Talk:Ion channel/Archive 1

Auxiliary subunits
A section on auxiliary subunits would be of interest. English_adler

"common currency of biological energy, ATP" -- someone please expand (and link) this acronym!

- What about non-gated ion channels? (Leak-channels), appreciate some expansion on that subject / Afx

Ion channels as enzymes
The Classification of Membrane Transport Proteins is described here: http://www.chem.qmul.ac.uk/iubmb/mtp/intro.html Note that this classification work is performed by the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology.

Here is the definition of “channel” from their glossary: “membrane protein (or an oligomeric cluster) involved in specific transport of ions or uncharged molecules down their chemical or electrochemical potential gradient. Most channels exist in two conformational states, open and closed. The opening can be accomplished (a) by a spreading electric field (potential-gated channels), (b) by binding a specific ligand (chemically gated channels), (c) by mechanical stress or strain (mechanically gated channels). When open, the specific site in the channel can transiently bind solutes from both sides of the membrane.” Note that being an enzyme is not part of the definition.

You can search the membrane transport protein data base at http://tcdb.ucsd.edu/tcdb/ Put  1.A.1.10   into the TC# lookup box and you will be shown some major types of ion channels such as the Voltage-sensitive Na+ channel.

3.A.3  will direct you to the P-type ATPase (P-ATPase) Superfamily which includes the “sodium pump”(discussed further below). This class of membrane transport proteins (3.A.3) provide examples of enzymes because of their associated ATP-splitting (or forming) activities.

In contrast with membrane transport proteins discussed above, enzymes have been classified in accordance with the recommendations of the Enzyme Commission of the International Union of Biochemistry (see http://www.chem.qmul.ac.uk/iupac/jcbn/index.html#6 for details)

You can search the IUBMB Enzyme listings at http://www.chem.qmul.ac.uk/iubmb/enzyme/search.html

First, note that some membrane transport proteins do have an associated enzyme activity. Try putting “ion” into the enzyme search engine (URL given above). Go down the resulting list to EC 3.6.3.7, one of the most famous ion transport proteins, the “sodium pump”. This ion transport protein is an enzyme because it splits ATP molecules and uses the chemical energy of the terminal phosphate bond of ATP to change the conformation of the pump protein so that the pumped ions can be moved against a concentration gradient.

Try putting “channel” into the enzyme search engine. The first choice should be EC 3.6.3.49, another famous ion transport protein, the one that is defective in the disease Cystic Fibrosis. This ion transport protein is an enzyme because it also catalyses the typical ATPase reaction: ATP + H2O = ADP + phosphate.

Note that you will not find proteins such as the Voltage-sensitive Na+ channel in the enzyme data base.

Summary. Enzymologists like to limit the term “enzyme” to proteins and other macromolecules that catalyze chemical reactions that involve changes in specific chemical bonds. Some ion transport proteins are enzymes, but not all. In particular, most proteins that form transmembrane ion channels are not enzymes.

There is nothing wrong with an analogy between ion channels and enzymes that points out how ion channels can provide a low energy path across a cell membrane for the transport of an ion, but there is no need to insist that ion channels are enzymes.68.109.166.14 03:56, 4 Dec 2004 (UTC)

Why do these count as enzymes? They typically don't catalyze a chemical reaction, do they? AxelBoldt 01:24 Mar 11, 2003 (UTC)


 * Ions diffuse across a pure lipid bilayer at a very low rate. Ion channels lower the activation energy barrier for their diffusion through the bilayer core and so accelerate their rate of crossing. Since diffusion falls under the heading of chemistry and since the acceleration is brought about in the same way (stearics, stabilization of the substrate, lowering of the activation energy etc) as in more stereotypical catalytic scenarios, many enzymologists and biophysicists count channels as enzymes, and many other scientists who haven't reflected on it would concede the point when pressed, even if they wouldn't want to start calling them enzymes themselves. 168... 06:25 Mar 11, 2003 (UTC)


 * It took some searching on Google to find someone calling channels "enzymes," but here's a person: 168... 06:50 Mar 11, 2003 (UTC)

Well done Axel, ion channels are not enzymes. This is really old hat, a hangover from the days when it was thought by some that electrical signalling was due to carriers or enzymes. Although similar in ways (as the tortuous argument above outlines) it is not useful to state identity between the two where there is only analogy -see below. I don't agree that most biophysicists would describe channels as enzymes. Enzymologists might, but anyway Google seems to disagree! This should be changed. One simple example of difference: Generally, each enzyme catalyses at most a few substrates at a time in it's catalytic cycle. Once an individual channel has opened, any number up to trillions of ions, which I think are identified above as the 'substrate' of the channel, can cross the membrane more easily than otherwise, before the channel closes again. Dependent, of course, on any chemical or electrical potential that may act on the ions.

