Protein pKa calculations

In computational biology, protein pKa calculations are used to estimate the pKa values of amino acids as they exist within proteins. These calculations complement the pKa values reported for amino acids in their free state, and are used frequently within the fields of molecular modeling, structural bioinformatics, and computational biology. In computational biology, protein pKa calculations are used to estimate the pKa values of amino acids as they exist within proteins. These calculations complement the pKa values reported for amino acids in their free state, and are used frequently within the fields of molecular modeling, structural bioinformatics, and computational biology. pKa values of amino acid side chains play an important role in defining the pH-dependent characteristics of a protein. The pH-dependence of the activity displayed by enzymes and the pH-dependence of protein stability, for example, are properties that are determined by the pKa values of amino acid side chains. The pKa values of an amino acid side chain in solution is typically inferred from the pKa values of model compounds (compounds that are similar to the side chains of amino acids). See Amino acid for the pKa values of all amino acid side chains inferred in such a way. There are also numerous experimental studies that have yielded such values, for example by use of NMR spectroscopy. The table below lists the model pKa values that are often used in a protein pKa calculation, and contains a third column based on protein studies.