Deciphering the Kinetic Mechanism of Spontaneous Self-Assembly of Icosahedral Capsids

Nguyen, Hung D.; Reddy, Vijay; Brooks, Charles L.

doi:10.1021/nl062449h

Cited by 189 publications

(317 citation statements)

References 41 publications

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“…A variety of such misassembled structuressincluding dumbbellsshave also been observed in molecular dynamics simulations of coarse-grained models of capsid proteins. 9 These have been compared to socalled "monster" structures that were found in in vitro studies of the assembly of turnip crinkle virus and capsid protein around the viral RNA. 10 12 correspond to Caspar-Klug structures with T ) 1, 3, 4, and 7; a so-called pseudo-Caspar-Klug structure with T ) 2 is also known.…”

Section: Resultsmentioning

confidence: 99%

Phase Diagram of Self-assembled Viral Capsid Protein Polymorphs

et al. 2009

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We present an experimental study of the self-assembly of capsid proteins of the cowpea chlorotic mosaic virus (CCMV), in the absence of the viral genome, as a function of pH and ionic strength. In accord with previous measurements, a wide range of polymorphs can be identified by electron microscopy, among them single and multiwalled shells and tubes. The images are analyzed with respect to size and shape of aggregates, and evidence is given that equilibrium has been achieved, allowing a phase diagram to be constructed. Some previously unreported structures are also described. The range and stability of the polymorphs can be understood in terms of electrostatic interactions and the way they affect the spontaneous curvature of protein networks and the relative stabilities of pentamers and hexamers.

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Section: Resultsmentioning

confidence: 99%

Phase Diagram of Self-assembled Viral Capsid Protein Polymorphs

et al. 2009

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“…We show in appendix A that the average timescales of these phases for an individual capsid can be described by τ = τ nuc + τ elong , with and , where f is the subunit-subunit binding rate constant, C S is the concentration of free subunits, n nuc is the number of subunits in the nucleus. Because elongation requires N − n nuc assembly events, it introduces a minimum timescale for the overall assembly process, which is primarily responsible for the lag time in assembly kinetics reported in experiments [9,12,53], theory [21,48], and simulations [26,28,80], and results in a distribution of assembly times for an individual capsid that cannot be fit with a sum of pure exponential functions [81]. The observed assembly rate constant, f, can be considered an average quantity, since computational models [26,28] suggest that it varies for different intermediates and decreases due to excluded volume constraints as assembly nears completion.…”

Section: A the Kinetics Of Core-controlled Assemblymentioning

confidence: 99%

“…Thus, in addition to their biomedical and technological applications, studying viral capsids has revealed fundamental principles of assembly. Although specific assembly mechanisms are poorly understood for most viruses, a general mechanism has emerged for the spontaneous assembly of empty capsids [10][11][12][12][13][14][15]21,26,28,[47][48][49][50][51][52][53]. Assembly occurs through a sequential addition process in which individual subunits or larger intermediates [26,52] bind to a growing capsid.…”

Section: Introductionmentioning

confidence: 99%

Controlling viral capsid assembly with templating

Hagan

2008

Phys. Rev. E

104

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We develop coarse-grained models that describe the dynamic encapsidation of functionalized nanoparticles by viral capsid proteins. We find that some forms of cooperative interactions between protein subunits and nanoparticles can dramatically enhance rates and robustness of assembly, as compared to the spontaneous assembly of subunits into empty capsids. For large core-subunit interactions, subunits adsorb onto core surfaces en masse in a disordered manner, and then undergo a cooperative rearrangement into an ordered capsid structure. These assembly pathways are unlike any identified for empty capsid formation. Our models can be directly applied to recent experiments in which viral capsid proteins assemble around the functionalized inorganic nanoparticles [Sun et al., Proc. Natl. Acad. Sci (2007) 104, 1354. In addition, we discuss broader implications for understanding the dynamic encapsidation of single-stranded genomic molecules during viral replication and for developing multicomponent nanostructured materials.

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“…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.

115

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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Deciphering the Kinetic Mechanism of Spontaneous Self-Assembly of Icosahedral Capsids

Cited by 189 publications

References 41 publications

Phase Diagram of Self-assembled Viral Capsid Protein Polymorphs

Phase Diagram of Self-assembled Viral Capsid Protein Polymorphs

Controlling viral capsid assembly with templating

A precise packing sequence for self-assembled convex structures

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