Talk:Alpha helix

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Untitled

Just an an FYI, Linus Pauling won his first Nobel for the discovery of the alpha helix, so a good reference source for this entry would be Pauling's Nobel Prize lecture... Dwmyers 18:05, 20 Sep 2003 (UTC)

I don't trust some of the stuff on this page. —Preceding unsigned comment added by Bensaccount (talk • contribs) 04:16, 18 February 2004 (UTC)[reply]

Don't make a comment like that without qualifying it with a valid reason. —Preceding unsigned comment added by 70.18.106.30 (talk • contribs) 02:46, 18 October 2004 (UTC)[reply]

Correct dimensions?

50 nanometers is not equal to 5 angstroms, which is the correct measure? If it is 50 nanometers, then it would be 500 angstroms, and if it is 5 angstroms, it would be 0.5 nanometers. —Preceding unsigned comment added by 172.157.138.41 (talk • contribs) 23:30, 14 May 2005

It is cerainly not 50 nanometers!! Proteins would be gigantic!! Some mycoplasmas are only 500 nanometers big, and they contain a vast number of proteins still. 5 Angstoms is the correct value, so 0.5 nanometers... Edward Mitchard —Preceding unsigned comment added by 163.1.42.165 (talk • contribs) 21:53, 18 June 2005 (UTC)[reply]

I changed the diameter of the alpha helix to 1.2 nanometers from 120 nanometers. Note that 10 angstroms is 1 nanometer, this should be the subject of a new page introducing the unit Ångström, which equals 0.1 nanometer. The diameter of the alpha helix is qouted as 12 Ångströms (Å). —Preceding unsigned comment added by 155.198.232.196 (talk • contribs) 11:22, 29 November 2005 (UTC)[reply]

Why 1.2 nm? Is there a reference? Alberts (Molecular Biology of the Cell. 4th edition. Alberts B, Johnson A, Lewis J, et al.

New York: Garland Science; 2002.) gives 0.5 nm = 5 Angstrom in Figure 3-11 Section: The shape and structure of Proteins. — Preceding unsigned comment added by 132.187.23.124 (talk) 09:38, 17 July 2012 (UTC)[reply]

I've tried to clarify the wording about helix diameter. Also will try to get back some time soon to adding more refs to this article. Dcrjsr (talk) 21:03, 17 July 2012 (UTC)[reply]

Page cleanup

I think this page needs to be cleaned up a bit, espicially the section on the helical geometry. I'm not one to do this, but i'm just commenting on the formatting. Dave —Preceding unsigned comment added by 72.225.63.56 (talk • contribs) 04:13, 18 August 2006 (UTC)[reply]

About William Astbury

According to my biochemistry text book "Principles of Biochemistry" by Lehninger (4th ed) on p.154 problem 2 specifically says that the unit spacing Astbury detected was 5.2 angstroms not 5.1 as reported in this article. Additionally, the textbook says he was not able to interpret the results as an alpha helix at the time. I trust this textbook over the uncited info here, but anyone willing to double check (as I'm studying for an exam at the moment) please do so! Thanks! —Preceding unsigned comment added by 140.192.135.35 (talk • contribs) 20:08, 3 October 2006 (UTC)[reply]

I'll check Lehninger for this. Probably what they mean is that Astbury did not have sufficient structural data to show that the present α-helix model was the sole correct possibility. In other words, his data allowed for a variety of models although, as pointed out in the text, not all of them were physically plausible, since they had steric clashes or poor hydrogen bonds. Talk to you soon, Willow 11:33, 18 October 2006 (UTC)[reply]

Question on bonding

In $\alpha$ -helix there are 3 spines of hydrogen bonds, so the bonding should be i -> i + 3. Thus the peptide group of aminoacid 1 should form an H-bond with peptide group of aminoacid 4. I hope the person who created the entry will be able to reply, or I have misunderstood something. But if you see the figure of $\alpha$ -helix, there also the bonding is 1->4, so i -> i + 3. Danko Georgiev MD 09:17, 18 October 2006 (UTC)[reply]

I think you may be right that the picture in the article is incorrect; if I'm not mistaken, it shows a 3₁₀ helix, not an α-helix. However, the definition is correct as written: the alpha helix is defined by i+4→i hydrogen bonds. I'm sorry for the picture snafu; I haven't checked the article in a while and mistakes can sometimes creep in, even with the best-intended editors. Willow 11:33, 18 October 2006 (UTC)[reply]

Drat! I just looked and that incorrect picture was there even when I was editing back in May. :( I'm really sorry for letting that slip by! I'll replace it with a correct model later today, something that looks like my pi helix, 3_10 helix and polyproline helix models. Willow 11:42, 18 October 2006 (UTC)[reply]

Hi but the figures are correct! I work on Davydov solitons recently, so I was interested in the indexing, and then I remembered the Wiki-entry realizing that there is some error. The

