Molecular Dynamics Simulation Reveals Specific Interaction Sites between Scorpion Toxins and Kv1.2 Channel: Implications for Design of Highly Selective Drugs

Figures

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  Figure 1. Scorpion toxins and K+ channels. (A) The rKv1.1-rKv1.3 pore region sequences. Amino acids conserved across the alignment are marked in yellow, and turret, pore helix, and filter are colored in green, blue, and red, respectively; (B) The α-KTxs studied in this work. Their functional sites identified by mutational experiments are highlighted with a double underline. New interaction sites predicted by reported molecular dynamics (MD) simulation data are underlined once. For the affinity of each toxin, Kd (dissociation constant), Ki (equilibrium constant), or IC50 (half maximal inhibitory concentration) (asterisks) are shown in nanomole (nM) [8,13,14,15,16,17].

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  Figure 2. Construction of toxin-channel complex for MD simulation analysis. Three experimentally determined functional sites of α-KTxs are shown as sticks. Superimposed structure of these five toxins are emphasized by red box and root-mean-square deviations (RMSDs) between these four toxins and ChTx are listed below the structure.

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  Figure 3. Structural flexibilities of four toxin-Kv1.2 complexes. (A) RMSDs of four toxin-Kv1.2 pore region complexes; (B) root-mean-square fluctuations (RMSFs) of the Cα atoms of Kv1.2 pore region in these four complexes from 15 ns to 40 ns. A–D indicate four different chains in Kv1.2. The range of A–D chains’ pore region residue number is marked by red, blue, light blue, and green string, respectively. Turret regions are outlined by black rectangular boxes and pore helix and filter regions are outlined by pink rectangular boxes; (C) average Cα-RMSF of Kv1.2 pore region in sole Kv1.2 and these four complexes from 15 ns to 40 ns. Turret, pore helix, and filter in x-coordinate represent the turret, pore helix, and filter region of Kv1.2 channel. A–D indicate four different chains in Kv1.2.

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  Figure 4. Structural flexibilities of four toxins. (A) RMSDs; (B) average RMSF; (C–F) RMSFs of the Cα atoms of four toxins. Toxins’ sequences are written under x-coordinate and their α-helical and β-fold are colored in red and green, respectively.

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  Figure 5. Interactions between toxins and Kv1.2. (A) A–D chains of Kv1.2 pore region; (B–F) showing the interaction residues of toxins and channel. H-bonds are shown in green and hydrophobic interactions in red. Interaction sites of toxins are highlighted in red and sites of the channel in blue. Sites involved in hydrophobic interactions are shown as lines and sticks in H-bonds or salt bridges.

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  Figure 6. Hydrogen bonds and salt bridges distances of toxin-Kv1.2 complexes. (A,C,E,G) showing the average distances of hydrogen bonds and salt bridges from 15 ns to 40 ns. (B,D,F,H) showing the changes of hydrogen bonds and salt bridges distances between toxins and Kv1.2 channel in 40 ns.

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  Figure 7. Interaction sites between toxins and Kv1.2. Sites participating in salt bridges, H-bonds, and hydrophobic effect are highlighted in golden, green, and purple, respectively. Four variable channel sites implicated in the interaction with α-KTxs are labeled with red arrows.

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  Figure 8. Kv1.2 specific amino acids involved in the interactions with the toxins. (A) A–D chains of Kv1.2 channels pore region; (B–F) interaction sites of toxins are highlighted in cyan; unconservative sites in the channel are highlighted in magentas. Amino acids at the interface between a toxin and the channel are shown as spheres.