Polyglutamate also exhibits pH-dependent unfolding. This transition occurs at a pH of about 7; below that pH the polypeptide chain is predominantly a-helical. Why is this transition for polyglutamate promoted by lowering the pH while the opposite applies to polylysine

Explanation:

As the pH drops, the NH2groups on the lysine side chains become charged and helices can no longer form because of charge repulsion between these groups. This might occur below the pKa of lysine if more than 50% of the lysine residues is to be charged in order to ‘break’ the helix. Another possibility is that the pKa of lysine residues might be different when in polylysine as compared with the monomer (free amino acid) in solution.

One will expect other residues that are positively charged at neutral pH to have a similar profile; namely, arginine and possibly histidine. Both arginine and histidine are bulkier than lysine. Even if there were some rotation of their side chains, steric interference would probably be so severe as to prohibit the formation of an -helix. The transition is inverted because at a low pH glutamate will be neutral whereas at a high pH it will assume a net negative charge (through dissociation of the carboxyl groups on its side chains). One will easily speculate that a polypeptide chain containing both glutamate and lysine residues will be able to form an helix at relatively neutral pHs. Under these conditions, lysines will be mostly positively charged and glutamates will be mostly negatively charged. This will allow these residues to make ionic bonds and salt bridges to stabilize the helix. At very low pH, however, lysine will be mostly positively charged, but it will be near to neutral glutamate residues. At very high pH, the Glu will be negatively charged, but it will be near neutral.