As Bertil Hille in *the* textbook on this subject* says: "Ion channels bear the same relation to electrical signalling in nerve, muscle and synapse as enzymes do to metabolism".


 * 'Ion Channels of Excitable Membranes' Bertil Hille (3rd ed., 2001, Sinauer Associates) Aplested 13:02, 22 Sep 2004 (UTC)

Question about external link
Is the newly added link to http://www.ionchannels.org useful? It seems to be a company website with ads and dead links to academic research labs that might provide information about ion channels...if they worked. Memenen 02:54, 14 Dec 2004 (UTC)


 * No, it's not a very userful link. I've removed it. Thanks -Dpryan 22:55, 2 August 2006 (UTC)

You obviously know nothing about ion channels. It is THE ion channel resource on the net. Shows your ignorance.


 * Actually I am an expert on them, anonymous user from 67.68.200.34, which happens to be the same place that ionchannels.org is located (not that I'm implying that you're promoting your own commercial site, of course). The ion channel resource would be pubmed or perhaps OMIM, not some add-filled commercial site. I see that someone from the same IP block as you replaced the link and has been adding it to other pages on wikipedia. Consider them all removed. If ionchannels.org wants to advertise its owners can pay to do so elsewhere. --Dpryan 08:18, 7 February 2007 (UTC)

G-protein and cyclic nucleotide gated channels
I believe that cyclic nucleotide gated channels are an example of what is listed as G-protein gated channels. The cyclic nucloetide entry even mentions the visual system, e.g., cyclic nucleotide gated channels in photoreceptors. These are the textbook examples of G-protein gated channels. Any objection to merging these in the list?

--- Yes, I would object as that would be incorrect. These are separate classes of ion channels. You should consult Hille for more information. Cheers...

Could you be more specific? In my version of Hille, I don't think the term G-protein-gated channel is used. I presume you are referring to channels which are directly modulated by activated G-proteins, which, at the time my version of Hille was published (Second Edition, 1992), is presented as an unproven hypothesis. If the mechanism of these chanels has been worked out, and a structurally distinct family of channels has been established, then I take back what I said. Could you provide a reference? Either version and page info from a newer edition of Hille, or a review article or something? References on the internet are much more helpful for those of us that don't have access to a university library. (I doubt Borders carries Hille...)


 * We should start the process of adding references to the ion channel article. I suggest we use this method. Some full text articles available online:

"CNG channels strongly select cations over anions, discriminate poorly among monovalent cations, and are also permeable to divalent cations, in particular Ca2+." "Cyclic nucleotides directly activate CNG channels by binding to a site on the channel protein." Note that the photoreceptor G-protein called transducin regulates cGMP production, and only indirectly regulates ion channel function.
 * Cyclic Nucleotide-Gated Ion Channels

Two important types of G-protein-gated channels are calcium channels and potassium channels: See G protein: part of the trimeric G-protein (the beta/gamma complex) interacts directly with the ion channels. --JWSchmidt 23:49, 5 December 2005 (UTC)
 * G Protein Modulation of Voltage-Gated Calcium Channels
 * Cell signal control of the G protein-gated potassium channel and its subcellular localization

Thermodynamics
What about a discussion of their disproving the second law of thermodynamics?


 * Huh?!? -- Boris 13:45, 11 January 2006 (UTC)

Definition
Is (2) of the definition not wrong? All the quotes on the talk page emphasize ion diffusion down its gradient; contrary to using ATP to pump ions across. It seems to me it should be changed. --Peiter 11:17, 4 August 2006 (UTC)
 * In general, the transmembrane parts of ion pumps are not described as being ion channels, but some of them do look like ion channels (see). I would like to see a citation to an authoritative source that describes the transmembrane parts of ion pumps as channels. --JWSchmidt 14:24, 4 August 2006 (UTC)


 * I agree with JWSchmidt, I've been working on ion channels for quite a while and I've never heard anyone refer two pumps as channels. That's the reason that I didn't include them in my edits of the diversity section. Perhaps JoeHall45 can provide a reference. I'll try and contact him either through his talk page or email. --Dpryan 07:55, 6 August 2006 (UTC)

