pKa's of ionizable groups and energetics of protein conformational transitions

It is well-known that the stability of proteins is pH-dependent because proteins contain groups capable of exchanging protons with their environment. In general, all conformational transitions of proteins might be expected to exhibit some pH-dependence. Using structural data for folded and partially unfolded forms of the Drosophila melanogaster engrailed homeodomain, we show that knowledge of the pK(a)'s of ionizable groups in different structural forms of a protein is not sufficient to determine pH-dependence of the free energy of its conformational transitions with accuracy better than 1 kcal/mol. We also describe a convenient computational approach for predicting expected errors when free energy of conformational transition is derived exclusively from the pK(a) values. This approach uses the full interaction free energy matrix between the ionizable sites, for the two forms of the protein, which can be determined when appropriate structural information is available.