nanoscience and nanotechnology where similar hollow convex structures are relevant.

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Section: Introductionmentioning

confidence: 99%

A minimal representation of the self-assembly of virus capsids

2014

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“…Insight into empty capsid formation has been obtained in recent years from theoretical (33)(34)(35)(36)(37) and in vitro experimental studies (31,38,39). In this case, a sequential assembly principle has been proposed in which either preformed intermediates or individual structural subunits adhere to a proto-capsomer or initial nucleation center to form a capsid (33,40).…”

Section: Spectroscopic Properties Of 3d Crystals Of Mixtures Of R3bmvmentioning

confidence: 99%

Core-controlled polymorphism in virus-like particles

Sun

Dufort²,

Daniel³

et al. 2007

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

272

363

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This study concerns the self-assembly of virus-like particles (VLPs) composed of an icosahedral virus protein coat encapsulating a functionalized spherical nanoparticle core. The recent development of efficient methods for VLP self-assembly has opened the way to structural studies. Using electron microscopy with image reconstruction, the structures of several VLPs obtained from brome mosaic virus capsid proteins and gold nanoparticles were elucidated. Varying the gold core diameter provides control over the capsid structure. The number of subunits required for a complete capsid increases with the core diameter. The packaging efficiency is a function of the number of capsid protein subunits per gold nanoparticle. VLPs of varying diameters were found to resemble to three classes of viral particles found in cells (T ‫؍‬ 1, 2, and 3). As a consequence of their regularity, VLPs form three-dimensional crystals under the same conditions as the wild-type virus. The crystals represent a form of metallodielectric material that exhibits optical properties influenced by multipolar plasmonic coupling. metamaterials ͉ protein cage ͉ self-assembly ͉ surface plasmon ͉ virus assembly E ngineered virus capsids and protein cage structures have shown increasing promise as therapeutic and diagnostic vectors (1-6), imaging agents (7-10), and as templates and microreactors for advanced nanomaterials synthesis (11)(12)(13)(14)(15)(16)(17). Here, we address the rules for the formation of symmetric protein cages consisting of viral capsid subunits formed over a functionalized inorganic nanoparticle core, called virus-like particles (VLPs).VLPs provide an example of how biomimetic self-organization can combine the natural characteristics of virus capsids with the exquisite physical properties of nanoparticles (18)(19)(20). Interactions between the artificial cargo and the protein carrier affects both the self-assembly and the stability of the resulting structure, yet very little is known about them. Progress toward the basic development and the practical use of VLPs requires an understanding of how relevant parameters contribute to complex formation.Symmetric VLPs may provide a technology for therapeutic or diagnostic agent delivery that is improved over amorphous shell nanoparticles that are already known to be efficient in similar applications (21). The advantage of a regular surface protein motif is that the binding domains are functionally identical by virtue of their equivalent environment. It has been shown in several situations that receptor-mediated targeting can be achieved even when using amorphous coatings (22). However, the principle challenges for nanoparticle delivery currently include: limited life-time in body fluids, nanoparticle transduction across the cellular membrane, avoidance of the exocytotic pathways, and target specificity. To optimize their infectivity, viruses have evolved to overcome these challenges. We still must learn how to apply virus strategies to targeted delivery. A simple question is central to this o...

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“…It is instructive to compare our predicted packing sequence to self-assembled viral capsids since both share the same icosahedral symmetry and shape for certain N. The origin of the precise packing of protein capsomers in a virus capsid shell has been the focus of much recent theoretical work (29,(34)(35)(36)(37)(38)(39)(40). About half of all viruses found in humans, animals, and plants are sphere-like, and most of them have protein shells possessing icosahedral symmetry.…”

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

confidence: 99%

“…Several theoretical models have explored the underlying mechanism of virus capsid assembly (29,(34)(35)(36)(37)(38)(39)52). Most models strictly impose spherical geometry and/or icosahedral symmetry at all times, and the simplest models generate unwanted multiplicity or degeneracy of structures not observed in nature.…”

Section: Relation To Previous Simulation Studies Of Virus Assemblymentioning

confidence: 99%

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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Self-assembly of polyhedral shells: A molecular dynamics study

Cited by 155 publications

References 20 publications

A minimal representation of the self-assembly of virus capsids

A minimal representation of the self-assembly of virus capsids

Core-controlled polymorphism in virus-like particles

A precise packing sequence for self-assembled convex structures

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