JMOL + Uniprot + Secondary Structure: Visualisation mismatch?

Question

[ldpubsec]

Dear everyone :-),

I am struggling with (maybe very newbie) questions and one problem.

1. For example, when I look up Titin_Human secondary structure (http://www.uniprot.org/uniprot/Q8WZ42#structure) my first question is: How can a helix consist of only 3 amino acids (position 72-74)? And a beta-strand of another 3 amino acids? What is the difference between those two three-amino-acid sequences, so that one is a helix and one is a beta-strand? (What determines that one will be a helix and one will be a beta-strand?)
2. When thinking about the question above, I've downloaded JMOL to try visualize first helix position at 72-74. At UniProt secondary structure list I clicked "combined sources" and copied PDB reference 2A38. JMOL visualized it nicely. Then, by simple commands:

select all
color blue
select 72-74
color red
cartoons only

I received:

this really confuses me, because what I suppose, is one red helical secondary structure at one location. The last question is, then: how can position 72-74 be visualised as three various structures at different places within the protein? Did I do something wrong? Or am I missing something?

Thank you in advance

Answer 1

[Elisabeth Gasteiger]

From the UniProt helpdesk (please do not hesitate to contact the helpdesk directly if you have additional questions):

Secondary structure elements are identified based on the backbone angles of the amino acid residues. Alpha-helices and beta-strands have characteristic backbone angles and fall into distinct regions in the Ramachandran plot (see the Wikipedia article)

You might also consult this site for information about the properties of secondary structure elements: http://www.proteinstructures.com/Structure/Structure/secondary-sructure.html

Since it takes 3.6 residues for one turn of an alpha-helix, a lower limit of three residues (almost one turn!) looks reasonable. Likewise, a lower limit of three residues has been imposed for beta-strands. These limits are a bit arbitrary, but not unreasonable.

The structure you looked at (2a38) contains three chains (A,B,C), all from the same protein, as explained in the PDB header document (found e.g. here).

This explains why you can see three very small helices in JMOL.