Talk:Alpha helix

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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. —The preceding unsigned comment was added by Bensaccount (talk • contribs) 04:16, 18 February 2004 (UTC).

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

Contents 1 Correct dimensions? 2 Page cleanup 3 About William Astbury 4 Question on bonding

[edit] 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. —The preceding unsigned comment was 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 —The preceding unsigned comment was added by 163.1.42.165 (talk • contribs) 21:53, 18 June 2005 (UTC).

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). —The preceding unsigned comment was added by 155.198.232.196 (talk • contribs) 11:22, 29 November 2005 (UTC).

[edit] 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 —The preceding unsigned comment was added by 72.225.63.56 (talk • contribs) 04:13, 18 August 2006 (UTC).

[edit] 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! —The preceding unsigned comment was added by 140.192.135.35 (talk • contribs) 20:08, 3 October 2006 (UTC).

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)

[edit] Question on bonding

In α-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 α-helix, there also the bonding is 1->4, so i -> i + 3. Danko Georgiev MD 09:17, 18 October 2006 (UTC)

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)

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)

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 α-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 π-helix is indeed i+4 -> i bonding. That is aa1 binds to aa5 by H-bond. In all papers on α-helix the H-bond spines are 3! In the π-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)

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)

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)