User:Ralf Stephan/Sandbox 2

From Proteopedia

Revision as of 19:49, 13 February 2009

Ion channels are membrane proteins that catalyze the passive transport of ions through the cell membrane. Most ion channels are specific to an ion, like the natrium channels, or the chloride channels. Some, like the TRP channels, let through a bunch of cations. Another property of ion channels is that they can be either driven by voltage or concentration gradients, or they can be gated (by voltage, ligands, touch and other sensory signal). Finally, ion channels are the fastest of all membrane transporters, with 10^6 to 10^8 transported units per second versus 10^2 to 10^4 molecules per second for porters/carriers, or 10^0 to 10^3 for ATP-driven pumps.

Classification

TCDB, the most sophisticated classification of transport proteins to date, classify ion channels as a heterogenous subset of all α-type channels, whose singular property is to consist mainly of α-helices that span the membrane. They are distinct in this from the beta-barrel porins, but also from non-ribosomally synthesized channels like gramicidin, polyglutamine or digitoxin. All these proteins are passive transport proteins.

Available structures

Membrane transport proteins are notoriously difficult to crystallize while in a working state. So, it's no surprise that there are preciously few structure data for ion channels. At the moment, the following α-type ion channels have been at least partly resolved:

• the voltage-dependent potassium channel from Rattus norvegicus (1exb, 2a79, 2r9r)
• the voltage-dependent calcium channel from Rattus norvegicus (L-type: 3bxk, R-type: 3bxl)
• the voltage-gated potassium channel from Streptomyces lividans with the structures 1bl8, 1k4c, 1k4d
• the voltage-gated potassium channel K_vAP from Aeropyrum pernix (1orq, 2a0l), and human K_v7 (2ovc)
• the voltage-gated calcium channel Ca_v (1toh, 1toj)
• the calcium-gated potassium channel mthK from Methanobacterium thermoautotrophicum (1lnq)
• the hyperpolarization-activated and cyclic nucleotide-gated K+ channel HCN from Mus musculus (1q3e, 1q43, 1q5o, 2ptm, 2q0a, 3bpz)
• the inward rectifier potassium channels KirBac3.1 (1xl4,1xl6) and Kir3.1 (Cyt. only: 1n9p, 1u4e, 1u4f, 1p7b, 2e4f)
• the acid-sensitive (proton-gated) cation channel ASIC from Gallus gallus (2qts)
• the nicotinic acetylcholine-activated cation-selective channel from Torpedo marmorata (1oed, 2bg9)
• a potassium channel from Burkholderia pseudomallei (1p7b)
• the ammonium transporter from Archaeoglobus fulgidus (2b2f)
• the small-conductance mechanosensitive channel from E. coli K12 (2oau)
• TRP channels (3e7k)
• human phospholamban (1zll)
• the P7 viroporin of Hepatitis C virus (2k8j)
• the M2 protein from Influenza A (2rlf, 3c9j)

Additionally the following non-ribosomally synthesized channel proteins constitute ion channels, and have their structure resolved:

• Gramicidin (1av2, 1c4d, 1mag)
• fungal Antiamoebin (1joh, 1gq0)
• fungal Trichotoxin (1m24)
• further Peptaibol antibiotics (1ob4, 1ob6, 1ob7)

We do not count ClC chloride carriers as ion channels, as they are secondary active carriers.

Weblinks

• The TCDB database
• TCDB: 1.A α-Type channels
• TCDB: Transport proteins with PDB structures