The role of proton bridges in selective cleavage of Ser-, Thr-, Cys-, Met-, Asp-, and Asn-containing peptides

Abstract

Fragmentation patterns of doubly charged peptides containing serine (Ser), threonine (Thr), cysteine (Cys), homoserine (Hse), methionine (Met), aspartic acid (Asp), or asparagine (Asn) and terminating with arginine (Arg) were investigated. Stronger cleavages N-terminal to Ser, Thr, Cys, Asp, and Asn were observed in comparison to their C-terminal cleavages. In contrast, stronger cleavages C-terminal to Hse and Met were observed compared to their N-terminal cleavages. These fragmentation patterns can be explained by the relative stabilities of intramolecular proton bridges that form between the side chain heteroatoms (hydroxyl oxygen, carbonyl oxygen or sulfur) and the neighboring backbone carbonyl oxygens. Literature data and results from molecular dynamics are used to explain the stabilities of the proton bridges with different ring sizes based on the site of the bridge. For Ser, Thr, Cys, Asn and Asp, the proton bridge between the side chain and the adjacent N-terminal carbonyl is more stable and thus favored over the one to the adjacent C-terminal carbonyl, resulting in N-terminal enhanced cleavage. For Met and Hse, the proton bridge between the side chain and the C-terminal carbonyl is more stable, leading to C-terminal enhanced cleavages.