Figure 4.

The local conformational landscape of α6,7,8 in apo-PhuS. (A) The kernel density estimation (KDE) plot generated from the 11 significantly upweighted clusters using the distance between the C_α atoms of H212 and F114 (Å) versus the percent α-helicity of the α6,7,8 region. Numbered points indicate the average coordinate of one of the 11 significantly upweighted clusters, labeled according to its corresponding average upweighting rank (most upweighted to least upweighted). The coordinates of apo- and holo-PhuS structures are indicated as an A and an H, respectively. From the KDE plot, four substates (S1–S4) are delineated as indicated by the gray circles. The scale bar represents the probability desnsity at each point. (B) A representative structure from each of the four substates, with the close-up highlighting the α6,7,8 region (red) overlaid with that in 4IMH (purple). (C) SASA calculations of the distal and backside heme-interacting residues. Bar graphs show the SASA of the contact residues in the holo-PhuS MD simulations (red), apo-PhuS MD simulations (gray), and significantly upweighted clusters (blue) the error bars are the standared error of the SASA calculated over each frame. To the right, the corresponding residues are shown in surface rendering for a representative frame from the holo-PhuS MD simulations and from a significantly upweighted cluster in substate S4.