Figure 7.

(A,B) Snapshots from all-atom MD simulations comparing mutual orientations of the two monomers in dimers of the WT (A) and F220C (B) constructs. TM5 and TM6 helices are shown in purple and silver, respectively. The rest of the protein is in transparent white color. Solid lines connect C_α atoms of residues 200 and 234 (yellow spheres) used to define the orientation of TM5 helix in each monomer (see text). (C) Probability distributions of the splay angle α between the two TM5 helices in the dimers of various constructs described in the text. The color coding of the systems follows the same pattern as in Fig. 6. The results for each replicate are shown separately (i.e. 6 plots per constructs). (D) Histogram of water counts in the interior of each monomer of the WT (Modes 1 and 2) and F220C dimers. For this analysis, in each trajectory, for a given dimer, water oxygen atoms within 7 Å of the sidechains of residues 264, 268, 272, 127, and 131 were counted in each monomer. The data was then combined for two monomers and for all the trajectories per construct (i.e. WT 1, WT 2, and F220C) and binned using a bin size of 2. (E) Histogram of C_α-C_α distance between residues 252 and 308 on each monomer of the WT (Modes 1 and 2) and F220C dimers. To construct the histogram, the data for each monomer and for all trajectories of each construct was combined and binned using a bin size of 1 Å. (F) A snapshot of the F220C dimer as in panel B, highlighting water penetration (yellow spheres show water oxygens in the protein interior) and the distance between TM6-TM7 distance reported in panel E (blue spheres are C_α atoms of residues 252 and 308).