pH has a major influence on protein structure by altering electrostatic interactions. In order to illustrate this point, let us think about polylysine (a polypeptide chain consisting of only L-lysine residues). At pH 10 and above, polylysine forms an ahelix. At a pH of 7 and below, however, this same polypeptide chain assumes an unfolded conformation (often referred to as ‘random coil’ or ‘random conformation’).

1) Can you explain why this transition occurs at pHs below the pKa of Lys?

2) What other residue(s) might you expect to show a similar pattern of pH-dependent folding and unfolding?

3) The residue(s) you might expect based on charge to be capable of forming α-helices do not do so in water when they alone make up a polypeptide chain. Can you come up with a reasonable explanation for why this might be?

4) Speculate on what you think might happen to the pH-dependence of α-helix formation if you had a polypeptide chain consisting of both glutamate and lysine residues.

(1) Remember that this occurred in a polylysine which consists only of L-Lys, the pKa of Lys residues might be different in polylysine as compared with the free amino acid in the solution.

The transition can also occur if more than 50% of the lysine residues need to be charged in order to ‘break’ the helix. Note that there is a 50:50 ratio of the coordinated bond of protons and dissociated forms.

(2) Other residues that are positively charged at neutral pH. They are arginine and histidine.

(3) Both arginine and histidine are more voluminous than Lys. Steric interference can prohibit the formation of an α-helices.