1
|
Peris-Díaz MD, Wu S, Mosna K, Liggett E, Barkhanskiy A, Orzeł A, Barran P, Krężel A. Structural Characterization of Cu(I)/Zn(II)-metallothionein-3 by Ion Mobility Mass Spectrometry and Top-Down Mass Spectrometry. Anal Chem 2023; 95:10966-10974. [PMID: 37440218 PMCID: PMC10372872 DOI: 10.1021/acs.analchem.3c00989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 06/29/2023] [Indexed: 07/14/2023]
Abstract
Mammalian zinc metallothionein-3 (Zn7MT3) plays an important role in protecting against copper toxicity by scavenging free Cu(II) ions or removing Cu(II) bound to β-amyloid and α-synuclein. While previous studies reported that Zn7MT3 reacts with Cu(II) ions to form Cu(I)4Zn(II)4MT3ox containing two disulfides (ox), the precise localization of the metal ions and disulfides remained unclear. Here, we undertook comprehensive structural characterization of the metal-protein complexes formed by the reaction between Zn7MT3 and Cu(II) ions using native ion mobility mass spectrometry (IM-MS). The complex formation mechanism was found to involve the disassembly of Zn3S9 and Zn4S11 clusters from Zn7MT3 and reassembly into Cu(I)xZn(II)yMT3ox complexes rather than simply Zn(II)-to-Cu(I) exchange. At neutral pH, the β-domain was shown to be capable of binding up to six Cu(I) ions to form Cu(I)6Zn(II)4MT3ox, although the most predominant species was the Cu(I)4Zn(II)4MT3ox complex. Under acidic conditions, four Zn(II) ions dissociate, but the Cu(I)4-thiolate cluster remains stable, highlighting the MT3 role as a Cu(II) scavenger even at lower than the cytosolic pH. IM-derived collision cross sections (CCS) reveal that Cu(I)-to-Zn(II) swap in Zn7MT3 with concomitant disulfide formation induces structural compaction and a decrease in conformational heterogeneity. Collision-induced unfolding (CIU) experiments estimated that the native-like folded Cu(I)4Zn(II)4MT3ox conformation is more stable than Zn7MT3. Native top-down MS demonstrated that the Cu(I) ions are exclusively bound to the β-domain in the Cu(I)4Zn(II)4MT3ox complex as well as the two disulfides, serving as a steric constraint for the Cu(I)4-thiolate cluster. In conclusion, this study enhances our comprehension of the structure, stability, and dynamics of Cu(I)xZn(II)yMT3ox complexes.
Collapse
Affiliation(s)
- Manuel David Peris-Díaz
- Department
of Chemical Biology, Faculty of Biotechnology, University of Wrocław, F. Joliot-Curie 14a, 50-383 Wrocław, Poland
- Michael
Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United
Kingdom
| | - Sylwia Wu
- Department
of Chemical Biology, Faculty of Biotechnology, University of Wrocław, F. Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Karolina Mosna
- Department
of Chemical Biology, Faculty of Biotechnology, University of Wrocław, F. Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Ellen Liggett
- Michael
Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United
Kingdom
| | - Alexey Barkhanskiy
- Michael
Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United
Kingdom
| | - Alicja Orzeł
- Department
of Chemical Biology, Faculty of Biotechnology, University of Wrocław, F. Joliot-Curie 14a, 50-383 Wrocław, Poland
| | - Perdita Barran
- Michael
Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United
Kingdom
| | - Artur Krężel
- Department
of Chemical Biology, Faculty of Biotechnology, University of Wrocław, F. Joliot-Curie 14a, 50-383 Wrocław, Poland
| |
Collapse
|
2
|
Peris-Díaz MD, Barkhanskiy A, Liggett E, Barran P, Krężel A. Ion mobility mass spectrometry and molecular dynamics simulations unravel the conformational stability of zinc metallothionein-2 species. Chem Commun (Camb) 2023; 59:4471-4474. [PMID: 36960761 PMCID: PMC10089061 DOI: 10.1039/d2cc06559b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 02/10/2023] [Indexed: 03/25/2023]
Abstract
Ion mobility-mass spectrometry (IM-MS) unraveled different conformational stability in Zn4-7-metallothionein-2. We introduced a new molecular dynamics simulation approach that permitted the exploration of all of the conformational space confirming the experimental data, and revealed that not only the Zn-S bonds but also the α-β domain interactions modulate protein unfolding.
