The effects of solution additives and gas-phase modifiers on the molecular environment and conformational space of common heme proteins

Investigating direct current potentials that affect native protein conformation during trapped ion mobility spectrometry-mass spectrometry

Trapped ion mobility spectrometry-time-of-flight mass spectrometry (TIMS-TOFMS) has emerged as a tool to study protein conformational states. In TIMS, gas-phase ions are guided across the IM stages by applying direct current (DC) potentials (D1-6), which, however, might induce changes in protein structures through collisional activation. To define conditions for native protein analysis, we evaluated the influence of these DC potentials using the metalloenzyme bovine carbonic anhydrase (BCA) as primary test compound. The variation of DC potentials did not change BCA-ion charge and heme content but affected (relative) charge-state intensities and adduct retention. Constructed extracted-ion mobilograms and corresponding collisional cross-section (CCS) profiles gave useful insights in (alterations of) protein conformational state. For BCA, the D3 and D6 potential (which are applied between the deflection transfer and funnel 1 [F1] and the accumulation exit and the start of the ramp, respectively) had most profound effects, showing multimodal CCS distributions at higher potentials indicating gradual unfolding. The other DC potentials only marginally altered the CCS profiles of BCA. To allow for more general conclusions, five additional proteins of diverse molecular weight and conformational stability were analyzed, and for the main protein charge states, CCS profiles were constructed. Principal component analysis (PCA) of the obtained data showed that D1 and D3 exhibit the highest degree of correlation with the ratio of folded and unfolded protein (F/U) as extracted from the mobilograms obtained per set D potential. The correlation of D6 with F/U and protein charge were similar, and D2, D4, and D5 showed an inverse correlation with F/U but were correlated with protein charge. Although DC boundary values for induced conformational changes appeared protein dependent, a set of DC values could be determined, which assured native analysis of most proteins.

Ion-shift reagent binding energy and the mass-mobility shift correlation in ion mobility spectrometry

RATIONALE

Ion mobility spectrometry (IMS) detects illegal substances and explosives in airports, ports, and customs. This is complicated by false positives caused by overlapping peaks. Shift reagents selectively change ion mobilities through adduction with analyte ions. This discriminates false positives because interferents and illegal substances respond differently to shift reagents.

METHODS

We introduced five different shift reagents using electrospray ionization-IMS-mass spectrometry to study the effect of interaction energy, intermolecular bonds, and analyte size on ion mobility shifts. Analyte ion-shift reagent interactions were calculated using Gaussian.

RESULTS

The mobility shifts showed a decreasing trend as the molecular weight increased for a series of ten compounds. The shift in drift time better reflected the pure effect of shift reagents. Valinol was an exception to this trend because it had a low binding energy interaction with all shift reagents and, consequently, its clusters were short-lived. This produced fewer collisions against the buffer gas and a shorter drift time, compared to ions of similar molecular weight.

CONCLUSIONS

The results of this investigation are important for understanding the behavior of shift reagents in resolving overlapping peaks that cause interferences. The suppression of false positives eases the transit of passengers and cargos, increases the confiscation of illicit substances, and saves money and distress due to needless delays in customs and airports.

Condensable Vapor Sorption by Low Charge State Protein Ions

Measurement of the gas-phase ion mobility of proteins provides a means to quantitatively assess the relative sizes of charged proteins. However, protein ion mobility measurements are typically singular values. Here, we apply tandem mobility analysis to low charge state protein ions (+1 and +2 ions) introduced into the gas phase by nanodroplet nebulization. We first determine protein ion mobilities in dry air and subsequently examine shifts in mobilities brought about by the clustering of vapor molecules. Tandem mobility analysis yields mobility-vapor concentration curves for each protein ion, expanding the information obtained from mobility analysis. This experimental procedure and analysis is extended to bovine serum albumin, transferrin, immunoglobulin G, and apoferritin with water, 1-butanol, and nonane. All protein ions appear to adsorb vapor molecules, with mobility "diameter" shifts of up to 6-7% at conditions just below vapor saturation. We parametrize results using κ-Köhler theory, where the term κ quantifies the extent of uptake beyond Köhler model expectations. For 1-butanol and nonane, κ decreases with increasing protein ion size, while it increases with increasing protein ion size for water. For the systems probed, the extent of mobility shift for the organic vapors is unaffected by the nebulized solution pH, while shifts with water are sensitive to pH.

