Protein Ions Generated by Native Electrospray Ionization: Comparison of Gas Phase, Solution, and Crystal Structures

Experiments and molecular dynamics (MD) simulations in the literature indicate that gaseous proteins generated by electrospray ionization (ESI) can retain native-like structures. However, the exact properties of these ions remain to be explored. Focusing on ubiquitin and lysozyme, we examined several pertinent questions. (1) We applied solvent MD runs to test whether the X-ray structures of both proteins are affected by crystal packing. Main and side-chain orientations were retained in solution, providing a justification for the hitherto unscrutinized approach of relying on crystal data for "solution" versus gas-phase comparisons. (2) Most earlier gas-phase protein MD investigations employed short (ns) simulation windows. By extending this time frame to 1 μs, we were able to observe rare unfolding/folding transitions in ubiquitin. These predicted fluctuations were consistent with a semi-unfolded subpopulation detected by ion mobility spectrometry (IMS). (3) Most earlier modeling studies did not account for the high H⁺ mobility in gaseous proteins. For the first time, we compared static and mobile H⁺ simulations, focusing on both positively and negatively charged ions. The MD runs revealed a strong preference for retention of a solution-like backbone fold, whereas titratable/polar side chains collapsed onto the protein surface. This side-chain collapse was caused by a multitude of intramolecular salt bridges, H-bonds, and charge-dipole interactions. Our results generalize the findings of Steinberg et al. ( ChemBioChem, 2008, 9, 2417-2423) who had first proposed the occurrence of such side-chain contacts on the basis of short-term simulations with static H⁺. (4) Calculated collision cross sections of the MD conformers were in close agreement with IMS experiments. Overall, this study supports the view that solution-like protein structures can be retained because of kinetic trapping on the time scale of typical ESI-IMS experiments.