Collapse
Affiliation(s)
- Manuel David Peris-Díaz
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, F. Joliot-Curie 14a, 50-383 Wrocław, Poland.
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Alexey Barkhanskiy
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Ellen Liggett
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Perdita Barran
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Artur Krężel
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, F. Joliot-Curie 14a, 50-383 Wrocław, Poland.
| |
Collapse
|
3
|
Rolland AD, Biberic LS, Prell JS. Investigation of Charge-State-Dependent Compaction of Protein Ions with Native Ion Mobility-Mass Spectrometry and Theory. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:369-381. [PMID: 35073092 DOI: 10.1021/jasms.1c00351] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The precise relationship between native gas-phase protein ion structure, charge, desolvation, and activation remains elusive. Much evidence supports the Charge Residue Model for native protein ions formed by electrospray ionization, but scaling laws derived from it relate only to overall ion size. Closer examination of drift tube CCSs across individual native protein ion charge state distributions (CSDs) reveals deviations from global trends. To investigate whether this is due to structure variation across CSDs or contributions of long-range charge-dipole interactions, we performed in vacuo force field molecular dynamics (MD) simulations of multiple charge conformers of three proteins representing a variety of physical and structural features: β-lactoglobulin, concanavalin A, and glutamate dehydrogenase. Results from these simulated ions indicate subtle structure variation across their native CSDs, although effects of these structural differences and long-range charge-dependent interactions on CCS are small. The structure and CCS of smaller proteins may be more sensitive to charge due to their low surface-to-volume ratios and reduced capacity to compact. Secondary and higher order structure from condensed-phase structures is largely retained in these simulations, supporting the use of the term "native-like" to describe results from native ion mobility-mass spectrometry experiments, although, notably, the most compact structure can be the most different from the condensed-phase structure. Collapse of surface side chains to self-solvate through formation of new hydrogen bonds is a major feature of gas-phase compaction and likely occurs during the desolvation process. Results from these MD simulations provide new insight into the relationship of gas-phase protein ion structure, charge, and CCS.
Collapse
Affiliation(s)
- Amber D Rolland
- Department of Chemistry and Biochemistry, University of Oregon, 1253 University of Oregon, Eugene, Oregon 97403-1253, United States
| | - Lejla S Biberic
- Department of Chemistry and Biochemistry, University of Oregon, 1253 University of Oregon, Eugene, Oregon 97403-1253, United States
| | - James S Prell
- Department of Chemistry and Biochemistry, University of Oregon, 1253 University of Oregon, Eugene, Oregon 97403-1253, United States
- Materials Science Institute, University of Oregon, 1252 University of Oregon, Eugene, Oregon 97403-1252, United States
| |
Collapse
|
4
|
Lee JH, Pollert K, Konermann L. Testing the Robustness of Solution Force Fields for MD Simulations on Gaseous Protein Ions. J Phys Chem B 2019; 123:6705-6715. [DOI: 10.1021/acs.jpcb.9b04014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Justin H. Lee
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Katja Pollert
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| |
Collapse
|
5
|
Pukala T. Importance of collision cross section measurements by ion mobility mass spectrometry in structural biology. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2019; 33 Suppl 3:72-82. [PMID: 30265417 DOI: 10.1002/rcm.8294] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 09/17/2018] [Accepted: 09/19/2018] [Indexed: 06/08/2023]
Abstract
The field of ion mobility mass spectrometry (IM-MS) has developed rapidly in recent decades, with new fundamental advances underpinning innovative applications. This has been particularly noticeable in the field of biomacromolecular structure determination and structural biology, with pioneering studies revealing new structural insight for complex protein assemblies which control biological function. This perspective offers a review of recent developments in IM-MS which have enabled expanding applications in protein structural biology, principally focusing on the quantitative measurement of collision cross sections and their interpretation to describe higher order protein structures.