Hi...I'll find the reference. An ion channel is a specialized protein that is embedded in the lippoprotein bilayer of animal cells. They function as a channel in that they only allow one type of ion to enter or depart the cell membrane such as the Na/K pump operates in muscle contraction and relaxation (depolarization/repolarization). The term pump is used to describe the fact that channels can operate using diffusion principle to move ions with the gradient, (downslope), however the channel may be activated by cellular mechanisms of active transport which uses ATP to move ions against the gradient (upslope) just like a mechanical pump. Does this help? Joe Hall P.S. I teach A&P, so let me know if you have other questions. Reference: http://www.prism.gatech.edu/~gh19/b1510/memtra.htm Another really good reference I give my students: http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/D/Diffusion.html#facilitated
 * The first reference that you (JoeHall) provide states at the bottom of the page: "Ion channels are not coupled to an energy source, which means that the transport is always passive, in direction from the high concentration side to the low concentration."  This hardly supports including pumps in the ion channel definition of wikipedia. --Peiter 14:19, 7 August 2006 (UTC)


 * "they only allow one type of ion to enter or depart the cell" <-- this is wrong. Some channels are fairly selective, others allow several types of ions to move across the membrane. See Acetylcholine receptor for an example. --JWSchmidt 16:12, 7 August 2006 (UTC)
 * Yeah, I agree with you and User:Peiter and have changed the intro paragraph to remove references to pumps as being channels. I also changed some unrelated inaccuracies elsewhere. --Dpryan 20:39, 7 August 2006 (UTC)


 * Added additional functions of ion channels and their comparison to other carrier molecules to 'definition/intro' in response to complaints. Russot1 (talk) 07:29, 30 December 2012 (UTC)

Cyclic nucleotide-gated channels
Under "Cyclic nucleotide-gated channels, it says that these are a superfamily containing CNG and HCN channels. According to the potassium channel dendrogram in Hille's "Ion Channels of Excitable Membranes," this is incorrect.  In this figure, CNGs are most similar to eag/hERG channels, and HCNs are far relatives to the whole Kv section of channels.  Obviously, CNGs and HCNs have features in common, but not particularly their ancestry.  Shouldn't this be corrected?  --Peiter 12:55, 6 September 2006 (UTC)
 * What was written was directed more toward functional categorization rather than evolutionary, as per the IUP nomenclature committee's report. I've made an edit to the article to explicitly state that the grouping is functional rather than evolutionary. Hopefully that'll clarify things sufficiently. --Dpryan 20:12, 13 September 2006 (UTC)

α2δ
Sorry to intrude with such layperson question, what is that α2δ subunit mentioned in 'diversity'? It must have something different to the 'normal' (usual?) α, yes/no? (am working on phytoremediation and hyperaccumulators, just starting or so to speak). Thanks for some clue about this. Basicdesign 13:55, 30 October 2006 (UTC)
 * Yes, α2 and δ are different from α1 and should be thought of as auxiliary subunits with β and γ. Please refer to the IUPAC section on calcium channels for a brief review and some references. --Dpryan 21:03, 2 November 2006 (UTC)

Definition much too narrow
First - ion channels are not only found on cell surrounding membranes but inside membranes as well, as an example take a look at a botany text books for vacuole and/or tonoplast. Second, ion flow certainly has impact on the voltage gradient across a membrane but this is not necessarily the prime function of many ion channel types, like nitrate- or malate-channels. Actually the control is primarily exerted by active transport proteins like ion pumps, which should not be considered ion channels. Certainly the article as whole is strongly biased towards animal cells, thus ignoring the complete field of plant ion channels. Burkhard -- 19:51, 2 December 2007 (UTC)

Picture for ion channel
I have made some simple picture for the ion channel, could somebody insert this here? (Of course I cold, but actually desription is only polish) The link is: http://pl.wikipedia.org/wiki/Plik:Ion_channel.png Outslider (talk) 18:51, 30 January 2009 (UTC

Names of subunits
I don't think that this statement: "The pore-forming subunit(s) are called the α subunit, while the auxiliary subunits are denoted β, γ, and so on." from the Basic Features section is true for all ion channels. For example, the nicotinic acetylcholine receptor and glycine receptor. I would like to reword in a week unless I'm mistaken. Shanata (talk) 21:27, 27 October 2009 (UTC)
 * That's a good point. I think that sentence is referring only to voltage-gated ion channels. --Tryptofish (talk) 21:33, 27 October 2009 (UTC)

1st Paragraph
The first sentence is pretty outdated in that ion channels are responsible for so much more than generating and regulating the resting potential. I would replace it with something more general. Actually the first sentence in the Basic Properties section is more correct.Desoto10 (talk) 05:59, 8 November 2009 (UTC)

Plant ion channels
Why no mention? — Preceding unsigned comment added by 143.117.78.27 (talk • contribs) 11:21, July 18, 2013‎