Figure 9

Mapping functional dynamics in the hexamer of P4 from bacteriophage ϕ8 [114]. Mass/charge (m/z) spectra corresponding to the peptic fragment encompassing residues 139–158 (m = 2210.14 Da, z = 3) during H/D exchange (only interval 0 to 60 min shown). (B) Increase of deuterium content in the peptide (symbols) and the corresponding maximum entropy fit (MEM) for P4 alone (black circles, solid line), P4+1 mM poly(C) (blue triangles, dotted), P4 + 1 mM poly(C) + 1 mM ATP (red squares, dashed line), P4 + 1 mM poly(C) + 1 mM AMP-PNP (green diamonds, dash-dot-dot) and P4 + 1 mM ADP (cyan inverted triangles, dash-dot). Standard deviations (error bars) were estimated from three independent experiments. (C) Rate distributions obtained by MEM fitting of data in panel B. The color bar under the panel indicates the three integration regions which were used to obtain the number of sites within each rate class (blue = slow/protected, green = intermediate, red = fast/unprotected). (D) Number of amide sites in the three classes and under different conditions (nucleotide di/triphosphates, RNA binding) obtained from data in panel C, bar colors as in panel C. (E) RGB representation of the HDX kinetics for subunit interfaces. The two facets (left and right) represent the facing interfaces from the neighboring subunits in a surface representation. Bound ATP molecule is shown in yellow ball-and-stick representation. Several regions of interest are delineated: NT-nucleotide binding pocket; L2H-loop 2 and α-helix 6 which constitute the moving lever of the motor; IH-interfacial helix which becomes transiently exposed during ring opening and RNA loading. (F) Three-color, RGB scale for number of amides exchanging in the three classes.