Collapse
Affiliation(s)
- Tara Pukala
- Discipline of Chemistry, University of Adelaide, North Terrace, Adelaide, South Australia, 5005
| |
Collapse
|
6
|
Chen X, Raab SA, Poe T, Clemmer DE, Larriba-Andaluz C. Determination of Gas-Phase Ion Structures of Locally Polar Homopolymers Through High-Resolution Ion Mobility Spectrometry-Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:905-918. [PMID: 30993642 DOI: 10.1007/s13361-019-02184-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 02/18/2019] [Accepted: 03/05/2019] [Indexed: 06/09/2023]
Abstract
The strong synergy arising from coupling two orthogonal analytical techniques such as ion mobility and mass spectrometry can be used to separate complex mixtures and determine structural information of analytes in the gas phase. A tandem study is performed using two systems with different gases and pressures to ascertain gas-phase conformations of homopolymer ions. Aside from spherical and stretched configurations, intermediate configurations formed by a multiply charged globule and a "bead-on-a-string" appendix are confirmed for polyethylene-glycol (PEG), polycaprolactone (PCL), and polydimethylsiloxane (PDMS). These intermediate configurations are shown to be ubiquitous for all charge states and masses present. For each charge state, configurations evolve in two distinctive patterns: an inverse evolution which occurs as an elementary charge attached to the polymer leaves the larger globule and incorporates itself into the appendage, and a forward evolution which reduces the globule without relinquishing a charge while leaving the appendix relatively constant. Forward evolutions are confirmed to form self-similar family shapes that transcend charge states for all polymers. Identical structural changes occur at the same mass over charge regardless of the system, gas or pressure strongly suggesting that conformations are only contingent on number of charges and chain length, and start arranging once the ion is at least partially ejected from the droplet, supporting a charge extrusion mechanism. Configurational changes are smoother for PDMS which is attributed to the larger steric hindrance caused by protruding pendant groups. This study has implications in the study of the configurational space of more complex homopolymers and heteropolymers. Graphical Abstract.
Collapse
Affiliation(s)
- Xi Chen
- Department of Mechanical Engineering, IUPUI, 723 W Michigan st, Indianapolis, IN, 46202, USA
- Department of Mechanical Engineering, Purdue Universiy, West Lafayette, IN, 47907, USA
| | - Shannon A Raab
- Department of Chemistry, Indiana University, 800 E Kirkwood Ave, Bloomington, IN, 47405, USA
| | - Timothy Poe
- Department of Mechanical Engineering, IUPUI, 723 W Michigan st, Indianapolis, IN, 46202, USA
| | - David E Clemmer
- Department of Chemistry, Indiana University, 800 E Kirkwood Ave, Bloomington, IN, 47405, USA
| | - Carlos Larriba-Andaluz
- Department of Mechanical Engineering, IUPUI, 723 W Michigan st, Indianapolis, IN, 46202, USA.
| |
Collapse
|
7
|
Kirk AT, Bohnhorst A, Raddatz CR, Allers M, Zimmermann S. Ultra-high-resolution ion mobility spectrometry-current instrumentation, limitations, and future developments. Anal Bioanal Chem 2019; 411:6229-6246. [PMID: 30957205 DOI: 10.1007/s00216-019-01807-0] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 03/15/2019] [Accepted: 03/25/2019] [Indexed: 12/29/2022]
Abstract
With recent advances in ionization sources and instrumentation, ion mobility spectrometers (IMS) have transformed from a detector for chemical warfare agents and explosives to a widely used tool in analytical and bioanalytical applications. This increasing measurement task complexity requires higher and higher analytical performance and especially ultra-high resolution. In this review, we will discuss the currently used ion mobility spectrometers able to reach such ultra-high resolution, defined here as a resolving power greater than 200. These instruments are drift tube IMS, traveling wave IMS, trapped IMS, and field asymmetric or differential IMS. The basic operating principles and the resulting effects of experimental parameters on resolving power are explained and compared between the different instruments. This allows understanding the current limitations of resolving power and how ion mobility spectrometers may progress in the future. Graphical abstract.
