A Stochastic Model of Icosahedral Capsid Growth

Kerner, Richard

doi:10.1080/10273660500149521

Cited by 6 publications

(5 citation statements)

References 11 publications

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“…Several other in general more complex modelling strategies were proposed to describe viral capsid assembly based on molecular dynamics [11] , thermodynamics as self-organization of discs on a sphere [12] , combinatorial optimization studies [10] , “local rules” approach [13] , stochastic icosahedral capsid growth [14] and protein aggregation by nucleated polymerization [15] . In Hagan and Chandler 2006, a class of capsomer models was created to simulate the assembly of capsid-like objects from subunits of different geometries using Newtonian dynamics [16] .…”

Section: Introductionmentioning

confidence: 99%

On the Effect of Thermodynamic Equilibrium on the Assembly Efficiency of Complex Multi-Layered Virus-Like Particles (VLP): the Case of Rotavirus VLP

et al. 2012

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Previous studies have reported the production of malformed virus-like-particles (VLP) in recombinant host systems. Here we computationally investigate the case of a large triple-layered rotavirus VLP (RLP). In vitro assembly, disassembly and reassembly data provides strong evidence of microscopic reversibility of RLP assembly. Light scattering experimental data also evidences a slow and reversible assembly untypical of kinetic traps, thus further strengthening the fidelity of a thermodynamically controlled assembly. In silico analysis further reveals that under favourable conditions particles distribution is dominated by structural subunits and completely built icosahedra, while other intermediates are present only at residual concentrations. Except for harshly unfavourable conditions, assembly yield is maximised when proteins are provided in the same VLP protein mass composition. The assembly yield decreases abruptly due to thermodynamic equilibrium when the VLP protein mass composition is not obeyed. The latter effect is more pronounced the higher the Gibbs free energy of subunit association is and the more complex the particle is. Overall this study shows that the correct formation of complex multi-layered VLPs is restricted to a narrow range of association energies and protein concentrations, thus the choice of the host system is critical for successful assembly. Likewise, the dynamic control of intracellular protein expression rates becomes very important to minimize wasted proteins.

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Section: Introductionmentioning

confidence: 99%

On the Effect of Thermodynamic Equilibrium on the Assembly Efficiency of Complex Multi-Layered Virus-Like Particles (VLP): the Case of Rotavirus VLP

et al. 2012

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“…Such "islands" exist also among the capsid types corresponding to higher values of T , even when one considers the Tables (17), (18) and (19) as cylinders, with their right and left borders glued together. There are single isolated species corresponding to T = 124; T = 196 and T = 268 (the last one beyond the range of observed types).…”

Section: Classification Of Icosahedral Capsidsmentioning

confidence: 99%

“…To define a notion of a distance between various types of capsids is a challenge for further research in this direction ( [18], [19], [20]). …”

Section: Classification Of Icosahedral Capsidsmentioning

confidence: 99%

Self-Assembly of Icosahedral Viral Capsids: the Combinatorial Analysis Approach

Kerner

2011

Math. Model. Nat. Phenom.

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Abstract. An analysis of all possible icosahedral viral capsids is proposed. It takes into account the diversity of coat proteins and their positioning in elementary pentagonal and hexagonal configurations, leading to definite capsid size. We show that the self-organization of observed capsids during their production implies a definite composition and configuration of elementary building blocks. The exact number of different protein dimers is related to the size of a given capsid, labeled by its T -number. Simple rules determining these numbers for each value of T are deduced and certain consequences concerning the probabilities of mutations and evolution of capsid viruses are discussed.

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“…Second, the final size of the capsid must depend on particular assembly schemes. We investigate here the rules that define the type and the size of the capsids, simultaneously optimizing the production rate [13].…”

Section: Introductionmentioning

confidence: 99%

Classification and Evolutionary Trends of Icosahedral Viral Capsids

Kerner

2000

Computational and Mathematical Methods in Medicine

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A classification of icosahedral viral capsids is proposed. We show how the self-organization of capsids during their formation implies a definite composition of their elementary building blocks. The exact number of hexamers with three different admissible symmetries is related to capsids' sizes, labelled by theirT-numbers. Simple rules determining these numbers for each value ofTare deduced and certain consequences concerning the probabilities of mutations and evolution of viruses are discussed.

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A Stochastic Model of Icosahedral Capsid Growth

Cited by 6 publications

References 11 publications

On the Effect of Thermodynamic Equilibrium on the Assembly Efficiency of Complex Multi-Layered Virus-Like Particles (VLP): the Case of Rotavirus VLP

On the Effect of Thermodynamic Equilibrium on the Assembly Efficiency of Complex Multi-Layered Virus-Like Particles (VLP): the Case of Rotavirus VLP

Self-Assembly of Icosahedral Viral Capsids: the Combinatorial Analysis Approach

Classification and Evolutionary Trends of Icosahedral Viral Capsids

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