Salt bridges govern the structural heterogeneity of heme protein interactions and porphyrin networks: microperoxidase-11

In this work, a proteolytic digest of cytochrome c (microperoxidase 11, MP-11) was used as a model to study the structural aspects of heme protein interactions and porphyrin networks. The MP-11 structural heterogeneity was studied as a function of the starting pH (e.g., pH 3.1-6.1) and concentration (e.g., 1-50 μM) conditions and adduct coordination. Trapped ion mobility spectrometry coupled to mass spectrometry (TIMS-MS) showed the MP-11 structural dependence of the charge state distribution and molecular ion forms with the starting pH conditions. The singly charged (e.g., [M]+, [M - 2H + NH4]+, [M - H + Na]+ and [M - H + K]+) and doubly charged (e.g., [M + H]2+, [M - H + NH4]2+, [M + Na]2+ and [M + K]2+) molecular ion forms were observed for all solvent conditions, although the structural heterogeneity (e.g., number of mobility bands) significantly varied with the pH value and ion form. The MP-11 dimer formation as a model for heme-protein protein interactions showed that dimer formation is favored toward more neutral pH and favored when assisted by salt bridges (e.g., NH4 +, Na+ and K+ vs. H+). Inspection of the dimer mobility profiles (2+ and 3+ charge states) showed a high degree of structural heterogeneity as a function of the solution pH and ion form; the observation of common mobility bands suggest that the different salt bridges can stabilize similar structural motifs. In addition, the salt bridge influence on the MP-11 dimer formations was measured using collision induced dissociation and showed a strong dependence with the type of salt bridge (i.e., a CE50 of 10.0, 11.5, 11.8 and 13.0 eV was observed for [2M + H]3+, [2M - H + NH4]3+, [2M + Na]3+ and [2M + K]3+, respectively). Measurements of the dimer equilibrium constant showed that the salt bridge interactions increase the binding strength of the dimeric species.

Following Structural Changes by Thermal Denaturation Using Trapped Ion Mobility Spectrometry-Mass Spectrometry

The behavior of biomolecules as a function of the solution temperature is often crucial to assessing their biological activity and function. While heat-induced changes of biomolecules are traditionally monitored using optical spectroscopy methods, their conformational changes and unfolding transitions remain challenging to interpret. In the present work, the structural transitions of bovine serum albumin (BSA) in native conditions (100 mM aqueous ammonium acetate) were investigated as a function of the starting solution temperature (T ∼ 23-70 °C) using a temperature-controlled nanoelectrospray ionization source (nESI) coupled to a trapped ion mobility spectrometry-mass spectrometry (TIMS-MS) instrument. The charge state distribution of the monomeric BSA changed from a native-like, narrow charge state ([M + 12H]12+ to [M + 16H]16+ at ∼23 °C) and narrow mobility distribution toward an unfolded-like, broad charge state (up to [M + 46H]46+ at ∼70 °C) and broad mobility distribution. Inspection of the average charge state and collision cross section (CCS) distribution suggested a two-state unfolding transition with a melting temperature Tm ∼ 56 ± 1 °C; however, the inspection of the CCS profiles at the charge state level as a function of the solution temperature showcases at least six structural transitions (T1-T7). If the starting solution concentration is slightly increased (from 2 to 25 μM), this method can detect nonspecific BSA dimers and trimers which dissociate early (Td ∼ 34 ± 1 °C) and may disturb the melting curve of the BSA monomer. In a single experiment, this technology provides a detailed view of the solution, protein structural landscape (mobility vs solution temperature vs relative intensity for each charge state).

Evaluating Separation Selectivity and Collision Cross Section Measurement Reproducibility in Helium, Nitrogen, Argon, and Carbon Dioxide Drift Gases for Drift Tube Ion Mobility-Mass Spectrometry

Previous ion mobility (IM) studies have demonstrated that varying the drift gas composition can be used to enhance chemical selectivity and resolution, yet there are few drift gas studies aimed at achieving quantitatively reproducible mobility measurements. Here, we critically evaluate the conditions necessary to achieve reproducible collision cross section (CCS) measurements in pure drift gases (helium, nitrogen, argon, and carbon dioxide) using a commercial uniform field drift tube instrument. Optimal experimental parameters are assessed based on the convergence of CCS measurements to reproducible values which are compared with literature values. A suite of calibration standards with diverse masses, biological classes, and charge states are examined to assess chemical selectivity and resolution achievable in each drift gas. Results indicate nitrogen and argon perform similarly and are sufficient for most applications where high resolving power and high peak capacity are desired. Carbon dioxide exhibits more selectivity for resolving structurally heterogeneous compounds, which may be preferable in specific analyte pair separations. Helium demonstrated modest separation capabilities but has utility for comparison to theoretical values and previously published work. In drift gases other than nitrogen, pressure differentials up to 230 mTorr between the drift tube and upstream chamber were optimal for improving correlation to literature values, while in nitrogen, the recommended pressure differential of 150 mTorr was found appropriate. We present recommended experimental parameters as well as gas-specific CCS measurements for structurally homogeneous sets of analytes which are suitable for use by other laboratories as standards for purposes of instrument calibration and overall assessment of IM separation performance.