Collapse
Affiliation(s)
- Ansgar T Kirk
- Institute of Electrical Engineering and Measurement Technology, Department of Sensors and Measurement Technology, Leibniz Universität Hannover, Appelstr. 9A, 30167, Hannover, Germany.
| | - Alexander Bohnhorst
- Institute of Electrical Engineering and Measurement Technology, Department of Sensors and Measurement Technology, Leibniz Universität Hannover, Appelstr. 9A, 30167, Hannover, Germany
| | - Christian-Robert Raddatz
- Institute of Electrical Engineering and Measurement Technology, Department of Sensors and Measurement Technology, Leibniz Universität Hannover, Appelstr. 9A, 30167, Hannover, Germany
| | - Maria Allers
- Institute of Electrical Engineering and Measurement Technology, Department of Sensors and Measurement Technology, Leibniz Universität Hannover, Appelstr. 9A, 30167, Hannover, Germany
| | - Stefan Zimmermann
- Institute of Electrical Engineering and Measurement Technology, Department of Sensors and Measurement Technology, Leibniz Universität Hannover, Appelstr. 9A, 30167, Hannover, Germany
| |
Collapse
|
8
|
Bakhtiari M, Konermann L. Protein Ions Generated by Native Electrospray Ionization: Comparison of Gas Phase, Solution, and Crystal Structures. J Phys Chem B 2019; 123:1784-1796. [DOI: 10.1021/acs.jpcb.8b12173] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Maryam Bakhtiari
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| |
Collapse
|
9
|
Lippens JL, Ranganathan SV, D'Esposito RJ, Fabris D. Modular calibrant sets for the structural analysis of nucleic acids by ion mobility spectrometry mass spectrometry. Analyst 2018; 141:4084-99. [PMID: 27152369 DOI: 10.1039/c6an00453a] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
This study explored the use of modular nucleic acid (NA) standards to generate calibration curves capable of translating primary ion mobility readouts into corresponding collision cross section (CCS) data. Putative calibrants consisted of single- (ss) and double-stranded (ds) oligo-deoxynucleotides reaching up to ∼40 kDa in size (i.e., 64 bp) and ∼5700 Å(2) in CCS. To ensure self-consistency among reference CCS values, computational data obtained in house were preferred to any experimental or computational data from disparate sources. Such values were obtained by molecular dynamics (MD) simulations and either the exact hard sphere scattering (EHSS) or the projection superposition approximation (PSA) methods, and then plotted against the corresponding experimental values to generate separate calibration curves. Their performance was evaluated on the basis of their correlation coefficients and ability to provide values that matched the CCS of selected test samples mimicking typical unknowns. The results indicated that the predictive power benefited from the exclusion of higher charged species that were more susceptible to the destabilizing effects of Coulombic repulsion. The results revealed discrepancies between EHSS and PSA data that were ascribable to the different approximations used to describe the ion mobility process. Within the boundaries defined by these approximations and the challenges of modeling NA structure in a solvent-free environment, the calibrant sets enabled the experimental determination of CCS with excellent reproducibility (precision) and error (accuracy), which will support the analysis of progressively larger NA samples of biological significance.
