Hello,
I was wondering how to tackle secondary structure prediction. I realize that it is an imperfect type of prediction given that it seems that any amino acids can potentially form an alpha helix or beta sheet.
My textbook says that the presence of hydrophobic residues, such as valine and isoleucine are less likely to form alpha helixes because they are bulky. However, a problem that I was given (determine the secondary structure of : ile-lys-ser-leu-phe-val-asn-met-ala-leu-tyr-glu-ile) seems to contradict this because the correct answer is an alpha helix. They say that the alpha helix can be amphipathic in that it alternates around every 3 residues from hydrophobic to hydrophilic, but in the example the whole A.A doesn't follow this - so I am wondering why the answer is an alpha helix and not a beta sheet. I was also wondering does it matter at which A.A. you start counting from?
I guess the biggest problem for me is because there is no cut and dry method of predicting it. The rules of thumb that are put in the textbook don't really seem to be helpful. I was wondering what exactly takes precedence when predicting secondary structure? Is it the residues polarity / size ??
I read also somewhere else that in an alpha helix one is less likely to find two hydrophobic residues spaced 3-4 A.A apart as well as amino acids with the same charge (because of like charges repelling). I understand this but they also go on to say that a hydrophobic residues that are spaced one or two A.A. would also disfavour an alpha helix, but I have trouble understanding this concept because it the residues coil into a turn i.e., even if you had a hydrophobic residue at A.A. # 1, shouldn't there would be an difference in angle to perhaps accommodate another hydrophobic residue?
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