Figure 1.
Figure 1. Identification of a conserved cluster of contiguous residues in the KV channel. (A) A heat map showing part of the symmetric version of the adjacency matrix showing the proximity scores between residues within the S4–S6 segments, deduced from the paddle chimera structure (PDB ID 2R9R, chain B). The proximity scores are colored from black to white according to the color legend shown alongside the matrix. The locations of the different helical segments are shown along the axes of the matrix, with the S4–S5 linker helix in gray and the tail end of the S6 helix in black. Within the matrix, the elements that depict the contacts between the S4–S5 linker and the S6 tail are shown within the dotted white ellipses. The heat map of the full sequence is shown in Fig. S1, and the full adjacency matrix is shown in the supplemental worksheet. (B) The full adjacency matrix that transforms the protein structure into a “graph” was clustered to find groups of residues with high interresidue contact density, which identifies six clusters. In each cluster, the circles (or nodes) represent an amino acid residue, numbered according to the Shaker KV channel sequence (based on an alignment of Shaker and the paddle chimera; Fig. S2). The lines between the nodes (or edges) depict whether the two nodes have a proximity score greater than the cut-off. In the yellow, gray, and green clusters, all residues are within the same subunit. In the cyan, white, and red clusters, not all residues are in the same subunit; residues that belong to different subunits are separated by dark curved lines. The edges are solid for intrasubunit contacts and dashed for intersubunit contacts. (C) The green, yellow, and red clusters are mapped on the structure of the KV channel, with the residues colored according to the cluster in B. For clarity, the intrasubunit green and yellow clusters, which are housed in the VSDs, are shown on different subunits. The red cluster lies at the intracellular interface between the two subunits. (D) For each of the six clusters, the standard deviation of the conservation entropy of the residues of a cluster (σc.e.) is plotted against the mean conservation entropy of the residues of the same cluster (μc.e.), derived from the multiple sequence alignment (MSA). Each circle represents a cluster and is colored according to B. The smaller dark circle, at the intersection of the two dashed lines, indicates the σc.e. and μc.e. for all of the residues of the protein (paddle chimera [2R9R, chain B] residues 158–417). (E–I) The frequency distribution of amino acids, at positions corresponding to each of the five residues of the intersubunit red cluster, derived from the MSA, is compared against the frequency distribution of amino acids in the overall MSA. The enrichment of particular amino acids at these positions underlies the high μc.e. and low σc.e. for the red cluster.

Identification of a conserved cluster of contiguous residues in the KV channel. (A) A heat map showing part of the symmetric version of the adjacency matrix showing the proximity scores between residues within the S4–S6 segments, deduced from the paddle chimera structure (PDB ID 2R9R, chain B). The proximity scores are colored from black to white according to the color legend shown alongside the matrix. The locations of the different helical segments are shown along the axes of the matrix, with the S4–S5 linker helix in gray and the tail end of the S6 helix in black. Within the matrix, the elements that depict the contacts between the S4–S5 linker and the S6 tail are shown within the dotted white ellipses. The heat map of the full sequence is shown in Fig. S1, and the full adjacency matrix is shown in the supplemental worksheet. (B) The full adjacency matrix that transforms the protein structure into a “graph” was clustered to find groups of residues with high interresidue contact density, which identifies six clusters. In each cluster, the circles (or nodes) represent an amino acid residue, numbered according to the Shaker KV channel sequence (based on an alignment of Shaker and the paddle chimera; Fig. S2). The lines between the nodes (or edges) depict whether the two nodes have a proximity score greater than the cut-off. In the yellow, gray, and green clusters, all residues are within the same subunit. In the cyan, white, and red clusters, not all residues are in the same subunit; residues that belong to different subunits are separated by dark curved lines. The edges are solid for intrasubunit contacts and dashed for intersubunit contacts. (C) The green, yellow, and red clusters are mapped on the structure of the KV channel, with the residues colored according to the cluster in B. For clarity, the intrasubunit green and yellow clusters, which are housed in the VSDs, are shown on different subunits. The red cluster lies at the intracellular interface between the two subunits. (D) For each of the six clusters, the standard deviation of the conservation entropy of the residues of a cluster (σc.e.) is plotted against the mean conservation entropy of the residues of the same cluster (μc.e.), derived from the multiple sequence alignment (MSA). Each circle represents a cluster and is colored according to B. The smaller dark circle, at the intersection of the two dashed lines, indicates the σc.e. and μc.e. for all of the residues of the protein (paddle chimera [2R9R, chain B] residues 158–417). (E–I) The frequency distribution of amino acids, at positions corresponding to each of the five residues of the intersubunit red cluster, derived from the MSA, is compared against the frequency distribution of amino acids in the overall MSA. The enrichment of particular amino acids at these positions underlies the high μc.e. and low σc.e. for the red cluster.

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