Conformational landscapes of ubiquitin, cytochrome c, and myoglobin: Uniform field ion mobility measurements in helium and nitrogen drift gas

Abstract

In this study, a commercial uniform field drift tube ion mobility-mass spectrometer (IM-MS) was utilized to measure the gas-phase conformational populations of three well-studied proteins: ubiquitin (8566Da), cytochrome c (12,359Da), and myoglobin in both apo and holo forms (16,951 and 17,567Da, respectively) in order to evaluate the use of this technology for broadscale structural proteomics applications. Proteins were electrosprayed from either acidic organic (pH∼3) or aqueous ammonium acetate (pH∼6.6) solution phase conditions, which generated a wide range of cation charge states corresponding to both extended (unfolded) and compact (folded) gas-phase conformational populations. Corresponding collision cross section (CCS) measurements were compiled for significant ion mobility peak features observed at each charge state in order to map the conformational landscapes of these proteins in both helium and nitrogen drift gases. It was observed that the conformational landscapes were similar in both drift gases, with differences being attributed primarily to ion heating during helium operation due to the necessity of operating the instrument with higher pressure differentials. Higher resolving powers were observed in nitrogen, which allowed for slightly better structural resolution of closely-spaced conformer populations. The instrumentation was found to be particularly adept at measuring low abundance conformers which are only present under gentle conditions which minimize ion heating. This work represents the single largest ion mobility CCS survey published to date for these three proteins with 266 CCS values and 117 ion mobility spectra, many of which have not been previously reported.