Figure 7.

Effect of pH on the exchange dynamics of different regions of CcdB. Hydrogen exchange rates of different regions were measured by using pepsin digestion, coupled to HX-MS. Shown are the observed masses of the sequence segments 1–16, 17–23, 24–41, 42–60, 61–68, and 80–96 obtained after different times of exchange in (a–f), respectively. Each panel shows the mass of the individual sequence segment at pH 4 (cyan circle) and pH 7 (pink circle). The solid lines in respective color represent the fit to the data using either one-, two-, or three-exponential equations. The kinetic parameters obtained upon fitting each peptide are listed in Tables S3 and S4. The red dashed lines and black dashed lines represent the rate of exchange for global unfolding at pH 7 and expected global unfolding rate at pH 4, respectively. (g) The pH-induced changes in the protection of different regions of CcdB are shown. The ratio of the protection values of different regions of CcdB at pH 4 to that at pH 7 is mapped on its structure as a heat map. The protection values were calculated as described in Materials and Methods. The regions with increased dynamics at pH 4 are marked with warmer colors, whereas those with decreased dynamics are marked with cooler colors. The uncharacterized regions are marked in gray color. The sequence segments containing β-strands colored in green, yellow, red, cyan, and orange marks the sequence segment 1–16, 17–23, 24–41, 42–60, and 61–68, respectively. The red colored segment with α-helix marks the region 80–96. The error bars represent standard error from two or more independent experiment. To see this figure in color, go online.