Empirical relationships between protein structure and carboxyl pKa values in proteins

Abstract

Relationships between protein structure and ionization of carboxyl groups were investigated in 24 proteins of known structure and for which 115 aspartate and 97 glutamate pK a values are known. Mean pK a values for aspartates and glutamates are ≤ 3.4 (±1.0) and 4.1 (±0.8), respectively. For aspartates, mean pK a values are 3.9 (±1.0) and 3.1 (±0.9) in acidic (pI < 5) and basic (pI > 8) proteins, respectively, while mean pK a values for glutamates are approximately 4.2 for acidic and basic proteins. Burial of carboxyl groups leads to dispersion in pK a values: pK a 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 pK a values and these correlations are not improved by including simple surface‐area‐based terms to account for the effects of desolvation. Mean aspartate pK a values decrease with increasing numbers of hydrogen bonds but this is not observed at glutamates. Only 10 pK a 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 pK a 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.