Pervasive Charge Solvation Permeates Native-like Protein Ions and Dramatically Influences Top-down Sequencing Data.

Abstract

Post-translational modifications create a diverse mixture of proteoforms, leading to substantial challenges in linking proteomic information to disease. Top-down sequencing of intact proteins and multiprotein complexes offers significant advantages in proteoform analysis, but achieving complete fragmentation for such precursor ions remains challenging. Intact proteins that undergo slow-heating generally fragment via charge directed (i.e., mobile proton) or charge remote fragmentation pathways. Our efforts seek to alter this paradigm by labeling proteins with trimethyl pyrylium (TMP), which forms a stable, positively charged label at lysine residues. Fixing positive charges to the protein sequence reduces the availability of mobile protons, driving fragmentation to charge remote channels. Furthermore, we demonstrate that capping acidic side chains with carbodiimide chemistry obstructs this pathway, restoring charge-directed fragmentation and resulting in more even coverage of the protein sequence. With large amounts of fixed charge and few mobile protons, we demonstrate that it is also possible to direct fragmentation almost exclusively to lysine residues containing the charged label. Finally, our data indicate that when electrosprayed under native conditions, protein ions possess an immense capacity to accommodate excess positive charge. Molecular dynamics simulations of such ions bearing intrinsically charged labels reveal evidence of numerous charge solvation processes, including the preferential formation of helices that solvate charged labels through interactions with their macro-dipoles. Thus, these studies reveal the extent to which intact gas-phase protein ions are capable of solvating charge, and provide the most complete indication to date of the extensive physical forces opposing the goal of comprehensive top-down protein sequencing.