Proton Dynamics in Protein Mass Spectrometry

Abstract

Native electrospray ionization/ion mobility-mass spectrometry (ESI/IM-MS) allows an accurate determination of low-resolution structural features of proteins. Yet, the presence of proton dynamics, observed already by us for DNA in the gas phase, and its impact on protein structural determinants, have not been investigated so far. Here, we address this issue by a multistep simulation strategy on a pharmacologically relevant peptide, the N-terminal residues of amyloid-β peptide (Aβ(1-16)). Our calculations reproduce the experimental maximum charge state from ESI-MS and are also in fair agreement with collision cross section (CCS) data measured here by ESI/IM-MS. Although the main structural features are preserved, subtle conformational changes do take place in the first ∼0.1 ms of dynamics. In addition, intramolecular proton dynamics processes occur on the picosecond-time scale in the gas phase as emerging from quantum mechanics/molecular mechanics (QM/MM) simulations at the B3LYP level of theory. We conclude that proton transfer phenomena do occur frequently during fly time in ESI-MS experiments (typically on the millisecond time scale). However, the structural changes associated with the process do not significantly affect the structural determinants.

HIV-1 Gag protein with or without p6 specifically dimerizes on the viral RNA packaging signal

“…While the presence of the p6 domain had minimal effect on the oligomeric states observed, it did influence the charge state distribution. The multimodal charge state distribution observed for WT Gag is attributed to the presence of the intrinsically disordered p6 domain (37). As expected, dimerization depended on the well-characterized dimer interface in the C-terminal domain of CA, as WM-GagΔp6 was exclusively monomeric (Figures 2C1 and S3) (38,39).…”

Conformational Characterization and Classification of Intrinsically Disordered Proteins by Native Mass Spectrometry and Charge‐State Distribution Analysis

“…Native‐MS has been compared to fluorescence and CD spectroscopy in evaluating the effect of ammonium acetate on the conformation and the metal‐binding properties of two zinc‐finger domains, the nucleocapsid protein (NCp7, residues 12–55) of human immunodeficiency virus 1 and the specificity protein 1 (Sp1‐2, residues 565–595). The addition of increasing concentrations of ammonium acetate to protein‐Zn 2+ mixtures have a dramatic effect on the apparent affinity, as well as on the CSD, which is narrower and shifted toward lower charge states in the presence of the salt . Ammonium acetate is known to promote detection of non‐covalent complexes and native‐like protein conformations by native‐MS, thanks to counter‐ion binding at interfaces and to the possibility to modulate ionic strength without interfering with the ESI process .…”

“…Thus, the combined sets of results suggest that these specific protein–metal interactions are promoted by ammonium acetate in solution, by a mechanism mediated by conformational changes. The analysis has been extended to other salts of the Hofmeister series …”

“…MS‐based compaction index. A) Logarithm of the average charge states obtained by native‐MS ( Z av ) plotted against the logarithm of ProtSA‐derived SASA values ( A s ) for a set of fully disordered proteins (chemically denatured proteins or high‐charge component of intrinsically disordered proteins) . The line represents the linear fitting of the experimental results.…”

“…This technique has proven useful for structural analysis of IDP/Rs, their non‐covalent complexes with protein interactors or small ligands, and their amyloid oligomeric forms, even in high‐throughput experimental design. Several interesting reviews have been recently published on this topic . The present review, instead, focuses specifically on CSD analysis for structural characterization of IDP/Rs.…”