Toward Site Specificity of Oxidative Damage in Proteins:  C−H and C−C Bond Dissociation Energies and Reduction Potentials of the Radicals of Alanine, Serine, and Threonine ResiduesAn ab Initio Study

High-level ab initio computations were used to characterize the parent species and α C radicals for alanine, serine, and threonine, both as free neutral amino acids (AH) and as residues in model peptides (PH) intended to mimic the midchain environment in proteins. The ab initio energies were used in isodesmic reactions to predict bond dissociation energies (BDEs, D α CH ) at 298 K, in kJ mol -1, to an estimated accuracy of ±10 kJ mol -1 . For the fully optimized systems the values of D α CH are AH(Gly), 331; AH(Ala), 317; AH(Ser), 327; AH(Thr), 328; PH(Gly), 348; PH(Ala), 344; PH(Ser), 348; PH(Thr), 356. All of the D α CH values are less than the BDE of a typical SH bond (370 kJ mol -1 ), as in cysteine or glutathione (GSH), a result that suggests that oxidative damage at the α C site will not be repaired efficiently by the mechanism of H donation from GSH. Values of D α CH in typical peptide conformations, such as β-sheet and α-helical secondary structure, were estimated by constraining the Ramachandran dihedral angles, Φ and Ψ, to values typical of these structures. Thus D α CH values are estimated as PH(Gly), 361; PH(Ala), 359; PH(Ser), 347; PH(Thr), 356 in the β-sheet conformation, and PH(Gly), 402; PH(Ala), 384; PH(Ser), 381; PH(Thr), 363 in the α-helix conformation. Hence, these residues are also expected to be susceptible to irreparable oxidative damage in β-sheet structures, but Gly, Ala, and Ser residues in α-helical regions should be less susceptible to damage and should be repairable by GSH. A consideration of reduction potentials calculated from the BDEs and entropies derived from the ab initio results leads to the same conclusions and indicates that certain radicals other than OH • that occur in cells (e.g., ROO • ) may also cause oxidative damage to β-sheet structures. Ab initio calculations were also done for the C-centered radicals formed by removal of H from the side chains. These showed that there is a marked increase in the ease of abstraction of this H in the series Ala, Ser, and Thr.