Linking Gas-Phase and Solution-Phase Protein Unfolding via Mobile Proton Simulations

• Published in: Analytical chemistry (Washington) Vol. 94; no. 46; pp. 16113 - 16121
• Main Authors: Eldrid, Charles, Cragnolini, Tristan, Ben-Younis, Aisha, Zou, Junjie, Raleigh, Daniel P., Thalassinos, Konstantinos
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 22-11-2022
• Subjects: Algorithms; Chemistry; Fluorescence; Fluorescent indicators; Ionic mobility; Ions - chemistry; Mass spectrometry; Mass spectroscopy; Molecular dynamics; Molecular Dynamics Simulation; Protein Conformation; Protein folding; Protein Unfolding; Proteins; Proteins - chemistry; Protons; Vapor phases
• ISSN: 0003-2700; 1520-6882; 1520-6882
• DOI: 10.1021/acs.analchem.2c03352

Native mass spectrometry coupled to ion mobility (IM-MS) combined with collisional activation (CA) of ions in the gas phase (in vacuo) is an important method for the study of protein unfolding. It has advantages over classical biophysical and structural techniques as it can be used to analyze small volumes of low-concentration heterogeneous mixtures while maintaining solution-like behavior and does not require labeling with fluorescent or other probes. It is unclear, however, whether the unfolding observed during collision activation experiments mirrors solution-phase unfolding. To bridge the gap between in vacuo and in-solution behavior, we use unbiased molecular dynamics (MD) to create in silico models of in vacuo unfolding of a well-studied protein, the N-terminal domain of ribosomal L9 (NTL9) protein. We utilize a mobile proton algorithm (MPA) to create 100 thermally unfolded and coulombically unfolded in silico models for observed charge states of NTL9. The unfolding behavior in silico replicates the behavior in-solution and is in line with the in vacuo observations; however, the theoretical collision cross section (CCS) of the in silico models was lower compared to that of the in vacuo data, which may reflect reduced sampling.