Computational Analysis of the Soluble Form of the Intracellular Chloride Ion Channel Protein CLIC1
Figure 5
Binding of GSH and mechanism of release from the noncovalently bound state. (a) Interactions of GSH with CLIC1. Final frame from the cov1 simulation ( ns). GSH and protein regions which interact with the ligand are shown in stick representation with nitrogen blue, oxygen red, and sulphur orange; carbon atoms of GSH are green and those of CLIC1 are tan. Residues and ligand are as labeled. Interactions discussed in the text are indicated by dotted lines and coloured as in Supplementary Figure 6 (Supplementary Material available at http://dx.doi.org/10.1155/2013/170586). (b) EV2 and (c) EV3 from PCA of the combined apo1 and cov1 simulations. Stereo image of the C trace of the superimposed maximum (green) and minimum (red) projection structures. The view is roughly orthogonal to that in Figure 1, equivalent to the perspective from the bottom of the page in Figure 1, along the axis of -helix 1; the N-terminal subdomain is on the right and the C-terminal subdomain on the left. (d) Concerted motions in the ncv2 and ncv3 simulations show a peak in the most concerted 50% of C atom fluctuations for residues 60–63. Per residue fluctuations due to EVs 1–5 from PCA analysis of the C trajectory of simulation ncv2 (black) and EVs 1–4 from simulation ncv3 (grey). Residues 145–165 were not included in the PCA analysis.
