Figure 3.

Ensemble refinement of WT apo-PhuS by ST, HDXer, and CD. (A) Plot of the trajectory-averaged RMSD (Å) of the C_α at each residue for the 5 μs conventional MD simulations of WT apo-PhuS (PDB: 4IMH) (black) and the combined six ST simulations of WT apo-PhuS (red). (B) The decision plot resulting from the reweighting of the combined ST ensemble to the target WT apo-PhuS HDX-MS data. The selected γ of 1 is displayed as a red dashed line. (C) Experimental CD spectra for apo-PhuS (red) and holo-PhuS (black). (D) Violin plots of the 11 significantly upweighted clusters ranked in order of average change in weight (log(Ω_f/Ω_i)). The tails represent the minimal and maximal weight in the cluster, the thick dashed lines are the mean weight, and the thin dashed lines bracket 50% of the population. The green dashed line represents the percent change in overall α-helicity (Δα_h) observed between apo- and holo-PhuS unbiased MD simulations. The blue dots represent the Δα_h between each of the 11 clusters and the holo-PhuS unbiased MD simulations, with the blue dashed-dot line representing the weighted average of the 11 blue dots. The red dotted line is the experimental Δα_h measured by CD.