PKAD-2: New Entries and Expansion of Functionalities of the Database of Experimentally Measured pKa's of Proteins

Abstract

Almost all biological reactions are pH-dependent and understanding the origin of pH dependence requires knowledge of the pKa's of ionizable groups. Here, we report a new edition of PKAD, the PKAD-2, which is a database of experimentally measured pKa's of proteins, both wild-type and mutant proteins. The new addition includes 117 wild-type and 54 mutant pKa values, resulting in total 1742 experimentally measured pKa's. The new edition of PKAD-2 includes eight new wild-type and 12 new mutant proteins, resulting in total of 220 proteins. This new edition incorporates a visual 3D image of the highlighted residue of interest within the corresponding protein or protein complex. Hydrogen bonds (HB) were identified, counted and implemented as a search feature. Other new search features include the number of neighboring <4 Å from the heaviest atom of the side chain of a given amino acid. Here, we present PKAD-2 with the intention to continuously incorporate novel features and current data with the goal to be used as a benchmark for computational methods.