Possible mechanisms for protecting N [sbnd]C α bonds in helical peptides from electron-capture (or transfer) dissociation

Abstract

Ab initio electronic structure simulations are carried out on small alanine-based peptide fragments with an excess electron added to a Coulomb-stabilized amide OCN π* orbital that forms a C O − radical anion center. A focus of the study is to determine to what extent and by what means helix-involved N C α bonds are “protected” against cleavage compared to similar bonds in non-helical peptides. The primary findings, many of which support earlier suggestions, include: (1) There is little or no increase in the energy barriers for N C α bond cleavage caused by an amino acid being in a helix where its carbonyl oxygen is involved in a hydrogen bond to an H N bond of an amino acid displaced by one helix turn. (2) When an electron attaches to a helix-involved Coulomb-stabilized OCN π* orbital and the N C α bond cleaves, three hydrogen bonds act to bind together the c and z fragment ions. One of these hydrogen bonds is especially strong (ca. 16 kcal mol −1) because it involves a negatively charged oxygen center. This suggests that the “protection” against N C α cleavage of helix-involved amino acids may, as others suggested earlier, result from the strong hydrogen bonding that binds the c and z fragment ions. (3) When an electron attaches to a helix-involved OCN π* orbital, an electron can migrate to the π* orbital of another amino acid one turn down the helix, but only by overcoming a barrier. After migrating to a new amino acid, N C α cleavage can occur at the latter site, also in line with what earlier workers have suggested. Suggestions of experiments that might test the hypotheses treated here are also put forth.