[Protein-analysis] Re: alpha helix decapeptide(10 residue)

Dr Engelbert Buxbaum via proteins%40net.bio.net (by engelbert_buxbaum from hotmail.com)
Tue Oct 30 14:25:20 EST 2007


Am 30.10.2007, 08:16 Uhr, schrieb thinktank <dibyadeep from gmail.com>:

> Actually I dont have a bio background, but need to find a small alpha
> helix protein. The type or nature of the protein is not that
> important, except that it be small (preferably 10 residue) and tat it
> be alpha helix in nature. I though that possible a polyalanine
> decapeptide would be good. However I couldnt understand what the name
> this specific protein would have, since I felt the same protein might
> exist in multiple forms. I tried using the protein data bank, but with
> the multitude of results that I obtained, I couldn't understand which
> one of them would qualify for my requirements.
>
> I know this might seem very insignificant, but could you please help
> me by providing me with the name of such a protein, or by showing me
> how to go about finding one. Perhaps by telling me how such proteins
> are named?

Polyalanine is perfectly fine. However, this is an artificial peptide and  
its structure may not have been solved, so you'd not find a PDB-file for  
it. You could however use a helical stretch from a protein like  
haemoglobin. An interesting example would be the mitochondrial import  
sequence MLSLRQSIRFFKPATRTL from cytochrome c oxidase, which forms an  
amphipatic helix (all positive residues in one quadrant of the helix). The  
PDB-code (http://bip.weizmann.ac.il/oca-bin/ocamain) for the bovine heart  
enzyme is IV54. A free program to view such structures is DeepView  
(http://www.expasy.org/spdbv/index.html).


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