Figure 1.
Dynamic fluctuations in the KcsA channel.
The K-channel may fluctuate between the open and closed conformations. The upper panels show a side view of the X-ray crystal structure of the channel (B; PDB identifier 1bl8) and the slowest mode of fluctuations in opposite directions (A and C). The lower panels show an intracellular view of the corresponding conformations: the X-ray structure (E) and the fluctuations (D and F). The outer (M1), inner (M2), and pore helices (PH) are displayed in red, yellow and blue, respectively. The Gly99 hinge is shown in green. To open the pore, i.e., to switch from the conformation in “C” and “F” to “A” and “D,” the inner and outer helices bend around their hinge sites, the inner helices rotate in a clockwise direction and swing away from the permeation pathway. The arrows indicate the rotations of the inner helices in each subunit. The picture was prepared using Pymol (http://www.pymol.org) [64].
Figure 2.
Dynamic fluctuations in the MthK channel.
The second slowest mode of fluctuations of the channel is presented from a side view in the upper panels ((A) and (C)) and from an intacellular view in the lower panels ((D) and (F)). The X-ray structure of MthK (PDB identifier 1lnq) is presented in the panels in the middle ((B) and (E)). The color scheme is the same as in Figure 1. To close the pore, i.e., to switch from the open conformation of “A” and “D” to the closed conformation of “C” and “F”, the inner and outer helices bend around their hinge sites, and the inner helices rotate in a counterclockwise direction. The arrows mark the rotations of the inner helices in each subunit. The picture was prepared using Pymol [64].
Figure 3.
Mean-square amino acid fluctuations in the KcsA channel.
The dips correspond to hinge regions. (A) Fluctuations in the first (solid) and second (dashed) slowest modes of motion of an isolated KcsA subunit. (B) Fluctuations in the first (solid black), second (dashed) and fifth (gray) slowest modes of motion of the subunit within the context of the homotetramer. (C) Structural elements and functionally important amino acids. The outer (M1), pore (PH), and inner (M2) helices are labeled in red, blue, and yellow bars, respectively, as in Figures 1 and 2. Elements and fragments of elements that are in the extracellular region of the cannel are presented using dashed bars; the bars of the inner and outer helices are dashed from the primary hinges identified in each ((A) and (B)). The approximate location of the selectivity filter is marked with “S”. The conserved Gly99 in the inner helix [2] is marked with a green triangle. Residues that are known to be functionally important based on single and double mutant experiments (Table S2 and Text S1) [8] are indicated with blank and solid red circles, respectively.
Figure 4.
ConSeq evolutionary conservation analysis [61] of the KcsA channel.
The ConSeq grades were mapped on the amino acids using the color bar with turquoise through purple marking variable through conserved amino acids.
Figure 5.
The dynamic coupling between residue pairs in the KcsA homotetramer.
The axes mark the residue numbers in each subunit. The magnitude of the positive and negative correlations between the dynamic fluctuations of the amino acids (average of the seven slowest modes) is color-coded using the red-through-blue scale on the right. (A) Interactions within subunit A; (B) interactions between residues in subunit A and residues in its nearest neighbor (subunit B; the right neighbor in the homotetrameric structure from the intracellular view of Figure 1E); (C) interactions between residues in subunit A and its juxtaposed neighbor (subunit C) in the tetramer. The structural elements (I to IV) and the helices are marked on the axes using the convention of Figure 3, and the approximate location of the selectivity filter is marked with “S”. The calculations were based on the average of the seven slowest modes of motion.
Figure 6.
The pairwise coupling measure (CM), between residue pairs in the KcsA tetramer; within the same subunit (A), between the near neighbor subunits (B), and between juxtaposed subunits (C). The axes mark the residue numbers in each subunit. The blue circles indicate the pairs of residues that are energetically-coupled with 90% confidence based on the z-score analysis. The lower-bound |CM| value that specifies this confidence is 0.31kT (A), 0.29kT (B), and 0.12kT (C) for interresidue distance 7 Å<r<16.5 Å. For r<7 Å, the lower-bound |CM| value that specifies the confidence is 0.57kT (A), 0.83kT (B), no data (C), respectively. The gray circles mark the pairs with |CM| values between these threshold values in the respective cases and 0.1kT, which is determined based on the distribution of all |CM| values. The solid red circles display pairs of residues that were found to be functionally-coupled to each other in experiments (Table S1) [11]. The structural elements (I to IV) and the helices are marked on the axes using the convention of Figure 3, and the approximate location of the selectivity filter is marked with “S”.