Figure 2.
Molecular insight into binding of Wu50 to the S3/S4 site.(A) Top view of a representative snapshot of the interaction between Wu50 and the S3/S4 site in the WT Shaker KV channel. The channel is shown as gray ribbons, and the Wu50 compounds are displayed using a space-filling representation, each atom type colored differently (black: C or Cl; red: O) Residues’ Cα coming in contact with Wu50 in at least one of the channel’s subunits (SUs) during MD simulations are represented as spheres and colored according to the subunit they belong to. (B) Distance between closest heavy atoms of Wu50 and ILE360 along a 1-µs-long MD simulation of the WT Shaker KV channel. Each of four subunits is depicted in a different color, following the color scheme presented in A. (C) Contact frequency between any heavy atom of Wu50 and S3/S4 site residues in the WT Shaker KV channel MD simulation. Each of the four subunits is depicted in a different color, following the color scheme presented in A. For each residue, each bar corresponds to the contact frequency in one of the four subunits. (D) Zoomed-in side view of the S3/S4 site for the WT Shaker KV channel. The residues identified in the contact frequency analysis are shown as sticks. Apolar, polar, and positively charged residues are represented as sticks and depicted in shades of gray, orange, and pink, respectively. Wu50 compounds are displayed using a CPK representation. (E) Top view of a representative snapshot of the interaction between Wu50 and the S3/S4 site in the Shaker channel with the 2R motif. (F) Distance between closest heavy atoms of Wu50 and ILE360 along a 500-ns-long MD simulation of the 2R motif–channel system. (G) Contact frequency between any heavy atom of Wu50 and S3/S4 site residues in the 2R motif channel simulation. (H) Zoomed-in side view of the S3/S4 site for the channel with the 2R motif. Colors and representations in E–H are the same as in A–D.

Molecular insight into binding of Wu50 to the S3/S4 site. (A) Top view of a representative snapshot of the interaction between Wu50 and the S3/S4 site in the WT Shaker KV channel. The channel is shown as gray ribbons, and the Wu50 compounds are displayed using a space-filling representation, each atom type colored differently (black: C or Cl; red: O) Residues’ Cα coming in contact with Wu50 in at least one of the channel’s subunits (SUs) during MD simulations are represented as spheres and colored according to the subunit they belong to. (B) Distance between closest heavy atoms of Wu50 and ILE360 along a 1-µs-long MD simulation of the WT Shaker KV channel. Each of four subunits is depicted in a different color, following the color scheme presented in A. (C) Contact frequency between any heavy atom of Wu50 and S3/S4 site residues in the WT Shaker KV channel MD simulation. Each of the four subunits is depicted in a different color, following the color scheme presented in A. For each residue, each bar corresponds to the contact frequency in one of the four subunits. (D) Zoomed-in side view of the S3/S4 site for the WT Shaker KV channel. The residues identified in the contact frequency analysis are shown as sticks. Apolar, polar, and positively charged residues are represented as sticks and depicted in shades of gray, orange, and pink, respectively. Wu50 compounds are displayed using a CPK representation. (E) Top view of a representative snapshot of the interaction between Wu50 and the S3/S4 site in the Shaker channel with the 2R motif. (F) Distance between closest heavy atoms of Wu50 and ILE360 along a 500-ns-long MD simulation of the 2R motif–channel system. (G) Contact frequency between any heavy atom of Wu50 and S3/S4 site residues in the 2R motif channel simulation. (H) Zoomed-in side view of the S3/S4 site for the channel with the 2R motif. Colors and representations in E–H are the same as in A–D.

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