Question

Suppose you were asked to design a program to search a protein sequence database for sequences that may form a-helices and β-strands on the surface of a protein (so one side of the helix or strand is surface-exposed, and one side is buried in the protein), a. What kinds of patterns in the sequence would you search for? b. Give 15 residue-long examples of a-helix and p-strand that could be found in this position in the native structure of a protein

Answer 1

1. Alpha helix is right handed coil and rod like structure with NH group of 1st aminoacid residue forms hydrogen bond with CO group of 4th aminoacid. Where as beta strands are sheet like with NH group of one strand forms hydrogen bonding with CO group of another strand. Aminoacid preference in alpha helix are ala, leu, met, Glu, gln, his, lys, arg which are oriented ouside of the helix and are single chain where as beta sheet has preference for tyr, trp, phe, met,ile,cys, Val,thr which may be oriented both outside or inside.

2. Lys glu lys lys arg met his lys (alpha helix surface exposed 8 residue part of protein )/ trp phe tyr tyr cys met Val(hydrophonic buried 7 residue part of the protein). This long 15 residue is composed of initial 8 surface exposed residue and later 7 residue buried residue.