PPD a database of protein ionization constants

Introduction
The propensity of a compound to donate a proton is measured as its dissociation constant, or Ka. These Ka values cover a wide range of 10¹⁰ for the strongest acids such as sulfuric acid to 10^-50 for the weakest acids such as methane. A more convenient scale of acidity is pKa which is the negative logarithm of the Ka (pKa = -log Ka). Thus a Ka of 10¹⁰ becomes a pKa of -10, and a Ka of 10^-50 becomes a pKa of 50. In general, more negative pKa values correspond to stronger acids and more positive pKa values correspond to weaker acids.

Amino acid residues within proteins have pKa values that are determined by their micro-environments, the nature of their near neighbours, extent of hydrogen bonding, etc. and can take on a range of values radically different from those quoted in undergraduate text book. These values can be measured experimentally using a variety of methods, such as NMR or calculated from the 3-dimensional structure of a protein using a variety of methods, including the linearized Poisson-Boltzmann equation.

The PPD Database No compilation of protein pKa values exists and so it is appropriate to develop such a database, which can then serve as a standard for benchmarking calculational methods and strategies.

The PPD data was sourced from the primary literature and contains in excess of 1400 entries. The database contains pK_a values for amino acid side-chains, as well as the N and C termini,  over 75% of which focus on Glutamate, Lysine, Histidine and Aspartate. These four residues are all key ionizable residues, and therefore the apparent bias is not driven by our selection, but by the available experimental data. Very little data is currently available for Arginine: its pK_a value (~12) essentially precludes measurement by titration as proteins will denature at high basic pH.