Abstract
Internal ionizable residues in proteins have shifted apparent pKa values with respect their intrinsic pKa in bulk water. To understand the atomistic mechanism responsible for this shift in pKa, we study the pH-dependent conformational changes in mutants of Staphylococcal Nuclease (SNase) having single internal ionizable residues. We used pH Replica Exchange Molecular Dynamics (pH-REMD) for our calculations. We present thermodynamic models to find the ‘conformation-specific pKa values’ of the internal ionizable residues and explain their association with the observed ‘apparent pKa’. Further, we study the pH-dependent structural and thermodynamic properties of ionizable residue pairs within the hydrophobic interior of SNase.
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