Category: New Publication

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New Publication: Ion Mobility of Proteins in Nitrogen Gas: Effects of Charge State, Charge Distribution, and Structure


Ion Mobility of Proteins in Nitrogen Gas: Effects of Charge State, Charge Distribution, and Structure. Daniele Canzani, Kenneth J. Laszlo, Matthew F. Bush. J. Phys. Chem. A 2018, in press. (Link)

Ion mobility is emerging as a rapid and sensitive tool for structural characterization. Collision cross-section (Ω) values determined using ion mobility are often compared to values calculated for candidate structures generated through molecular modeling. Several methods exist for calculating Ω values, but the trajectory method explicitly includes contributions from long-range, ion–neutral interactions. Recent implementations of the trajectory method have significantly reduced its expense and have made applications to proteins far more tractable. Here, we use ion mobility experiments and trajectory method calculations to characterize the effects of charge state, charge distribution, and structure on the ion mobility of proteins in nitrogen gas. These results show that ion-induced dipole interactions Continue reading “New Publication: Ion Mobility of Proteins in Nitrogen Gas: Effects of Charge State, Charge Distribution, and Structure”

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New Publication: Effects of Charge State, Charge Distribution, and Structure on the Ion Mobility of Protein Ions in Helium Gas

Effects of Charge State, Charge Distribution, and Structure on the Ion Mobility of Protein Ions in Helium Gas: Results from Trajectory Method Calculations. Kenneth J. Laszlo, Matthew F. Bush. J. Phys. Chem. A, 2017, in press. (Link)

Collision cross section (Ω) values of gas-phase ions of proteins and protein complexes are used to probe the structures of the corresponding species in solution. Ions of many proteins exhibit increasing Ω-values with increasing charge state but most Ω-values calculated for protein ions have used simple collision models that do not explicitly account for charge. Here we use a combination of ion mobility mass spectrometry experiments with helium gas and trajectory method calculations to characterize the extents to which increases in experimental Ω-values with increasing charge state may be attributed to increased momentum transfer concomitant with enhanced long-range interactions between the protein ion and helium atoms. Continue reading “New Publication: Effects of Charge State, Charge Distribution, and Structure on the Ion Mobility of Protein Ions in Helium Gas”

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New Publication: Nonspecific aggregation in native electrokinetic nanoelectrospray ionization

Droplets_TOCNonspecific Aggregation in Native Electrokinetic Nanoelectrospray Ionization. Kimberly L. Davidson; Derek R. Oberreit; Christopher J. Hogan; Matthew F. Bush. Int. J. Mass Spectrom. 2016, DOI: 10.1016/j.ijms.2016.09.013. (Link)

Native mass spectrometry is widely used to determine the stoichiometries and binding constants of noncovalent interactions in solution. One challenge is that multiple analytes in a single electrospray droplet can aggregate during solvent evaporation, which will bias the distribution of oligomeric states observed during gas-phase measurements. Here, measurements of solution flow rates, electrospray currents, droplet size distributions, and nonspecific aggregation are used in conjunction with Poisson statistics to characterize the factors that control nonspecific aggregation during typical native mass spectrometry experiments. Continue reading “New Publication: Nonspecific aggregation in native electrokinetic nanoelectrospray ionization”

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New Publication: Radio-Frequency (rf) Confinement in Ion Mobility Spectrometry

rf_cofinement_toc_2Radio-Frequency (rf) Confinement in Ion Mobility Spectrometry: Apparent Mobilities and Effective Temperatures
Samuel J. Allen, Matthew F. Bush
J. Am. Soc. Mass Spectrom. 2016, DOI: 10.1007/s13361-016-1479-9. (Link)

Ion mobility is a powerful tool for separating and characterizing the structures of ions. Here, a radio-frequency (rf) confining drift cell is used to evaluate the drift times of ions over a broad range of drift field strengths (E/P, V cm–1 Torr–1). The presence of rf potentials radially confines ions and results in excellent ion transmission at low E/P (less than 1 V cm–1 Torr–1), thereby reducing the dependence of ion transmission on the applied drift voltage. Non-linear responses between drift time and reciprocal drift voltages are observed for extremely low E/P and high rf amplitudes. Under these conditions, pseudopotential wells generated by the rf potentials dampen the mobility of ions. The effective potential approximation Continue reading “New Publication: Radio-Frequency (rf) Confinement in Ion Mobility Spectrometry”

