posted on 2024-03-01, 21:04authored byMichael
S. Cordes, Elyssia S. Gallagher
Unraveling the mechanism by which native proteins are
charged through
electrospray ionization (ESI) has been the focus of considerable research
because observable charge states can be correlated to biophysical
characteristics, such as protein folding and, thus, solution conformation.
Difficulties in characterizing electrosprayed droplets have catalyzed
the use of molecular dynamics (MD) to provide insights into the mechanisms
by which proteins are charged and transferred to the gas phase. However,
prior MD studies have utilized metal ions, primarily Na+, as charge carriers, even though proteins are primarily detected
as protonated ions in the mass spectra. Here, we propose a modified
MD protocol for simulating discrete Grotthuss diffuse H3O+ that is capable of dynamically altering amino-acid
protonation states to model electrospray charging and gaseous ion
formation of model proteins, ubiquitin, and myoglobin. Application
of the protocol to the evaporation of acidic droplets enables a molecular
perspective of H3O+ coordination and proton
transfer to/from proteins, which is unfeasible with the metal charge
carriers used in previous MD studies of ESI. Our protocol recreates
experimentally observed charge-state distributions and supports the
charge residue model (CRM) as the dominant mechanism of native protein
ionization during ESI. Additionally, our results suggest that protonation
is highly specific to individual residues and is correlated to the
formation of localized hydrated regions on the protein surface as
droplets desolvate. Considering the use of discrete H3O+ instead of Na+, the developed protocol is a necessary
step toward developing a more comprehensive model of protein ionization
during ESI.