\alpha

-helix is one with 3.6 aa per turn. This means that aa1 binds to aa4. The correct indexing is thus i+3 -> i bonding. The figure with the

\pi

-helix is indeed i+4 -> i bonding. That is aa1 binds to aa5 by H-bond. In all papers on

\alpha

-helix the H-bond spines are 3! In the

\pi

-helix I see 4 spines. Spine is the chain of H-bonded peptide groups. So I think I am right in my comment, you have overlooked something. Danko Georgiev MD 12:38, 18 October 2006 (UTC)[reply]

Forgive me, but I think there might be a mis-understanding about how residues are numbered. The carbonyl group is counted as belonging to the C^α before whereas the amide nitrogen is counted as belonging to the C^α after; thus, a "residue" in a protein is -NH-C^α-C(=O)-. So if you want to count peptide groups, yes, the (i+3)th peptide group hydrogen bonds to the (i)th peptide group in an alpha helix; but the carbonyl oxygen of residue i is hydrogen bonded to the nitrogen of residue i+4. Hoping that this makes sense, Willow 13:22, 18 October 2006 (UTC)[reply]

Agreed! Sorry, it was my overlook. I intuitively counted the peptide groups in the spines when I created the idexing, yet I did not consider the fact that the peptide group is created by 2 aa, thus indeed the correct bonding is i+4 aa -> i aa, but when it comes to peptide groups, the bonding is i+3 pg -> i pg. I admit that I had to be more careful before asking the question. But maybe it deserves all this to be clarified in the main text. Danko Georgiev MD 02:08, 19 October 2006 (UTC)[reply]

Spring shape

Do alpha helix proteins ever stretch or compress? Can one alpha helix be tighter than another? —Preceding unsigned comment added by 75.72.21.221 (talk) 01:31, 6 December 2007 (UTC)[reply]

No they are quite the same. Atoms don't have individuality. It would be more or less springy based on temperature, I'd assume

An alpha-helix can't get any tighter, since successive turns are already in van der Waals contact as well as hydrogen bonding, and the atoms can't get significantly closer. They can stretch out in a dynamic sense, but would return to the favorable equilibrium position. Of course, Astbury's experiment shows the ultimate in helix stretch - all the way to extended beta structure. Maybe the word "spring" in the intro is somewhat misleading; I'll replace it with "spiral". Dcrjsr (talk) 21:35, 31 January 2010 (UTC)[reply]

Main picture subtext

It says the sidechains point slightly downward. Does this refer to the hydrogen that have polar bonding to the oxygens? If so, it is pointing almost completely downward. Side-chains are usually amino chains such as this... We need to edit the text under the main picture. It is confusing. —Preceding unsigned comment added by Speshuldusty (talk • contribs) 09:56, 4 December 2009 (UTC)[reply]

I've clarified the figure caption, based on the above comment - hope this helps. Note that I've also done a very great deal of editing on this page over the past week - adding images and references, and clarifying/correcting many points, since it does lie within my expertise. There's still more to be done, but I'd appreciate any feedback very much. Dcrjsr (talk) 21:29, 31 January 2010 (UTC)[reply]

Art Section

I am not convinced this section should be here, but I still don't know enough about Wikipedia policy to formally justify its deletion. Xandrox (talk) 05:41, 11 December 2012 (UTC)[reply]

Caption of first figure

The caption of the first figure includes this text:

"Two hydrogen FOR the same peptide group"

On the face of it, this is ungrammatical, and the capitalization of "FOR" is weird. Or is FOR an acronym for something? At any rate, it could use clarification. Gwideman (talk) 21:29, 6 October 2014 (UTC)[reply]

Information in (removed) "2D representation" section - how to deal with it? Reference for "helical net" rep?

I don't know about "Headbomb" being a sockpuppet for one of the researchers cited, but the information (I assume) is legitimate. How are cases like this handled? I don't have the expertise to rewrite the section without basically copying it. Are there secondary references covering the same material? I did find this article^[1] which appears to be about the "helical net" diagram. Jimw338 (talk) 05:04, 14 February 2020 (UTC)[reply]

References

^ Dunnill, P (July 1968). "The use of helical net-diagrams to represent protein structures". Biophysical journal. 8 (7): 865–75. doi:10.1016/S0006-3495(68)86525-7. PMID 5699810.

Crambin animation.

The animation at the top of the article with the caption "Three-dimensional structure of an alpha helix in the protein crambin" is great, except there is no way to pause it, or at least, no obvious way. It's really important to be able to pause an animation like this, to take a close look at part or all of it while it's not moving. Polar Apposite (talk) 16:31, 9 November 2022 (UTC)[reply]

[1] Dunnill, P (July 1968). "The use of helical net-diagrams to represent protein structures". Biophysical journal. 8 (7): 865–75. doi:10.1016/S0006-3495(68)86525-7. PMID 5699810.

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