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New Publication: Folding of Protein Ions in the Gas Phase after Cation-to-Anion Proton-Transfer Reactions (CAPTR)

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Folding of Protein Ions in the Gas Phase after Cation-to-Anion Proton-Transfer Reactions (CAPTR)
Kenneth J Laszlo, Eleanor B. Munger, and Matthew F Bush
J. Am. Chem. Soc. 2016, DOI: 10.1021/jacs.6b04282. (Link)

The structure and folding of a protein in solution depends on noncovalent interactions within the protein and those with surrounding ions and molecules. Decoupling these interactions in solution is challenging, which has hindered the development of accurate physics-based models for structure prediction. Investigations of proteins in the gas phase can be used to selectively decouple factors affecting the structures of proteins. Here, we use Cation to Anion Proton Transfer Reactions (CAPTR) to reduce the charge states of denatured ubiquitin ions in the gas phase, and ion mobility to probe their structures. Continue reading “New Publication: Folding of Protein Ions in the Gas Phase after Cation-to-Anion Proton-Transfer Reactions (CAPTR)”

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New Publication: Analysis of Native-Like Proteins and Protein Complexes Using Cation to Anion Proton Transfer Reactions (CAPTR)

CAPTR_TOC_250Analysis of Native-Like Proteins and Protein Complexes Using Cation to Anion Proton Transfer Reactions (CAPTR). Kenneth J. Laszlo; Matthew F. Bush. J. Am. Soc. Mass Spectrom. 2015, in press. (Link)

Mass spectra of native-like protein complexes often exhibit narrow charge-state distributions, broad peaks, and contributions from multiple, coexisting species. These factors can make it challenging to interpret those spectra, particularly for mixtures with significant heterogeneity. Here we demonstrate the use of ion/ion proton transfer reactions to reduce the charge states of m/z-selected, native-like ions of proteins and protein complexes, a technique that we refer to as cation to anion proton transfer reactions (CAPTR). We then demonstrate that CAPTR can increase the accuracy of charge state assignments and the resolution of interfering species in native mass spectrometry. The CAPTR product ion spectra for pyruvate kinase exhibit ~30 peaks and enable unambiguous determination of the charge state of each peak, whereas the corresponding precursor spectra exhibit ~6 peaks and the assigned charge states have an uncertainty of ±3%. 15+ bovine serum albumin and 21+ yeast enolase dimer both appear near m/z 4450 and are completely unresolved in a mixture. After a single CAPTR event, the resulting product ions are baseline resolved. The separation of the product ions increases dramatically after each subsequent CAPTR event; 12 events resulted in a 3000-fold improvement in separation relative to the precursor ions. Finally, we introduce a framework for interpreting and predicting the figures of merit for CAPTR experiments. More generally, these results suggest that CAPTR strongly complements other mass spectrometry tools for analyzing proteins and protein complexes, particularly those in mixtures.

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New Publication: Collision cross section calibrants for negative ion mode traveling wave ion mobility-mass spectrometry

malic_acid_tocCollision cross section calibrants for negative ion mode traveling wave ion mobility-mass spectrometry. Jay G. Forsythe, Anton S. Petrov, Chelsea A. Walker, Samuel J. Allen, Jarrod S. Pellissier, Matthew F. Bush, Nicholas V. Hud, Facundo M. Fernández. Analyst 2015, 140, 6853-6861. (Link|PUBMED)

Abstract. Unlike traditional drift-tube ion mobility-mass spectrometry, traveling-wave ion mobility-mass spectrometry typically requires calibration in order to generate collision cross section (CCS) values. Although this has received a significant amount of attention for positive-ion mode analysis, little attention has been paid for CCS calibration in negative ion mode. Here, we provide drift-tube CCS values for [M − H]− ions of two calibrant series, polyalanine and polymalic acid, and evaluate both types of calibrants in terms of the accuracy and precision of the traveling-wave ion mobility CCS values that they produce.

