Question

When you mutate a Gly residue that immediately follows an alpha-helix to an Ala residue, the protein becomes less stable of 2.0 kcal/mol. Explain the molecular basis of this result.

Answer 1

The energetics of alpha-helix formation are fairly well understood and the helix content of a given amino acid sequence can be calculated with reasonable accuracy from helix-coil transition theories that assign to the different residues specific effects on helix stability.

In internal helical positions, alanine is regarded as the most stabilizing residue, whereas glycine, after proline, is the more destabilizing.

The difference in stabilization afforded by alanine and glycine has been explained by invoking various physical reasons, including the hydrophobic effect and the entropy of folding.

Alanine consistently stabilizes the helical conformation relative to glycine because it buries more apolar area upon folding and because its backbone entropy is lower.

However, the relative contribution of polar area burial (which is shown to be destabilizing) and of backbone entropy critically depends on the approximation used to model the structure of the denatured state.

In this respect, the excised-peptide model of the unfolded state, proposed by Creamer and coworkers (1995), predicts a major contribution of polar area burial, which is in good agreement with recent quantitations of the relative enthalpic contribution of Ala and Gly residues to alpha-helix formation.