Are Acidic and Basic Groups in Buried Proteins Predicted to be Ionized? Original Research Article

Ionizable residues play essential roles in proteins, modulating protein stability, fold and function. Asp, Glu, Arg, and Lys make up about a quarter of the residues in an average protein. Multi-conformation continuum electrostatic (MCCE) calculations were used to predict the ionization states of all acidic and basic residues in 490 proteins. Of all 36,192 ionizable residues, 93.5% were predicted to be ionized. Thirtyfive percent have lost 4.08 kcal/mol solvation energy (ΔΔGrxn) sufficient to shift a pKa by three pH units in the absence of other interactions and 17% have ΔΔGrxn sufficient to shift pKa by five pH units. Overall 85% of these buried residues (ΔΔGrxn>5ΔpK units) are ionized, including 92% of the Arg, 86% of the Asp, 77% of the Glu, and 75% of the Lys. Ion-pair interactions stabilize the ionization of both acids and bases. The backbone dipoles stabilize anions more than cations. The interactions with polar side-chains are also different for acids and bases. Asn and Gln stabilize all charges, Ser and Thr stabilize only acids while Tyr rarely stabilize Lys. Thus, hydroxyls are better hydrogen bond donors than acceptors. Buried ionized residues are more likely to be conserved than those on the surface. There are 3.95 residues buried per 100 residues in an average protein.