Regulating Self-Assembly of Spherical Oligomers

Johnson, Jennifer M.; Tang, Jinghua; Nyame, Yaw A.; Willits, Deborah A.; Young, Mark; Zlotnick, Adam

doi:10.1021/nl050274q

Cited by 110 publications

(161 citation statements)

References 25 publications

(77 reference statements)

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“…Following the early work of Fraenkel-Conrat and Williams [10], it was found that many small RNA viruses can assemble spontaneously under in-vitro conditions in solutions containing the capsid proteins and the RNA genome molecules. The self-assembly of empty capsids has been shown to have the character of a first-order, activated process [11]. This is consistent with the nucleation-and-growth of "proteinby-protein" assembly models [12] where capsid proteins diffuse in towards partially assembled protein shells.…”

Section: Introductionsupporting

confidence: 71%

“…An interesting extension of the theory would be to study its kinetics and the relation to the current nucleation-and-growth description of capsid assembly [11,46]. Based on numerical simulations [47], it is expected that when the binding affinity between different capsid proteins increases with respect to the binding affinity between capsid proteins and RNA then nucleation and growth will start to dominate over the collective scenario that is the focus of this paper.…”

Section: Hk97mentioning

confidence: 99%

“…Note that the capsid has a pronounced chiral character. In solution, picorna virus capsid proteins are organized into stable pentagons [11]. The pentagons are composed of five asymmetric units, each of which is composed of three proteins.…”

Section: Picornavirusmentioning

confidence: 99%

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Orientational phase transitions and the assembly of viral capsids

et al. 2017

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We present a generalized Landau-Brazovskii free energy for the solidification of chiral molecules on a spherical surface in the context of the assembly of viral shells. We encounter two types of icosahedral solidification transitions. The first type is a conventional first-order phase transition from the uniform to the icosahedral state. It can be described by a single icosahedral spherical harmonic of even l. The chiral pseudo-scalar term in the free energy creates secondary terms with chiral character but it does not affect the thermodynamics of the transition. The second type, associated with icosahedral spherical harmonics with odd l, is anomalous. Pure odd l icosahedral states are unstable but stability is recovered if admixture with the neighboring l + 1 icosahedral spherical harmonic is included, generated by the non-linear terms. This is in conflict with the principle of Landau theory that symmetry-breaking transitions are characterized by only a single irreducible representation of the symmetry group of the uniform phase and we argue that this principle should be removed from Landau theory. The chiral term now directly affects the transition because it lifts the degeneracy between two isomeric mixed-l icosahedral states. A direct transition is possible only over a limited range of parameters. Outside this range, non-icosahedral states intervene. For the important case of capsid assembly dominated by l = 15, the intervening states are found to be based on octahedral symmetry.

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Section: Introductionsupporting

confidence: 71%

Section: Hk97mentioning

confidence: 99%

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Orientational phase transitions and the assembly of viral capsids

et al. 2017

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“…In this discussion we assume that cores are commensurate with the size and geometry of capsids; we discuss the general case elsewhere. If there is no assembly of adsorbed subunits, the equilibrium surface concentration of subunits can be calculated for Langmuir adsorption (8) where β = 1/k B T is the inverse of the thermal energy, and g c is the surface-subunit free energy. The adsorption timescale is τ ad = n s /k ad C S , with k ad the adsorption rate constant, and the number of adsorbed subunits at saturation, n s = N σ 3 c surf .…”

Section: A the Kinetics Of Core-controlled Assemblymentioning

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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“…[7][8][9][10][11][12] Multiscale analysis is a natural way to understand these phenomena. [13][14][15] In the present approach, OPs are used to capture the slow overall transformation of a system from one state to another.…”

Section: Introductionmentioning

confidence: 99%

Thermal nanostructure: An order parameter multiscale ensemble approach

Cheluvaraja

Ortoleva²

2010

The Journal of Chemical Physics

100

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Deductive all-atom multiscale techniques imply that many nanosystems can be understood in terms of the slow dynamics of order parameters that coevolve with the quasiequilibrium probability density for rapidly fluctuating atomic configurations. The result of this multiscale analysis is a set of stochastic equations for the order parameters whose dynamics is driven by thermal-average forces. We present an efficient algorithm for sampling atomistic configurations in viruses and other supramillion atom nanosystems. This algorithm allows for sampling of a wide range of configurations without creating an excess of high-energy, improbable ones. It is implemented and used to calculate thermal-average forces. These forces are then used to search the free-energy landscape of a nanosystem for deep minima. The methodology is applied to thermal structures of Cowpea chlorotic mottle virus capsid. The method has wide applicability to other nanosystems whose properties are described by the CHARMM or other interatomic force field. Our implementation, denoted SIMNANOWORLD ™ , achieves calibration-free nanosystem modeling. Essential atomic-scale detail is preserved via a quasiequilibrium probability density while overall character is provided via predicted values of order parameters. Applications from virology to the computer-aided design of nanocapsules for delivery of therapeutic agents and of vaccines for nonenveloped viruses are envisioned.

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Regulating Self-Assembly of Spherical Oligomers

Cited by 110 publications

References 25 publications

Orientational phase transitions and the assembly of viral capsids

Orientational phase transitions and the assembly of viral capsids

Controlling viral capsid assembly with templating

Thermal nanostructure: An order parameter multiscale ensemble approach

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