Exploring the Symmetry and Mechanism of Virus Capsid Maturation Via an Ensemble of Pathways  Eric R. May, Jun Feng, Charles L. Brooks  Biophysical Journal  Volume 102, Issue 3, Pages 606-612 (February 2012) DOI: 10.1016/j.bpj.2011.12.016 Copyright © 2012 Biophysical Society Terms and Conditions

Figure 1 T = 7 capsids. (A) An idealized representation of a capsid, with the pentamers labeled as first neighbors (N1), 2nd neighbors (N2), or opposite (OPP) of the pentamer denoted by ⋆. In a T = 7, each pentamer (red dot) is surrounded by five unique hexamers (blue dots). (B) The immature PHII structure of HK97 (PDB 3e8k). (C) The mature HII structure of HK97 (PDB 1ohg). Biophysical Journal 2012 102, 606-612DOI: (10.1016/j.bpj.2011.12.016) Copyright © 2012 Biophysical Society Terms and Conditions

Figure 2 Native-state simulations. Fraction of native contacts and Cv are plotted against temperature. Biophysical Journal 2012 102, 606-612DOI: (10.1016/j.bpj.2011.12.016) Copyright © 2012 Biophysical Society Terms and Conditions

Figure 3 Convergence of a sample trajectory. (A) The fraction of native contacts and the mean radius value over the course of the trajectory (solid lines); also shown are the target values, Θ★, and R¯⋆ (dashed lines). (B) The potential energy (U) profile over the first 100 ns of the trajectory. (C) The buckling variable (β) for each of the 12 pentameric sites. Biophysical Journal 2012 102, 606-612DOI: (10.1016/j.bpj.2011.12.016) Copyright © 2012 Biophysical Society Terms and Conditions

Figure 4 Histograms of convergence times and symmetry-breaking. The histograms of the times to reach Θ★,R¯⋆, and β★ are shown in A–C, respectively. (D) Histogram of symmetry breaking. Biophysical Journal 2012 102, 606-612DOI: (10.1016/j.bpj.2011.12.016) Copyright © 2012 Biophysical Society Terms and Conditions

Figure 5 Symmetry conserving and breaking pathways. (A) Buckling of the most cooperative trajectory. (B) Buckling of the trajectory with the most significant degree of symmetry breaking. (C) Potential energy profiles of the trajectories shown in A (cooperative) and B (symmetry-breaking) (D) Snapshots from the symmetry-breaking trajectory shown in B. The brown trend in B corresponds to the brown pentamer in D (arrows). Biophysical Journal 2012 102, 606-612DOI: (10.1016/j.bpj.2011.12.016) Copyright © 2012 Biophysical Society Terms and Conditions

Figure 6 Mechanism and characterization of transition pathways. (A) The fraction of native pentameric (Θpent) and hexameric contacts (Θhex) are plotted in black for all 66 trajectories, and a single sample trajectory (same trajectory as in Fig. 3) is shown in red. (B) The squared mode projections of the normal modes of PHII projected onto displacement vectors between PHII and intermediate states. The first two icosahedral modes (I1 and I2) and the sum of the low-frequency nonicosahedral (NI) modes are shown for all trajectories. (Inset) Same projection calculation, but with the displacement vectors calculated between subsequent intermediate structures and the projections averaged over all trajectories. Biophysical Journal 2012 102, 606-612DOI: (10.1016/j.bpj.2011.12.016) Copyright © 2012 Biophysical Society Terms and Conditions