Energy landscapes for shells assembled from pentagonal and hexagonal pyramids

Abstract

We present new rigid body potentials that should favour efficient self-assembly of pentagonal and hexagonal pyramids into icosahedral shells over a wide range of temperature. By adding an extra repulsive site opposite the existing apex sites of the pyramids considered in a previously published model, frustrated energy landscapes are transformed into systems identified with self-assembling properties. The extra interaction may be considered analogous to a hydrophobic-hydrophilic repulsion, as in micelle formation.

Viral genome structures are optimal for capsid assembly

“…We model the capsid as a dodecahedron, composed of 12 pentagonal subunits (each of which represents a rapidly forming and stable pentameric intermediate, which then more slowly assembles into the complete capsid, as is the case for SV40 [Li et al, 2002]). Our model extends those of Wales (2005), Fejer et al (2009), Johnston et al (2010), with subunits attracted to each other via attractive pseudoatoms at the vertices (type ‘A’) and driven toward a preferred subunit–subunit angle by repulsive ‘Top’ pseudoatoms (type ‘T’) and ‘Bottom’ pseudoatoms (type ‘B’) (see Figure 1 and the ‘Methods’). In contrast to previous models for polyelectrolyte encapsidation (Angelescu et al, 2006; Elrad and Hagan, 2010; Kivenson and Hagan, 2010; Mahalik and Muthukumar, 2012), the proteins contain positive charges located in flexible polymeric tails, representing the ARM (arginine-rich motif) NA binding domains typical of positive-sense ssRNA virus capsid proteins.

10.7554/eLife.00632.003Figure 1.Schematics and representative images of model systems.

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“…We have extended a model for empty capsid assembly (Wales, 2005; Fejer et al, 2009; Johnston et al, 2010) to describe assembly around NAs. A complete listing of the interaction potentials is provided below; here we present a concise description of our model.…”

A minimal representation of the self-assembly of virus capsids

“…The simplest models represent the capsomers as isotropic bodies, but they require additional geometrical constraints such as a template of the virus capsid [14][15][16][17][18][19] . In other more complex models each capsomer is represented as a discrete set of either isotropic 17,[20][21][22][23][24] or anisotropic interaction centres [25][26][27] , or as a continuous body of interaction points plus some extra discrete centres 28 .…”

Global minima of transition metal clusters described by Finnis–Sinclair potentials: A comparison with semi-empirical molecular orbital theory

“…Perhaps the most attractive feature of the basin-hopping approach is that only a small number of adjustable parameters need to be specified to produce acceptable results for a wide range of different systems, ranging from atomic and molecular clusters [16,22,23,29,30] to peptides [31][32][33][34][35][36][37], polymers [38], a glass-forming solid [39], and mesoscopic building blocks that form shells and helices [40,41]. The GMIN program [42], available for use under the GNU General Public License, contains a wide variety of different step-taking approaches, along with parallel basin-hopping implementations and taboo lists [43].…”