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Name Miss Ankita Sarkar
Organization or Institution University of Florida
Presentation Type Poster
Topic Biophysical

pH-dependent properties of Ionizable Residues in the Hydrophobic Interior of Staphylococcal Nuclease


Ankita Sarkar, Adrian E. Roitberg

Author Institution(s)

University of Florida


Ionizable residues present in the hydrophobic interior of proteins, despite being rare, play major roles in important biological processes like energy transduction and enzyme catalysis. These internal residues display anomalous pKa values. An atomistic understanding of factors determining the anomalous pKa values is very important. In the present work, we study the diversity of the pH dependent conformational changes undergone by several mutants of staphylococcal nuclease (SNase), due to the presence of single internal ionizable residues, using constant pH Replica Exchange molecular dynamics. We present thermodynamic models to calculate the ‘conformation-specific microscopic pKa’ of the water-exposed and buried conformations of the internal ionizable residues and explain it in association with its observed anomalous ‘apparent pKa’. We further investigate the thermodynamic and structural consequences of the presence of an ionizable residue pair, within the hydrophobic interior of SNase.