Electronic Thesis and Dissertation Repository


Master of Science




Lars Konermann


Here, we apply Molecular Dynamics (MD) simulations to investigate fundamental aspects of structural mass spectrometry (MS). We first examine microscopic phenomena underlying Hydrogen/Deuterium exchange (HDX). HDX interrogates structural dynamics of proteins by measuring the rate of Deuterium uptake into backbone amides. We perform microsecond MD simulations on ubiquitin to investigate this process. We find that HDX protection often cannot be explained by H‑bonding or solvent accessibility considerations. These findings caution against non-critical use of HDX data in structural contexts. We next use MD to examine the Electrospray ionization (ESI) mechanism of proteins. ESI is a soft ionization technique resulting in the production of gaseous protein ions. The mechanism of ion formation from nanometer sized droplets is unclear. We apply a trajectory stitching MD approach to simulate protein-containing nanodroplets, finding that natively‑folded proteins remain solvated as droplets shrink. Residual charge carriers remain following desolvation, consistent with Dole’s charged residue model.