FIGURE 6.

Cys¹⁶⁸ residue of SKOR is expected to reside in a water-filled pocket accessible from the outside in the open, but not in the closed conformation. Results of molecular dynamic simulations are shown in a side-on view of the SKOR channel assembly (top) with S2 and S3 α-helices of one monomer in ribbon (gray and orange, respectively) and Cys¹⁶⁸, Cys²²⁸, and Cys²³⁴ in van der Waals representations following equilibration (see supplemental Fig. S1). Expanded views of the S2 and S3 α-helices show amino acid residues (center) and the water-filled space in blue (bottom) adjacent to Cys¹⁶⁸. Protein structures were recorded every 10 ps and the root mean square deviation was calculated with the VMD trajectory tool (46) using α-C atoms to confirm equilibration. Root mean square deviation averages from 300 superimposed coordinates were determined at 10-ps intervals and gave a root mean square deviation of 0.863 ± 0.083 (±S.D.) in the open state and 0.457 ± 0.035 (±S.D.) in the closed state.