Defects and Chirality in the Nanoparticle-Directed Assembly of Spherocylindrical Shells of Virus Coat Proteins

Abstract

Virus coat proteins of small isometric plant viruses readily assemble into symmetric, icosahedral cages encapsulating noncognate cargo, provided the cargo meets a minimal set of chemical and physical requirements. While this capability has been intensely explored for certain virus-enabled nanotechnologies, additional applications require lower symmetry than that of an icosahedron. Here, we show that the coat proteins of an icosahedral virus can efficiently assemble around metal nanorods into spherocylindrical closed shells with hexagonally close-packed bodies and icosahedral caps. Comparison of chiral angles and packing defects observed by in situ atomic force microscopy with those obtained from molecular dynamics models offers insight into the mechanism of growth, and the influence of stresses associated with intrinsic curvature and assembly pathways.

Keywords: chirality; defects; nanoparticle-directed assembly; packing; virus-like particles.

Figure 1:

Transmission electron microscopy (TEM) of Au nanorod and spherocylindrical VLPs. A. “Long” NR sample and associated VLPs. B. “Short” NR sample and associated VLPs.

Figure 2:

A. TEM micrographs of spherocylindrical VLPs encapsulating long (left) and short (right ) NR particles. Long NR VLPs are more prone to defects, which are observable as gaps on the cylindrical side. B. Incidence of VLPs showing vacancy defects and defect-free VLPs for short rods (red = defect-free, short NR; green = with vacancies, short NR; orange = defect-free, long NR; cyan = with vacancies, long NR). C. Histogram of distance of the apparent ring defect from the closest NR end (for long NRs).

Figure 3:

Top: AFM images of single spherocylindrical VLPs in liquid provide suffcient spatial resolution to examine capsomer formation and packing. Cylindrical sides are characterized by hexagonal close packing with occasional vacancy defects. Spherical caps contain pentamers. A. Spherical VLP (28 nm diameter) formed around a 12 nm nanoparticle core is included for reference. B. A short NR VLP. C. NR VLP with chiral oligomeric arrangement. D. A VLP with two different widths separated by a defect. This situation may correspond to a T=3 cap at one end and a T=4, at the other. E. VLP of diameter consistent with T=4 caps. Bottom: Images of typical experimental outcomes and simulation outcomes with morphologies corresponding to those seen in experiments: F. Complete particle; G. Particle with one ring defect; H. Particle with two ring defects. Bead colors map the number of neighbors.

Figure 4:

A. Histograms of chiral angle characterizing cylindrical sides for: particles with no observable vacancies (red) and particles with vacancies (blue). B. Two T=3 end cap structures corresponding to 5-fold and 3-fold icosahedron symmetry axes collinear with the cylinder axis. A “zig-zag” lateral structure corresponds to θ = 0^°, 5-fold center axis, and the θ = 30^°, 3-fold center axis, corresponds to the “ring” lateral structure. C. Similar models for the T=4 end cap structure. In contrast with T=3, in this case: θ = 30^° “ring” has a 5-fold on center axis; θ = 0^°, “zig-zag”, has a 3-fold. D. Representation of the side hexagonal lattice, lattice vectors, and chiral angle. Dotted line: orientation of the NR long axis.

Figure 5:

A. Schematic of model capsomers, which are conical particles comprised of stacked spheres. Interparticle attractions are represented by Morse potentials between the four interior spheres, while excluded volume interactions are represented by a repulsive Lennard-Jones potentials. B. The nanorod template is modeled as a spherocylinder. The model includes attractive interactions between the subunit cone tip and the template surface which lead to adsorption. C. In the absence of the nanorod template, isometric shells with icosahedral symmetry assemble spontaneously due to subunit-subunit interactions. Bead colors map the number of neighbors.

Figure 6:

Representative snapshots of defect-free shells (A) and of shells with vacancies (B), assembled around short NRs. Colors indicate the number of nearest neighbors. Parameters are: NR radius R_nr = 5 nm, capsomer preferred curvature radius R_capsomer = 8 nm, and NR length L_nr = 22.5 nm in A, and L_nr = 22.5 nm in B. C. For comparison, TEM image examples from our experiments, with bold arrows pointing the presence of defect. D. Phase diagram showing the most frequent outcome (defect-free or with vacancies) of short nanorods as a function of the capsomer radius and NR length.

Figure 7:

Long NR simulations. A. A suffcient match between the preferred curvature of the capsomer and the curvature of the cylindrical template γ_nr ≳ 8/5 results in complete particles, such as this example for R_capsomer = 14 nm and R_nr = 9 nm. B,C. A mismatch between the preferred curvature of the capsomer and the curvature of the cylindrical template γ_nr < 8/5 leads to incomplete particles with ring defects, such as these examples for R_capsomer = 11 nm and R_nr = 9 nm (B) and R_capsomer = 8 nm and R_nr = 9 (C).

Figure 8:

Histogram of the chiral angles for particles assembled above and below the threshold curvature mismatch with the cylindrical portion of the nanorod, with R_nr = 8.0 nm, L_nr = 61.0 nm: (A)γ_nr = 1.63 and (B) γ_nr = 1.50, based on 75 independent simulations for each parameter set. A. (i) Representative snapshot of a defect-free particle assembled at conditions favoring a ring structure. (ii) Simulation snapshot showing a particle with vacancies. (iii) A typical particle with vacancies obtained in our experiments showing a ring orientation of the hexagonal lattice (θ ≈ 30^°) . B. (i) Representative snapshot of a defect-free particle with a roughly aligned lattice (θ = 2.9^°). (ii) Snapshot showing a defect-free particle with θ = 10.9^°. (iii) A typical defect-free particle from our experiments showing a roughly aligned orientation of the hexagonal lattice (θ ≈ 5^°).

Figure 9:

Density of adsorbed capsomers as a function of time, for the spherical (blue) and cylindrical (red) regions, for different capsomer curvatures: A. R_capsomer = 9.5nm, B. R_capsomer = 14.0nm, C. R_capsomer = 21.5nm. Each curve represents the average over ten independent simulations. The time at which nucleation occurs is indicated with a dashed line. Spherocylinder dimensions are: R_nr = 9.5nm and L_nr = 40.0nm. The lower panels show representative snapshots of an early stage of assembly for the three cases.