PKAD: a database of experimentally measured pKa values of ionizable groups in proteins.

Swagata Pahari,Lexuan Sun,Emil Alexov

doi:10.1093/database/baz024

Abstract

Ionizable residues play key roles in many biological phenomena including protein folding, enzyme catalysis and binding. We present PKAD, a database of experimentally measured pKas of protein residues reported in the literature or taken from existing databases. The database contains pKa data for 1350 residues in 157 wild-type proteins and for 232 residues in 45 mutant proteins. Most of these values are for Asp, Glu, His and Lys amino acids. The database is available as downloadable file as well as a web server (http://compbio.clemson.edu/pkad). The PKAD database can be used as a benchmarking source for development and improvement of pKa’s prediction methods. The web server provides additional information taken from the corresponding structures and amino acid sequences, which allows for easy search and grouping of the experimental pKas according to various biophysical characteristics, amino acid type and others.

Highlights

Ionizable side chains in proteins play a key role in various functionalities of the corresponding proteins and protein complexes
Ionizable residues play a key role in protein folding [4, 5]. pH dependence of protein stability and conformations can be explained in many cases by perturbed pKa values of ionizable residues [6,7,8]
The database is accessible via http:// compbio.clemson.edu/pkad

Summary

Introduction

Ionizable side chains in proteins play a key role in various functionalities of the corresponding proteins and protein complexes. The ionization state of titratable residues affects the function, stability, structure and solubility of protein [1,2,3]. Ionizable residues play a key role in protein folding [4, 5]. PH dependence of protein stability and conformations can be explained in many cases by perturbed pKa values of ionizable residues [6,7,8]. It is very important to understand and predict the pKa values of ionizable groups of proteins and which are the factors contributing to the corresponding pKa shifts. PKa’s measurements have been performed using indirect techniques [14, 15] such as potentiometric titration, calorimetry, electrophoresis and high-performance liquid chromatography, typically resulting in larger error

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Conclusion