The pH Dependence of Protonation States of Polar Amino Acid Residues Determined by Neutron Diffraction

Abstract

The charges of various amino-acid side chains depend on the pH. For example, at a high pH (low acidity conditions), carboxylic acids tend to be negatively charged (deprotonated), and amines tend to be uncharged (unprotonated). At a low pH (high acidity), the opposite is true. The pH at which exactly half of any ionized amino acid is charged in solution is called the pKa of that amino acid. These pKa values of such ionizable amino-acid side chains are tabulated in standard textbooks. However, the protonation state of a given amino-acid side chain in a protein cannot be estimated from standard pKa values measured from isolated amino acids in solution, because inside a protein it may vary significantly depending on the local environment. The electrically charged states of the amino-acid residues are very important in understanding the physiological function of the protein, the interaction between ligands and proteins, molecular recognition, structural stability, and so on. Neutron Protein Crystallography (NPC) is the unique method to provide the definite protonation states of the amino acid residue in proteins because neutron can identify not only hydrogen atoms but also protons. (N.Niimura et al. 2004,2006, N.Niimura & R. Bau 2008, N.Niimura & A. Podjarny 2011)