Correlations in Scattered X-Ray Laser Pulses Reveal Nanoscale Structural Features of Viruses

We use extremely bright and ultrashort pulses from an x-ray free-electron laser (XFEL) to measure correlations in x rays scattered from individual bioparticles. This allows us to go beyond the traditional crystallography and single-particle imaging approaches for structure investigations. We employ angular correlations to recover the three-dimensional (3D) structure of nanoscale viruses from x-ray diffraction data measured at the Linac Coherent Light Source. Correlations provide us with a comprehensive structural fingerprint of a 3D virus, which we use both for model-based and ab initio structure recovery. The analyses reveal a clear indication that the structure of the viruses deviates from the expected perfect icosahedral symmetry. Our results anticipate exciting opportunities for XFEL studies of the structure and dynamics of nanoscale objects by means of angular correlations.

Figure 1

(a),(b) Experimental SAXS profiles $⟨I_i(q,\phi ){⟩}_{\phi ,i}$ (log scale) determined for (a) RDV and (b) PR772 viruses. The insets in (a) and (b) display randomly chosen high-intensity single-particle diffraction patterns for corresponding particles. (c)–(f) Amplitudes of the FCs ${\tilde{C}}^n(q_1,q_2)$ for $n=1,\dots ,12$ determined for (c),(e) RDV and (d,f) PR772 viruses at (c,d) $q_1=q_2=q$ and (e,f) at fixed $q_2=0.3{\mathrm{nm}}^{-1}$ as a function of $q_1$.

Figure 2

Experimental 2D correlation maps (log scale, arb. units) of the amplitudes of the FCs $|{\tilde{C}}^n(q_1,q_2)|$ for $n=2$, 4, 6, 8, 10 and 12, determined for (a)–(f) RDV and (g)–(l) PR772 viruses. The legend and axes on the bottom-left map are the same for all 2D maps of the amplitudes $|{\tilde{C}}^n(q_1,q_2)|$ in this Letter. The dashed line ($q_1=q_2=q$) in (g) indicates a section through all 2D maps for $n\le 12$, which produce the plots in Figs. 1 and 1, while the dotted line corresponds to the plots in Figs. 1 and 1 for RDV and PR772, respectively.

Figure 3

Simulated 2D correlation maps (log scale, arb. units) of the amplitudes of the FCs $|{\tilde{C}}^{n=2}(q_1,q_2)|$ for $n=2$ determined for (a) the atomistic structure of the empty RDV capsid, and bead models of the (b) solid icosahedral particle, (c) hollow icosahedral particle with a spherical void, (d) empty RDV capsid model compressed by 3% along the fivefold symmetry axis, (e),(f) solid icosahedral particle compressed by (e) 3% and (f) 7% (see text). Notice prominent similarity of the simulated and experimental maps shown in Figs. 3 and 2, as well as Figs. 3 and 2.

Figure 4

Reconstructed images of RDV (top row) and PR772 (bottom row). Two different views (corresponding to a 72 degree rotation about the top axis) of the reconstructed RDV (a),(b) and PR772 (f),(g) particles, as well as density plots showing nonuniformities in the internal distribution of material inside the viruses (c),(h), 2D slices through the center of the reconstructed densities (d),(i), and 2D projections of the reconstructed densities (e),(j). The isosurfaces for the capsid and internal material were calculated at 45% and 84% of the maximum density for RDV, and at 47% and 78% for PR772, respectively. The viewing directions for the 2D slices and projections in (d),(e),(i), and (j) are given by the normal to the page for the structures shown in (a),(b),(f), and (g), respectively.