  • For a perspective on this work, please see the feature that appeared on the main page for NASA Astrobiology (Link)
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New Publication: Comprehensive Analysis of Gly-Leu-Gly-Gly-Lys Peptide Dication Structures and Cation-Radical Dissociations Following Electron Transfer

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Comprehensive Analysis of Gly-Leu-Gly-Gly-Lys Peptide Dication Structures and Cation-Radical Dissociations Following Electron Transfer: From Electron Attachment to Backbone Cleavage, Ion-Molecule Complexes, and Fragment Separation Robert Pepin, Kenneth J. Laszlo, Bo Peng, Aleš Marek, Matthew F. Bush, František Tureček. J. Phys. Chem. A 2014, 118, 308–324. (Link|PUBMED)

Experimental data from ion mobility measurements and electron transfer dissociation were combined with extensive computational analysis of ion structures and dissociation energetics for Gly-Leu-Gly-Gly-Lys cations and cation radicals. Experimental and computational collision cross sections of (GLGGK + 2H)2+ ions pointed to a dominant folding motif that is represented in all low free-energy structures. The local folding motifs were Continue reading “New Publication: Comprehensive Analysis of Gly-Leu-Gly-Gly-Lys Peptide Dication Structures and Cation-Radical Dissociations Following Electron Transfer”

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New Publication: Effects of Polarity on the Structures and Charge States of Native-like Proteins and Protein Complexes in the Gas Phase

toc_polarity_120-01Native mass spectrometry and ion mobility spectrometry were used to investigate the gas-phase structures of selected cations and anions of proteins and protein complexes with masses ranging from 6–468 kDa. Under the same solution conditions, the average charge states observed for all native-like anions were less than those for the corresponding cations. Using an RF-confining drift cell, similar collision cross sections were measured in positive and negative ion mode suggesting that anions and cations have very similar structures. This result suggests that for protein and protein complex ions within this mass range, there is no inherent benefit to selecting a specific polarity for capturing a more native-like structure. For peptides and low-mass proteins, polarity and charge-state dependent structural changes may be more significant. The charged-residue model is most often used to explain the ionization of large macromolecules based on the Rayleigh limit, which defines the upper limit of charge that a droplet can hold. Because ions of both polarities have similar structures and the Rayleigh limit does not depend on polarity, these results cannot be explained by the charged-residue model alone. Rather, the observed charge-state distributions are most consistent with charge-carrier emissions during the final stages of analyte desolvation, with lower charge-carrier emission energies for anions than the corresponding cations. These results suggest that the observed charge-state distributions in most native mass spectrometry experiments are determined by charge-carrier emission processes; although the Rayleigh limit may determine the gas-phase charge states of larger species, e.g., virus capsids.

Effects of Polarity on the Structures and Charge States of Native-like Proteins and Protein Complexes in the Gas Phase Samuel J. Allen, Alicia M. Schwartz, Matthew F. Bush. Anal. Chem. 2013, 85, 12055–12061. (Link|PUBMED)

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New Publication: Hexamers of the Type II Secretion ATPase GspE from Vibrio cholerae with Increased ATPase Activity

dn1eThe type II secretion system (T2SS), a multiprotein machinery spanning two membranes in Gram-negative bacteria, is responsible for the secretion of folded proteins from the periplasm across the outer membrane. The critical multidomain T2SS assembly ATPase GspEEpsE had not been structurally characterized as a hexamer. Here, four hexamers of Vibrio cholerae GspEEpsE are obtained when fused to Hcp1 as an assistant hexamer, as shown with native mass spectrometry. The enzymatic activity of the GspEEpsE-Hcp1 fusions is ∼20 times higher than that of a GspEEpsE monomer, indicating that increasing the local concentration of GspEEpsE by the fusion strategy was successful. Crystal structures of GspEEpsE-Hcp1 fusions with different linker lengths reveal regular and elongated hexamers of GspEEpsE with major differences in domain orientation within subunits, and in subunit assembly. SAXS studies on GspEEpsE-Hcp1 fusions suggest that even further variability in GspEEpsE hexamer architecture is likely.

Hexamers of the Type II Secretion ATPase GspE from Vibrio cholerae with Increased ATPase Activity Connie Lu, Stewart Turley, Samuel T. Marionni, Young-Jun Park, Kelly K. Lee, Marcella Patrick, Ripal Shah, Maria Sandkvist, Matthew F. Bush, Wim G.J. Hol. Structure 2013, 21, 1707–1717. (Link|PUBMED)