pH-Dependent Conformational Changes Due to Ionizable Residues in a Hydrophobic Protein Interior: The Study of L25K and L125K Variants of SNase

Ionizable residues in the hydrophobic interior of certain proteins are known to play important roles in life processes like energy transduction and enzyme catalysis. These internal ionizable residues show experimental apparent pKₐ values having large shifts as compared to their values in solution. In the present work, we study the pH-dependent conformational changes undergone by two variants of staphylococcal nuclease (SNase), L25K and L125K, using pH replica exchange molecular dynamics (pH-REMD) in explicit solvent. Our results show that the observed pKₐ of Lys25 and Lys125 are significantly different than their pKₐ in solution. We observed that the internal lysine residues prefer to be water-exposed when protonated at low pH, but they remain buried within the hydrophobic pocket when deprotonated at high pH. Using thermodynamic laws, we estimate the microscopic conformation-specific pKₐ of the water-exposed and buried conformations of the internal lysine residues and explain their relation to the macroscopic observed pKₐ values. We present the differences in the microscopic mechanisms that lead to similar experimentally observed apparent pKₐ of Lys25 and Lys125, and explain the need of thermodynamic models of different complexities to account for our calculations. We see that L25K displays pH-dependent fluctuations throughout the entire β barrel and the α1 helix. In contrast, pH-independent fluctuations are observed in L125K, primarily limited to the α3 helix. The present computational study offers a detailed atomistic understanding of the determinants of the observed anomalous pKₐ of internal ionizable residues, bolstering the experimental findings.