Pendular proteins in gases and new avenues for characterization of macromolecules by ion mobility spectrometry

Abstract

Polar molecules align in electric fields when the dipole energy (proportional to field intensity E ؋ dipole moment p) exceeds the thermal rotational energy. Small molecules have low p and align only at inordinately high E or upon extreme cooling. Many biomacromolecules and ions are strong permanent dipoles that align at E achievable in gases and room temperature. The collision cross-sections of aligned ions with gas molecules generally differ from orientationally averaged quantities, affecting ion mobilities measured in ion mobility spectrometry (IMS). Field asymmetric waveform IMS (FAIMS) separates ions by the difference between mobilities at high and low E and hence can resolve and identify macroion conformers based on the mobility difference between pendular and free rotor states. The exceptional sensitivity of that difference to ion geometry and charge distribution holds the potential for a powerful method for separation and characterization of macromolecular species. Theory predicts that the pendular alignment of ions in gases at any E requires a minimum p that depends on the ion mobility, gas pressure, and temperature. At ambient conditions used in current FAIMS systems, p for realistic ions must exceed Ϸ300 -400 Debye. The dipole moments of proteins statistically increase with increasing mass, and such values are typical above Ϸ30 kDa. As expected for the dipole-aligned regime, FAIMS analyses of protein ions and complexes of Ϸ30 -130 kDa show an order-of-magnitude expansion of separation space compared with smaller proteins and other ions. mass spectrometry ͉ protein structure S eparation and characterization of ions by using their drift in gases forced by electric field, called ion mobility spectrometry (IMS), is becoming common in analytical and structural chemistry (1-6). As with mass spectrometry (MS), initial applications were to small molecules (1, 5, 7) that could be readily ionized. Coupling to MS and to electrospray (ESI) and matrix-assisted laser desorption ionization (MALDI) ion sources in the 1990s (8, 9) brought IMS to biological analyses (2, 4, 6). In particular, peptide and protein folding (2, 4, 9-14) and amyloidogenic misfolding (15) were explored. Application of IMS and IMS/MS is expanding to ever-larger macromolecules, including noncovalent assemblies with mass (m) Ͼ 1 MDa (16-18). Such studies have used both drift tube (DT) IMS (1-5, 7-15) and differential mobility analyzers (DMA) (17, 18) to separate ions by absolute mobility (K). In DT IMS, ions are separated while being pulled through still gas by an electric field. In DMA (17-19) ions traverse a space between 2 electrodes while being displaced laterally by gas flow. Only ions of specific K (determined by the voltage across the gap and flow speed) exit the gap, and mobility spectra are obtained by scanning the voltage.Recently, field asymmetric waveform ion mobility spectrometry (FAIMS) or differential mobility spectrometry has emerged as a major analytical tool (6,(20)(21)(22)(23)(24)(25)(26)(27)(28). FAIMS filters ions based on th...

Ultrahigh-Resolution Differential Ion Mobility Separations of Conformers for Proteins above 10 kDa: Onset of Dipole Alignment?

“…Features in that region, previously consigned to proteins above ∼30 kDa, 42,44 are arguably due to pendular alignment of ions by strong field. The onset of alignment for proteins in the ∼10−20 kDa range is seconded by simulations 44 that show a miniscule fraction of unfolded protein conformers to reach the dipole moment threshold for alignment, despite much lower moment for the native conformation and average moment of the equilibrium geometry ensemble.…”

Differential Ion Mobility Separations in up to 100 % Helium Using Microchips

“…To quantify the E C shift upon transition from N 2 to He, we note that the FAIMS effect (except for large proteins that arguably exhibit dipole alignment [43]) mainly reflects that v deviates from a Maxwell-Boltzmann distribution when the drift velocity at peak field ( v D = KE D ) is not negligible relative to the mean ion-molecule velocity in Brownian motion ( v Br ). Thus, the scaling of E C as E D 3 (for type C ions) must fundamentally be due to the proportionality of Δ K to ( v D / v Br ) 3 .…”

Differential Mobility Spectrometry-Hydrogen Deuterium Exchange (DMS-HDX) as a Probe of Protein Conformation in Solution

“…The unfolded character of Tau is illustrated here both by the broad, high charge distribution and the exceptionally broad DMS profiles associated with each peak. Pendular alignment effects [10,12], which are expected for a 46 kDa protein, are observed in the bimodal appearance of the CV profile (Figure 2a, top panel). All proteins including Tau were subjected to extensive optimization of DMS separation, principally in the selection of modifier gas (Supplementary Figure S1).…”

“…For large proteins with significant molecular dipoles, a particular problem is field-induced alignment, which results in bimodal CV profiles for unimodal structural distributions [10,11]. As a result, there has been little effort to apply DMS to large biomolecules [12] and no success in linking gas-phase structural insights acquired by DMS to the liquid-phase conformational ensembles of proteins [13][14][15].…”