Figure 4.

Atomistic simulations explain experimentally observed structural properties of misfolded RBD. (a) Native contact map for RBD, alongside native structure. Contacts corresponding to the substructures a to j are indicated with different colors and labeled on structure as dashed lines. (b) Free energies of distinct “topological configurations,” defined as the collection of snapshots containing some subset of folded native substructures (defined as in a). Each dot represents one topological configuration, as labeled, with its x position corresponding to its respective number of folded substructures and y position corresponding to its respective free energy relative to the lowest energy state. (c) Example snapshot of fully folded structure (configuration abcdefghij) from the simulation with constraints. (d) Example snapshot of configuration bcdefgi, the lowest energy state from simulations without disulfide constraints. Cysteine pairs CYS46 (cyan) and CYS99 (light green), as well as CYS147-CYS145 (orange) remain in contact with each other, whereas other cysteine pairs corresponding to native disulfides do not form contacts. (e) Probability distribution of number of cysteine-cysteine contacts among snapshots from the simulation without disulfide constraints. (f) Root mean-square fluctuation relative to native state (top plot) of each residue in simulations with disulfide constraints (orange) and without constraints (blue line, cysteine positions indicated with red markers) and difference in solvent-accessible surface area (SASA) between the simulations as a function of residue (bottom plot). Positive $\Delta$SASA indicates the residue is more exposed in the simulation without constraints. The color of each bar represents the hydrophobicity of the residue, quantified by the Miyazawa-Jernigan scale (57). The secondary structure of each residue is indicated below the plots (arrows = beta strands, rectangles = helices, colored as in c and d).