Structural Stability from Solution to the Gas Phase: Native Solution Structure of Ubiquitin Survives Analysis in a Solvent-Free Ion Mobility–Mass Spectrometry Environment

TLDR

Desolvated ubiquitin ions were characterized by ion mobility spectrometry using an in‑house two‑meter helium drift tube coupled to a quadrupole time‑of‑flight mass spectrometer. Native‑state ubiquitin remains compact in the gas phase, matching the solution native cross‑section (~1000 Ų), while A‑state ions unfold to larger conformations (1800–2000 Ų) and decay more rapidly within ≤50 ms.

Abstract

The conformations of desolvated ubiquitin ions, lifted into the gas phase by electrospray ionization (ESI), were characterized by ion mobility spectrometry (IMS) and compared to the solution structures they originated from. The IMS instrument combining a two-meter helium drift tube with a quadrupole time-of-flight mass spectrometer was built in-house. Solutions stabilizing the native state of ubiquitin yielded essentially one family of tightly folded desolvated ubiquitin structures with a cross section matching the size of the native state (1000 Å(2)). Solutions favoring the A state yielded several well-defined families of significantly unfolded conformations (1800-2000 Å(2)) matching in size conformations between the A state and a fully unfolded state. On the basis of these results and a wealth of data available in the literature, we conclude that the native state of ubiquitin is preserved in the transition from solution to the desolvated state during the ESI process and survives for >100 ms in a 294 K solvent-free environment. The A state, however, is charged more extensively than the native state during ESI and decays more rapidly following ESI. A state ions unfold on a time scale equal to or shorter than the experiment (≤50 ms) to more extended structures.