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I know how they fold, but what causes some polypeptide chains to preferably fold into Alpha-helix rather than Beta-sheets (or vice-versa). What force makes it fold into one conformation over the other?

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    $\begingroup$ look into the primary sequence and the energy minimization if you are into the computational side of things. This (en.wikipedia.org/wiki/Protein_folding) should help. $\endgroup$ – Bez Oct 23 '14 at 0:57
  • $\begingroup$ I don't think this is homework. This is about relative preference of structures (this is usually not explained in detail in textbooks) $\endgroup$ – WYSIWYG Oct 23 '14 at 10:19
  • $\begingroup$ I'll answer this question in a while. Meanwhile you can have a look at Ramachandran Plot $\endgroup$ – WYSIWYG Oct 23 '14 at 10:26
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All the residues in a polypeptide chain tends to configure into their lowest potential energy state. except the peptide bond all the other bonds are free to rotate, alpha helix makes optimal use of internal H bonds. The overall structure is stabilized by H bond between the hydrogen atom attached to the electronegative nitrogen atom of peptide linkage and the electronegative carbonyl oxygen atom. The arrangement of amino acids in the peptide plays a very important role in forming alpha helix. Different combination of amino acids results in different combination of dihedral angels, hence it determines alpha helix conformation.

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