Release of lipid nanodiscs from charged nano-droplets in the electrospray ionization process revealed by microsecond atomistic molecular dynamics simulations

Electrospray ionization (ESI) prevents the analyte being split into fragments and is widely used to analyze biomolecules. Nanodiscs provide a native-like environment for membrane proteins, while making them accessible in aqueous solution for analysis. We performed microsecond (s) molecular dynamics simulations at different temperatures, to provide atomistic insight in the release of intact nanodiscs from charged nano-droplets, the late stage of the ESI process. Two distinct main scenarios, at-center and off-center, were observed. The at-center scenario follows the charged residue model, and in the process the nanodisc stays well in the droplet interior, with the membrane scaffold protein (MSP) keeping its annular geometry. As solvent evaporates, lipids turn over to protect the hydrophilic surface. The off-center scenario conforms to a hybrid model of the charged residue model and chain ejection model. The nanodisc migrates to the water/air interface, leading to lipids escaping from the dissociated dimer and the partial ejection of one monomer of MSP. A diversity of morphologies of product gaseous ions was observed, as evidenced by their structural details, collision cross sections and moments of inertia. Our results are in reasonable agreement with results of mass spectrometry in mass-to-charge ratio, charge state and collision cross section. Our work displays the first atomistic view of a heterogeneous system, a lipid nanodisc, releasing from highly charged nano-droplets into the gas phase, which may provide structural supports for the interpretation of mass spectra of complicated systems. What we observe in our simulations could also be generalized to other protein-lipid systems.