Empirical relationships between protein structure and carboxyl pKa values in proteins

AbstractRelationships between protein structure and ionization of carboxyl groups were investigated in 24 proteins of known structure and for which 115 aspartate and 97 glutamate pKa values are known. Mean pKa values for aspartates and glutamates are ≤ 3.4 (±1.0) and 4.1 (±0.8), respectively. For aspartates, mean pKa values are 3.9 (±1.0) and 3.1 (±0.9) in acidic (pI < 5) and basic (pI > 8) proteins, respectively, while mean pKa values for glutamates are approximately 4.2 for acidic and basic proteins. Burial of carboxyl groups leads to dispersion in pKa values: pKa values for solvent‐exposed groups show narrow distributions while values for buried groups range from < 2 to 6.7. Calculated electrostatic potentials at the carboxyl groups show modest correlations with experimental pKa values and these correlations are not improved by including simple surface‐area‐based terms to account for the effects of desolvation. Mean aspartate pKa values decrease with increasing numbers of hydrogen bonds but this is not observed at glutamates. Only 10 pKa values are > 5.5 and most are found in active sites or ligand‐binding sites. These carboxyl groups are buried and usually accept no more than one hydrogen bond. Aspartates and glutamates at the N‐termini of helices have mean pKa values of 2.8 (±0.5) and 3.4 (±0.6), respectively, about 0.6 units less than the overall mean values. Proteins 2002;48:388–403. © 2002 Wiley‐Liss, Inc.