Structure Relaxation Approximation (SRA) for Elucidation of Protein Structures from Ion Mobility Measurements

Ion mobility spectrometry-mass spectrometry methods offer the potential to correlate protein tertiary and quaternary structures to variations in their amino acid sequences and post-translational modifications. Because ion mobility spectrometry measures cross sections of ions in the gas phase, however, the structure of protein systems detected by ion mobility spectrometry will generally differ from their native solution structures. While it is now established that ion mobility spectrometry does not typically detect equilibrium gas-phase structures of protein systems, what remains disputed is which aspects, if any, of the detected ions resemble the native state present in solution. Here, we develop the structure relaxation approximation (SRA) method to predict charge-state specific ion mobility spectra from an ensemble of solution structures. This allows us to predict the "global" trends observed in the experiments for various experimental conditions and charge states, thereby enabling detailed structure elucidation. The SRA predicts (RMSD to experiment ∼4%) that even the small protein ubiquitin largely retains its native inter-residue contacts with an intact hydrophobic core when studied by "soft" ion mobility measurements. Because collisional activation is increasingly inefficient with increasing numbers of internal degrees of freedom, the SRA suggests that it is all the more likely that ion mobility spectrometry retains essentially the native state for protein systems larger than ubiquitin.