Master equation approach to the assembly of viral capsids

Keef, T.; Micheletti, Cristian; Twarock, Reidun

doi:10.1016/j.jtbi.2006.04.023

Cited by 54 publications

(63 citation statements)

References 32 publications

(20 reference statements)

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“…The simple geometrical construction model introduced by Caspar and Klug (CK) 2 to explain the architecture of icosahedral viruses is a milestone in modern virology. Generalizations of the CK rules properly account for the geometry of some exceptional icosahedral capsids [3][4][5][6] and other elongated virus capsids that share coordination numbers with the icosahedral ones [7][8][9] . Recent work [10][11][12] provides important further development about the effect of the geometrical and topological constraints on the capsid structure.…”

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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“…There is currently no feasible experimental method to directly observe a rapid, nanometer-scale assembly process such as that involved in building a capsid. Capsid assembly has thus been an important model for numerous simulation studies, where they have helped us elucidate general principles that may guide self-assembly [1,4,28,35], map out parameter spaces of possible assembly products and pathways [6,8,10,11,14,21,26], and perform model-based interpretation of indirect experimental measures of assembly progress in real virus systems [3,9,38,39].…”

Section: Introductionmentioning

confidence: 99%

Pathway Complexity of Model Virus Capsid Assembly Systems

Misra

Lees

Zhang

et al. 2008

Computational and Mathematical Methods in Medicine

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As computational and mathematical studies become increasingly central to studies of complicated reaction systems, it will become ever more important to identify the assumptions our models must make and determine when those assumptions are valid. Here, we examine that question with respect to viral capsid assembly by studying the 'pathway complexity' of model capsid assembly systems, which we informally define as the number of reaction pathways and intermediates one must consider to accurately describe a given system. We use two model types for this study: ordinary differential equation models, which allow us to precisely and deterministically compare the accuracy of capsid models under different degrees of simplification, and stochastic discrete event simulations, which allow us to sample use of reaction intermediates across a wide parameter space allowing for an extremely large number of possible reaction pathways. The models provide complementary information in support of a common conclusion that the ability of simple pathway models to adequately explain capsid assembly kinetics varies considerably across the space of biologically meaningful assembly parameters. These studies provide grounds for caution regarding our ability to reliably represent real systems with simple models and to extrapolate results from one set of assembly conditions to another. In addition, the analysis tools developed for this study are likely to have broader use in the analysis and efficient simulation of large reaction systems.

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“…However, symmetry impacts also on other stages of the viral life-cycle, such as the assembly of the protein containers. Insights from Keef et al have also been used in this context, 5,10,14,21,30 and have been instrumental in elucidating the cooperative roles of the viral genome in RNA virus assembly. This shows that the fundamental geometric principle in virology encoded by the library of point arrays has wide applications in virology.…”

Section: Resultsmentioning

confidence: 99%

A Mathematical Approach to Structural Transitions in Viral Capsids

Indelicato

Twarock

2012

Int. J. Mod. Phys. Conf. Ser.

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The majority of viruses have protein containers, called capsids, in which proteins are arranged with icosahedral symmetry. The capsids of these viruses follow structural blueprints that can be modelled as subsets of 3-dimensional aperiodic lattices called quasicrystals. These, in turn, can be obained by projection from 6-dimensional Bravais lattices. In this work we apply the crystallographic theory of phase transitions to these 6D lattices, and via projection of these results derive information on the structural transitions of viruses important for infection.

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Master equation approach to the assembly of viral capsids

Cited by 54 publications

References 32 publications

A minimal representation of the self-assembly of virus capsids

A minimal representation of the self-assembly of virus capsids

Pathway Complexity of Model Virus Capsid Assembly Systems

A Mathematical Approach to Structural Transitions in Viral Capsids

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