Article Figures & Data
Figures
- Fig. 1.
Representation of the amino acid relationships of the minimal pore regions of the voltage-gated ion channel superfamily. This global view of the 143 members of the structurally related ion channel genes highlights seven groups of ion channel families and their membrane topologies. Four-domain channels (CaV and NaV) are shown as blue branches, potassium-selective channels are shown as red branches, cyclic nucleotide-gated channels are shown as magenta branches, and TRP and related channels are shown as green branches. Background colors separate the ion channel proteins into related groups: light blue, CaV and NaV; light green, TRP channels; light red, potassium channels, except KV10-12, which have a cyclic nucleotide binding domain and are more closely related to CNG and HCN channels; light orange, KV10-12 channels and cyclic nucleotide-modulated CNG and HCN channels. Minimal pore regions bounded by the transmembrane segments M1/S5 and M2/S6 were aligned by ClustalX (Thompson et al., 1997) and refined manually. The pore regions of the fourth homologous domain of NaV and CaV channels, the second domain of the two-pore channels (TPC), and the first pore regions of the K2P channels were used to assemble the alignment, and an unrooted consensus tree was built by minimum evolution analysis using PAUP version 4.0b10 software (Swofford, 2003). To confirm the significance of the relationship among the families that comprise the VGL ion channel superfamily, we tested the significance of the amino acid sequence relationships using the HMM searching procedure. HMM searches of the complete RefSeq database revealed that each ion channel family profile identified another family of voltage-gated-like ion channels as the nearest relative in amino acid sequence of its pore. For example, for the KV channel profile, the nearest neighbor was CNGA1 (HMM e-value of 2.6 × 10-3); for the cyclic nucleotide-modulated channel profile, KV11.2 (HMM e-value of 1.5 × 10-6); for the TRP channel profile, CaV3.1 (HMM e-value of 1.8 × 10-3); and for the NaV/CaV profile, CatSper (HMM e-value of 9.4 × 10-6). The e-value is a measure of the number of hits from HMM searches that would be expected by chance; values less than 1.0 indicate a highly significant amino acid sequence relationship to the probe profile (Yu and Catterall, 2004).
- Fig. 2.
Structure of voltage-gated sodium channels. Left, schematic representation of the sodium channel α subunit. Roman numerals indicate the homologous domains. The α-helical transmembrane segments S5 and S6 and the pore loop region between them are highlighted in green. The positively charged S4 segments are highlighted in red. The inactivation gate with the isoleucine-phenylalanine-methionine-threonine (IFMT) motif that is crucial for inactivation is highlighted in yellow. The probable N-linked glycosylation sites are indicated by Ψ. The circles in the reentrant loops in each domain represent the amino acids that form the ion selectivity filter (the outer rings have the sequence EEDD and inner rings DEKA) (Noda et al., 1989; Heinemann et al., 1992, 2003). Right, three-dimensional structure of the NaV channel α subunit at 20 Å resolution, compiled from electron micrograph reconstructions. Adapted from Sato et al. (2001) and Yu and Catterall (2004).
- Fig. 3.
Structures of potassium channels. A, open and closed conformations of the potassium channel pore structures. Two subunits of the bacterial K+ channels of KcsA (Doyle et al., 1998), representing a “closed” conformation, and MthK (Jiang et al., 2002b), representing an “open” conformation, are shown in the figure. The selectivity filter is orange, and the outer helix (M1) is depicted adjacent to the lipid bilayer. The inner helix (M2) is marked with a space-filling model of the conserved glycine residue (red), which is thought to be critical for the bending of the M2 helix in the open conformation. B, cross-section through the three-dimensional structure of a tetrameric KV1.2 channel (Long et al., 2005a,b). Center, the pore regions S5-P-S6 of two subunits, designated 1 and 3, in blue-green. Left, S1 through S4 of subunit 4, whose S5-P-S6 segments project in front of the plane of the figure and form the near side of the pore. Right, S1 through S4 segments of subunit 2, whose S5-P-S6 segments project behind the plane of the figure and form the far side of the pore. As illustrated, the voltage-sensing domain composed of the S1 to S4 segments is positioned to interact with the S5-P-S6 segments of the adjacent subunit located clockwise (as seen from the extracellular side) in the symmetrical tetrameric array.
- Fig. 4.
Auxiliary subunits of the VGL ion channel superfamily. The transmembrane folding patterns of the auxiliary subunits of the VGL ion channel superfamily are illustrated, with cylinders representing predicted α-helices. Note that the intracellular and extracellular sides of the proteins are oriented in opposite directions for the top and bottom membranes, as in a cell. N-linked carbohydrate chains are indicated by Ψ. The intracellular auxiliary subunits are illustrated by their predicted or directly determined three-dimensional structures (Yu and Catterall, 2004).
