Supramolecular self-assembly: molecular dynamics modeling of polyhedral shell formation

Rapaport, D. C.; Johnson, John E.; Skolnick, Jeffrey

doi:10.1016/s0010-4655(99)00319-7

Cited by 106 publications

(99 citation statements)

References 3 publications

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“…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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Section: Introductionmentioning

confidence: 99%

Controlling viral capsid assembly with templating

Hagan

2008

Phys. Rev. E

104

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“…These results have been used to investigate the possibility of inhibiting assembly via an anti-viral drug in the case of Herpes Virus [28]. Related approaches include molecular dynamics studies of viral capsid assembly [13,14], and a molecular dynamics-like formalism that is implemented in connection with a "local rules" mechanism that regulates capsid assembly [1,18].…”

Section: Introductionmentioning

confidence: 99%

Master equation approach to the assembly of viral capsids

Keef

Micheletti

Twarock

2006

Journal of Theoretical Biology

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The distribution of inequivalent geometries occurring during self-assembly of the major capsid protein in thermodynamic equilibrium is determined based on a master equation approach. These results are implemented to characterize the assembly of SV40 virus and to obtain information on the putative pathways controlling the progressive build-up of the SV40 capsid. The experimental testability of the predictions is assessed and an analysis of the geometries of the assembly intermediates on the dominant pathways is used to identify targets for antiviral drug design.

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“…If the dynamics of transitioning between states along a pathway and thereby the density of states influencing the configurational integral computation [66] and other such factors nullify the vast differences in symmetry-induced numeracy factors between pathways, then that argument is yet to be made. The local rule theories using simple geometric rules, ODEs and other first principles physics-based simulations of the assembly of viral capsids [67][68][69][70][71][72][73][74][75][76][77] have been used to obtain the assembly kinetics, including rates and concentrations of intermediates, and implicitly provide a probability distribution over pathways. A cautionary note in [78] uses an ODE-based model of reaction kinetics to question simplistic models of assembly pathways.…”

Section: Depth Of An Assembly Pathwaymentioning

confidence: 99%

Symmetry in Sphere-Based Assembly Configuration Spaces

et al. 2016

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Many remarkably robust, rapid and spontaneous self-assembly phenomena occurring in nature can be modeled geometrically, starting from a collection of rigid bunches of spheres. This paper highlights the role of symmetry in sphere-based assembly processes. Since spheres within bunches could be identical and bunches could be identical, as well, the underlying symmetry groups could be of large order that grows with the number of participating spheres and bunches. Thus, understanding symmetries and associated isomorphism classes of microstates that correspond to various types of macrostates can significantly increase efficiency and accuracy, i.e., reduce the notorious complexity of computing entropy and free energy, as well as paths and kinetics, in high dimensional configuration spaces. In addition, a precise understanding of symmetries is crucial for giving provable guarantees of algorithmic accuracy and efficiency, as well as accuracy vs. efficiency trade-offs in such computations. In particular, this may aid in predicting crucial assembly-driving interactions. This is a primarily expository paper that develops a novel, original framework for dealing with symmetries in configuration spaces of assembling spheres, with the following goals.(1) We give new, formal definitions of various concepts relevant to the sphere-based assembly setting that occur in previous work and, in turn, formal definitions of their relevant symmetry groups leading to the main theorem concerning their symmetries. These previously-developed concepts include, for example: (i) assembly configuration spaces; (ii) stratification of assembly configuration space into configurational regions defined by active constraint graphs; (iii) paths through the configurational regions; and (iv) coarse assembly pathways. (2) We then demonstrate the new symmetry concepts to compute the sizes and numbers of orbits in two example settings appearing in previous work. (3) Finally, we give formal statements of a variety of open problems and challenges using the new conceptual definitions.Keywords: sphere assembly; configuration space; stratification; distance constraints; Cayley geometry; entropy; kinetics; pathways MotivationSupramolecular assembly is prevalent in nature, healthcare and engineering, but poorly understood. The assembly starts with identical copies of structures drawn from a small number of types. Modeling these starting structures as rigid bunches of spheres is well suited to assembly processes driven by so-called short-range or hard sphere interaction potentials.More formally, an input to a computational model of an assembly process is an assembly system consisting of the following:

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Supramolecular self-assembly: molecular dynamics modeling of polyhedral shell formation

Cited by 106 publications

References 3 publications

Controlling viral capsid assembly with templating

Controlling viral capsid assembly with templating

Master equation approach to the assembly of viral capsids

Symmetry in Sphere-Based Assembly Configuration Spaces

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