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Figure 2 | BMC Structural Biology

Figure 2

From: Monte Carlo-energy minimization of correolide in the Kv1.3 channel: possible role of potassium ion in ligand-receptor interactions

Figure 2

Random search for the energetically optimal binding site of correolide in model 2/4. The following coloring scheme is used: inner helices – violet ribbons; pore helices – green ribbons; outer helices – gray strands; the selectivity-filter region and extracellular segments – green rods; K+ ions – yellow spheres; water molecules – space filled; correolide – sticks with gray carbons and red oxygens. A and B, The side and extracellular views of 200 out of 20,000 randomly generated starting positions of correolide, in which its mass center occurred within a cylinder of 16 Å in diameter and 16 Å in length. C and D, The side and cytoplasmic views of the superposition of six lowest-energy structures found after energy minimizations from the 20,000 starting points. In the side view, only two domains are shown for clarity. In the cytoplasmic view, the P-loop domain is not shown for clarity. E and F, The structure with the most favorable ligand-receptor energy, whose characteristics are given in Table 2. Side chains of correolide-sensing residues found by Hanner et al. [15] are shown as sticks. G, Close-up view of the complex shown at E. Note that two oxygen atoms of correolide, one of which from the epoxide group, bind to the K+ ion in position 4, which is also coordinated by eight oxygen atoms from residues Thr392.

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