Peptide conformation

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BlackSails
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Peptide conformation

Postby BlackSails » Tue Sep 16, 2008 9:02 pm UTC

This was on a practice test given to us by my biochem prof:

You have the following peptide: (V-K)6-P-G-(V-K)5

In regular water, it exists in an extended conformation.

However, in an aqueous solution of high ionic strength, it exists in a much more compact configuration. What happens?



The only thing I can think of is: basically, by adding ions everywhere, you are making the solvent even more polar. This will force the peptide into a helix, proline residue be damned.

Is this correct, or does something else happen?

tantalum
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Re: Peptide conformation

Postby tantalum » Tue Sep 16, 2008 10:28 pm UTC

There are quite a few lysine residues on this peptide. All of these positively charged groups don't want to get close to each other (mutual charge repulsion), so the peptide spreads out. In a strongly ionic solution, the energy penalty for being spread out is much greater (think of it as the solvent being much 'thicker', so that it takes more energy to push the solvent molecules apart to make room for yourself). Also, the high ionic strength is better at stabilizing the positive charge.

These two effects combine to make the peptide fold up in a compact form. Dunno about the proline.. probably a red herring, as is the glycine.

Which university do you go to, btw? This is actually a pretty interesting question that I wouldn't expect from, say, a state school.

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BlackSails
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Re: Peptide conformation

Postby BlackSails » Tue Sep 16, 2008 10:37 pm UTC

NYU.


And duh, its not a glycine, its a glutamic acid. Thanks for pointing that out, thats something else I need to know for thursday. :oops:

Seli
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Re: Peptide conformation

Postby Seli » Wed Sep 17, 2008 11:08 am UTC

High ionic strength shields charges on the lysine residues.
The Valine-Lysine repeat should be prone to form beta-sheets, the proline-glycine/gutamic acid can easily form a turn.
I'd expect a hairpin turn with the KV repeats folded back on each other to form a (anti-parallel) beta-sheet.

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Sungura
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Re: Peptide conformation

Postby Sungura » Wed Sep 17, 2008 1:53 pm UTC

I am more inclined to think it will make a beta sheet.
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Yggdrasil
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Re: Peptide conformation

Postby Yggdrasil » Thu Sep 18, 2008 3:01 am UTC

The high ionic strength would also promote the hydrophobic effect which would act to bury the valines in a conformation with two beta strands stacked on eachother (remember on beta strands, every other residue ends up on the same side of the beta strand). The peptide would fold into a beta hairpin-like structure with the valine faces of the beta strands in the interior and the lysine faces solvent exposed. I wouldn't call this a beta hairpin or beta sheet because the beta strands in these structures are hydrogen-bonded together, not interacting via side-chains. Such a conformation is reminiscent of the stacking of beta strands in amyloid structures (i.e. prion proteins).


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