What do the structures do?

Case number:699969-998291
Topic:General
Opened by:spmm
Status:Open
Type:Question
Opened on:Sunday, August 10, 2014 - 11:49
Last modified:Friday, October 31, 2014 - 13:16

I had been thinking about this for some time and a new player in global asked and I certainly wasn't able to provide a good answer apart from 'well its probably complicated'.
So thought I'd ask the question.

(Sun, 08/10/2014 - 11:49  |  10 comments)


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Assuming we're talking about SS here.

I had the exact same questions as a newbie myself. And they're actually a pretty fundamental concept.

Secondary Structures basically define the shape and purpose of the section of the protein. That is, usually you want helices to be twirled and covering exposed areas of sheets, sheets should be fairly flat and lined up next to each other, and loops connect helices and sheets (they have certain shapes that are good, but you tend to find those more with experience). Though these aren't always the case, they often are.

My two cents.

mirp's picture
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Secondary Structures doesn't change the score. But they affect rebuild and wiggle. There are a few explanation in the Foldit Wiki.

http://foldit.wikia.com/wiki/Secondary_Structure
http://foldit.wikia.com/wiki/Rebuild
http://foldit.wikia.com/wiki/Wiggle

spmm's picture
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Thanks - I will add this one as well: http://foldit.wikia.com/wiki/Structure

Although none of this actually explains why a helix is a helix and what it does, as opposed to what a sheet does. That is 'why do they form those shapes? Are they more efficient or compact?

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Different amino acids have certain favored regions of phi,psi plots (Ramachandran plots) (http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=n/a&template=doc_procheck02.html). Different secondary structures also occur in certain favored regions of Ramachandran plots (http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=n/a&template=doc_procheck01.html).

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http://www.greeley.org/~hod/papers/Unsorted/Ramachandran.doc.pdf gives 21 pages explaining phi,psi angles and why certain regions of the Ramachandran plot are favored and others are not allowed.

mirp's picture
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The sequence of the amino acids (primary structure) makes certain angles of the backbone more likely due to interactions between the residues and residue-backbone-interactions. This results in certain secondary structures. But that is hard to predict. Some combinations of amino acids are found in helices and sheets.

spmm's picture
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I was hoping that someone that knows this inside out would provide a simple plain English explanation.

alwen's picture
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My simple English explanation is:

-a helix packs many amino acids into a relatively small space.

-a sheet uses the fewest possible amino acids to stretch from one part of the protein to another.

v_mulligan's picture
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Secondary structures are patterns that pop up over and over again in naturally-occurring protein structures. They form for two reasons: first, every amino acid in a stretch of secondary structure is in a good conformation for avoiding clashes, both with itself, and with other amino acids in the structure. (There exist some conformations, for example, in which an amino acid's backbone oxygen clashes with the first carbon atom in its side chain. This clash does not happen in either alpha-helices or in beta-strands, though.) Second, the backbone hydrogen bond donors and acceptors can by fully satisfied by bonding to other amino acids within the same piece of secondary structure (in the case of helices), or in adjacent pieces of the same type of secondary structure (in the case of strands). Both of these things make helices and sheets very energetically favourable -- i.e. very stable, which is why they form spontaneously. It is difficult to create a loop in which all the backbone hydrogen bonds are fully internally satisfied, which is one reason why you tend not to see very many large proteins that have no secondary structure at all.

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I'll take a crack at it, using my own twisted grunt logic.

Spmm, think torque when trying to explain the helices. Each piece has an intrinsic number of rotational positions it can enter into when connected to another piece. if attempt are made to make twist it beyond these rotations, it becomes rigid and in flexible. If a series of contiguous pieces favors a helical trend, a helix will form, simply to avoid (effective) torque stress. If a series of contiguous pieces
that has no such helical tendency is aligned with another series of contiguous pieces that has no such helical tendency, they will attempt to find EM balance by aligning themselves in such a way as to minimize the effective stress each of their individual members applies to its counterpart in the aligned series (if they have some freedom of movement, they will attempt to do so by aligning their em fields. If successful wee see bound sheets.

granted, if we examine minutia, the helices may also be encouraged by other bits around them and interactions with the external environment as well (when forming), but the dominant forces involved in forming a helix is direct internal stresses caused by its members. Sheets, I think are in part created by their positioning with other non contiguous pieces of the polypeptide.

Another way... When I was in the moment, I looked at helices as the muscles of proteins. They always seem to be associated with contraction or flexure points like the drive behind those trapdoors I've seen in many proteins (think what seems to be at one end of a barrel for instance) ... And the trapdoors? As I recall, they almost always seem to be made of chunks of sheets. Interesting if nothing else. Doors, walls...

back to the lurk.

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