Suppression of Protein Structural Perturbations in Native Electrospray Ionization during the Final Evaporation Stages Revealed by Molecular Dynamics Simulations

Native electrospray ionization was known to preserve the protein structure in solution, which overcame the uncontrollable acidification of droplets during transfer from solution into the gas phase in conventional electrospray ionization. However, detailed experimental studies on when and how could native electrospray ionization minimize structural perturbations remain quite unclear. Herein, we conducted molecular dynamics simulations to investigate the protein structure evolution during electrospray ionization. At a neutral droplet pH, the protein structure in solution could be retained after evaporation, which was in accordance with previous reports. As the droplet pH deviated from neutral, we have found that the compact protein structure would not unfold until the last 10 ns prior to the final desolvation, which demonstrated that the role of native electrospray ionization in preserving the protein structure was mainly reflected on the final evaporation stages. The present study might provide new insights into studying the microscopic biomolecular events occurring during the liquid–gas interface transition and their influence on solution–structure retention.