pH sensitive properties of ionizable residues in a hydrophobic protein interior

Internal ionizable residues in proteins display anomalous pKa values. An atomistic understanding of factors determining the shifted pKa values is important in obtaining insights into the mechanisms driving important biological processes such as enzyme catalysis and energy transduction. We study the diversity of the pH dependent conformational changes undergone by several mutants of staphylococcal nuclease (SNase), driven by the presence of a single internal ionizable residue, using pH Replica Exchange molecular dynamics simulations (pH-REMD). We present thermodynamic models to calculate the ‘conformation-specific pKa’ of the water-exposed and buried conformations of the internal ionizable residues and explain it in association with the observed anomalous ‘apparent pKa’. We further investigate the pH sensitive structural and thermodynamic properties driven by the presence of two ionizable residues within the hydrophobic interiors.