Please be patient while the structures in the left frame load. In order to display all of the structures in the tour properly, press 'View' buttons below in order (from 1 to the end).
Channels belong to a class of transmembrane proteins that mediate the transport of metal ions down a concentration gradient. This transport is passive: it does not require energy input. Channels are usually gated. They remain closed until a stimulus triggers the opening of the gate, allowing diffusion through the channel. The stimulus is usually a change in the membrane potential (voltage-gated channels) or ligand binding (ligand-gated channels). Generally, channels have a high selectivity for a specific substrate.
The display in the left frame shows a ball–and–stick model of the structure of a potassium (K+) channel from the bacterium Streptomyces lividans (KcsA channel). This remarkable protein is capable of allowing K+ cations to enter the intracellular space at rates that are close to K+ diffusion rates in solution (about 107 to 108 ions per second) while maintaining high selectivity for this cation over the chemically and physically similar Na+ ion (selectivity ratio K+/Na+ ≅ 104).
The KcsA channel consists of four identical subunits (homotetramer), each coloured differently. (Unless otherwise noted, in each view the extracellular side of the channel is always pointing upwards).
This is a look down the channel from the extracellular side emphasising its tetrameric structure and its approximately four – fold symmetry.
The KcsA channel is composed mostly of hydrophobic residues (white areas). This allows for the whole structure to be comfortably 'nested' inside the hydrophobic phospholipid bilayer of a cell membrane.
To see KcsA's potential surface map, click on thumbnails below:
The secondary structure of KcsA subunits (two of which are shown here, one on each side of the channel) are composed of three alpha helices (white) connected via two loops (blue). Each helix is important for the proper function of the channel:
The primary structure of these loops, Thr–Val–Gly–Tyr–Gly, is highly conserved and is found in selectivity filters of all potassium channels (see further below). The oxygen atoms (red spheres) from C=O groups of the peptide backbone lign the inner surface of the selectivity filter. They bear a partially negative charge, similar to the oxygen atoms in water molecules. The last oxygen atom at the end of the pore is from a deprotonated hydroxyl group of threonine (Thr) sidechain.
The pore has four potential K+ binding sites, S1 to S4 labelled from the extracellular side. Each binding site is a cage formed by eight oxygen atoms pointing at the vertices of a cube (only four O atoms from each cube are shown here, the other four are from two hidden subunits). However, inside the pore only every second site is actually occupied with K+, the other two sites are occupied by water molecules (red spheres inside the pore). The presence of water molecules reduces electrostatic repulsion between the two cations inside the pore. In this display the channel is in the 1, 3-configuartion with K+ ions occupying sites S1 and S3 and water molecules sites, S2 and S4.
A closer look at the pore architecture reveals the reasons behind the high selectivity for K+. The pore diameter (about 6 Å) and spacing between the oxygen atoms (about 3 Å) are a perfect match for the size of K+ (1.33 Å) and the K+-O distances (on average 2.8 Å). On the other hand, Na+ is too small (radius 0.95 Å) and makes significantly shorter distances to oxygen atoms (on average 2.3 Å). As smaller cation, Na+ prefers lower coordination numbers and different coordination geometries.
This display shows a 2, 4 conformation inside the pore as another possible distribution of potassium cations inside the pore. When K+ occupies either position 2 or position 3 the channel is in a conductive state and is able to let K+ pass. If potassium is not occupying either of these positions, the channel is in a collapsed state and is unable to conduct. Importantly, only potassium ions are of the right size to induce the switch from a collapsed to a conductive state.
Another potassium cation can enter the pore when cations inside are in the 2, 4-conformation. The hydrated potassium cation (labeled 'K out') approaches the pore from the extracellular side, attracted by the negative surface potential around the opening.
The K+ hydration sphere is partially removed at the very entrance, at a site referred to as S0. Note that the residual water molecules around the potassium cation at the extracellular side of the channel have not been located in the X-ray electron density map.
Finally, the K+ enters to occupy position S1 inside the pore pushing out the potassium cation from position S4 into the cavity (labeled 'K in'). Inside the cavity, the cations are re-hydrated and are ready to enter the intracellular space.
This display shows the cavity and the pore. The backbone oxygens from two remaining subunits defining the pore are now also shown. Note the similarities in coordination geometry and coordination number between hydrated K+ inside the cavity and K+ inside the pore. The two inner helices are displayed as a ball-and-stick model while the pore helices are visible as white strands. The potassium cation inside the cavity is now completely rehydrated with eight water molecules surrounding it.
The mechanism that regulates the opening and closing of the KcsA channel (Views 1-16) is poorly understood at the moment but both pH and K+ concentration have been implicated as possible regulators. However, for two other channels, KvAP and MthK, the gating mechanisms are somewhat better understood.
KvAP potassium channel: A voltage-gated channel
The display in the left frame shows the structure of a voltage-gated potassium channel KvAP from Archea Aeropyrum pernix viewed from the extracellular space. The helices defining the channel part are colored yellow while the voltage sensing part is white; the pore containing the selectivity filter is displayed in red (at the center of the structure). Potassium cations (purple spheres) are visible inside the pore. Note the similarities in structure between the KcsA channel (Views 1-16) and KvAP: an approximate four-fold symmetry, an all- α secondary structure and a selectivity filter defined with four loops.
It is believed that helix 4 (cartoon) and its five positively charged arginine residues (green, ball-and-stick) are responsible for sensing the changes in the membrane potential. This helix can move rather freely with respect to the rest of the channel components and is exposed to the intracellular space when the membrane potential is normal. However, when membrane depolarization occurs, this helix moves and it can probably be exposed to the extracellular environment during the depolarization process. These large changes in the protein's tertiary structure are transmitted through the other helices and loops of the voltage-sensing component that open and close the channel gates.
MthK channel: A ligand-gated channel
The display in the left frame shows a side view of the structure of MthK channel (red) and its gate (white) from Methanobacterium autotrophicum in their open states. The ligands that bind to the massive gate, change the gate's tertiary structure, and open the channel, are calcium cations (Ca2+) visible as green spheres inside the structure rendered in white. When the calcium ions dissociate from the gate, its tertiary structure collapses and the channel is closed.
Optional view: Click to pass through this channel: you will enter the space between the channel and its gate, turn for 180 degrees and look down the channel's axis from the intracellular space! (This animation takes a while!)
To see the selectivity filter consensus sequence, click on the first thumbnail below:
Scorpion toxins are small proteins found in scorpion venoms. They generally act by blocking various membrane channels and disrupting neuronal transmissions. Charybdotoxin, composed of only 37 amino acids, is a scorpion toxin that blocks potassium channels.
Charybdotoxin contains a number of arginine and lysine amino acids that are positively charged at physiological pH (blue areas). These residues make the surface of charybdotoxin positively charged.
To see charybdotoxin's potential surface map, click on the thumbnail below:
The positively charged surface of charybdotoxin is in turn an excellent match for the negatively charged surface around the pore of potassium channels. The display in the left frame shows the structure of charybdotoxin in complex with KcsA as obtained by solution NMR. The toxin (red) plugs the channel pore preventing potassium cations from entering the channel (white).