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Topic: Secondary structure of proteins - alpha-helix and beta-pleated  (Read 27270 times)

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Ah Beng

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Secondary structure of proteins - alpha-helix and beta-pleated
« on: January 29, 2006, 11:23:56 PM »
Hi,

What determines whether a polypeptide takes on the alpha-helix or beta-pleated secondary structure?

Put in another way, can the same polypeptide take on the alpha-helix structure under certain conditions, and yet take on the beta-pleated structure under other conditions?

Thanks for your help,
Ah Beng

Offline Yggdrasil

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Re:Secondary structure of proteins - alpha-helix and beta-pleated
« Reply #1 on: January 31, 2006, 12:44:32 AM »
In theory, the primary sequence of a polypeptide will determine the folding of that polypeptide completely.  Therefore, an alpha-helical structure should not be able to form a beta-pleated strcuture and vice versa.  However, our methods of ab initio protein structure prediction are not yet good enough to be able to fully predict protein structure from primary sequence.  Despite the shortcomming in protein structure prediction, there are some general guidelines to differentiate between alpha-helical sequences and beta-sheets.

Since alpha-helices are more compact than beta-sheets, sequences with few bulky groups are more likely to form alpha-helices whereas sequences with many bulky groups are more likely to form beta-sheets.  Many adjacent bulky groups or bulky groups spaced 3-4  residues apart (directly above each other or below in the helix) will disfavor helix formation.  The same goes with residues of the same charge.  Because of the sterics of helices, glycines and prolines disfavor helix formation, although there are notable exceptions (e.g. collagen fibers which consist of mostly glycine and hydroxyproline).

Amphipaticity (spatial separation of hydrophobic and hydrophillic groups) will also favor the formation of secondary-structures.  For a helix, spacing hydrophobic groups 3-4 residues apart will create an amphipathic helix, while having hydrophobic residues at every other residue will create an amphipathic beta-sheet.

Ah Beng

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Re:Secondary structure of proteins - alpha-helix and beta-pleated
« Reply #2 on: January 31, 2006, 01:02:29 AM »
That's a very comprehensive and enlightening answer. Thanks again for your reply, Yggdrasil! Much appreciated! :)

Offline Equi

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Re:Secondary structure of proteins - alpha-helix and beta-pleated
« Reply #3 on: January 31, 2006, 04:43:42 PM »
Put in another way, can the same polypeptide take on the alpha-helix structure under certain conditions, and yet take on the beta-pleated structure under other conditions?
Taking the spider web fluid proteins as an example this can happen. Inside the spider the filaments exist as alpha helices and change their conformation to a beta pleated sheets when used to build a spider web, due to dehydration.
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Ah Beng

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Re:Secondary structure of proteins - alpha-helix and beta-pleated
« Reply #4 on: January 31, 2006, 10:53:21 PM »
>>> Taking the spider web fluid proteins as an example this can happen. Inside the spider the filaments exist as alpha helices and change their conformation to a beta pleated sheets when used to build a spider web, due to dehydration. <<<

Ahhh, so from your work, you've confirmed that its possible for certain (but probably very few) polypeptides to take on either secondary structure (alpha-helix vs beta-pleated), under different conditions, such as hydration vs dehydration.

Thanks again, Equi and Yggdrasil both! :)

savoy7

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Re:Secondary structure of proteins - alpha-helix and beta-pleated
« Reply #5 on: March 18, 2006, 12:31:55 PM »
Reviewing some of the posts I noticed this one.  This is an interesting question to me.  

Can a protein with the same AA sequence have a different shape?

This question brought up Prion theory.  The PrP protein.  PrP stands for prion-related protein.  It earned Prusiner the 1997 Nobel.  The normal protein found in humans changes shape when in contact with the PrP protein.  

I have enclosed the shapes.  

Notice that the normal protein has more alpha-helixes than the prion protein which has more beta sheets.

Normal on the left, abnormal on the right
« Last Edit: March 18, 2006, 12:33:49 PM by savoy7 »

Offline Equi

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Re:Secondary structure of proteins - alpha-helix and beta-pleated
« Reply #6 on: March 19, 2006, 07:05:37 AM »
Reviewing some of the posts I noticed this one.  This is an interesting question to me.  

Can a protein with the same AA sequence have a different shape?

This question brought up Prion theory.  The PrP protein.  PrP stands for prion-related protein.  It earned Prusiner the 1997 Nobel.  The normal protein found in humans changes shape when in contact with the PrP protein.  

I have enclosed the shapes.  

Notice that the normal protein has more alpha-helixes than the prion protein which has more beta sheets.

Normal on the left, abnormal on the right
That's "relatively easy" to explain: Every protein fold can have several energy minima. This makes bioinformatics so damn difficult, as we cannot recognise, whether we reached the right minium or not (and the extreme amount of data associated with this process). In cells, chaperones (HSPs) assists for the more complex folds, leading the protein to the "right" energy minimum.
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savoy7

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Re:Secondary structure of proteins - alpha-helix and beta-pleated
« Reply #7 on: March 19, 2006, 03:40:11 PM »
My post wasn't a question, just an example for the initial post.


Offline Equi

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Re:Secondary structure of proteins - alpha-helix and beta-pleated
« Reply #8 on: March 19, 2006, 06:53:32 PM »
My post wasn't a question, just an example for the initial post.
Pardon me. I thought one good turn deserves another ;-)
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