Collapse
Affiliation(s)
| | | | | | - Daniele Fabris
- University at Albany, Albany, New York, USA. and SUNY, Albany, The RNA Institute, 1400 Washington Avenue, Albany, New York, USA
| |
Collapse
|
10
|
Structural Lipids Enable the Formation of Functional Oligomers of the Eukaryotic Purine Symporter UapA. Cell Chem Biol 2018; 25:840-848.e4. [PMID: 29681524 PMCID: PMC6058078 DOI: 10.1016/j.chembiol.2018.03.011] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 02/27/2018] [Accepted: 03/22/2018] [Indexed: 11/25/2022]
Abstract
The role of membrane lipids in modulating eukaryotic transporter assembly and function remains unclear. We investigated the effect of membrane lipids in the structure and transport activity of the purine transporter UapA from Aspergillus nidulans. We found that UapA exists mainly as a dimer and that two lipid molecules bind per UapA dimer. We identified three phospholipid classes that co-purified with UapA: phosphatidylcholine, phosphatidylethanolamine (PE), and phosphatidylinositol (PI). UapA delipidation caused dissociation of the dimer into monomers. Subsequent addition of PI or PE rescued the UapA dimer and allowed recovery of bound lipids, suggesting a central role of these lipids in stabilizing the dimer. Molecular dynamics simulations predicted a lipid binding site near the UapA dimer interface. Mutational analyses established that lipid binding at this site is essential for formation of functional UapA dimers. We propose that structural lipids have a central role in the formation of functional, dimeric UapA. Mass spectrometry reveals specific lipid binding to the eukaryotic transporter UapA Interfacial lipids stabilize the functional UapA dimer MD simulations reveal the lipid binding sites Mutagenesis of a lipid binding site disrupts UapA dimerization and function in vivo
Collapse
|
11
|
Nabuchi Y, Hirose K, Takayama M. pH Dependence of the Number of Discrete Conformers of Carbonic Anhydrase 2, as Evaluated from Collision Cross-Section Using Ion Mobility Coupled with Electrospray Ionization. ACTA ACUST UNITED AC 2018. [PMID: 29515944 PMCID: PMC5832482 DOI: 10.5702/massspectrometry.a0064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Ion mobility experiments coupled with electrospray ionization (ESI) were conducted to evaluate the folding states of bovine carbonic anhydrase 2 (CA2) under three different pH conditions. Collision cross-section (CCS) of the CA2 ions generated by ESI revealed the presence of six discrete conformers in the gas phase under the conditions employed in this study. The CCS of the most extended conformer was three times larger than that of the most compact one. The charge state distribution of the CA2 ions was indicative of three conformers being present. Although there was consistency in conformer assignment conducted by CCS and charge state distribution, the CCS measurement was shown to be more effective because the information obtained provided more detailed knowledge of the conformation of the protein.
Collapse
Affiliation(s)
- Yoshiaki Nabuchi
- Graduate School of Nanobioscience, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama 236-0027, Japan
| | - Kenji Hirose
- Biopharmaceutical Market Development, Waters Corporation Asia Pacific Headquarter, 5-14-10 Nishinakanoshima, Yodogawa-ku, Osaka 532-0011, Japan
| | - Mitsuo Takayama
- Graduate School of Nanobioscience, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama 236-0027, Japan
| |
Collapse
|
12
|
Ben-Nissan G, Sharon M. The application of ion-mobility mass spectrometry for structure/function investigation of protein complexes. Curr Opin Chem Biol 2018; 42:25-33. [PMID: 29128665 PMCID: PMC5796646 DOI: 10.1016/j.cbpa.2017.10.026] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Revised: 10/19/2017] [Accepted: 10/24/2017] [Indexed: 12/16/2022]
Abstract
Ion-mobility mass spectrometry (IM-MS) is an approach that can provide information on the stoichiometry, composition, protein contacts and topology of protein complexes. The power of this approach lies not only in its sensitivity and speed of analysis, but also in the fact that it is a technique that can capture the repertoire of conformational states adopted by protein assemblies. Here, we describe the array of available IM-MS based tools, and demonstrate their application to the structural characterization of various protein complexes, including challenging systems as amyloid aggregates and membrane proteins. We also discuss recent studies in which IM-MS was applied towards investigations of conformational transitions and stabilization effects induced by protein interactions.
Collapse
Affiliation(s)
- Gili Ben-Nissan
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Michal Sharon
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel.
| |
Collapse
|
13
|
Mortensen DN, Susa AC, Williams ER. Collisional Cross-Sections with T-Wave Ion Mobility Spectrometry without Experimental Calibration. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1282-1292. [PMID: 28432656 DOI: 10.1007/s13361-017-1669-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 03/21/2017] [Accepted: 03/27/2017] [Indexed: 06/07/2023]
Abstract
A method for relating traveling-wave ion mobility spectrometry (TWIMS) drift times with collisional cross-sections using computational simulations is presented. This method is developed using SIMION modeling of the TWIMS potential wave and equations that describe the velocity of ions in gases induced by electric fields. The accuracy of this method is assessed by comparing the collisional cross-sections of 70 different reference ions obtained using this method with those obtained from static drift tube ion mobility measurements. The cross-sections obtained here with low wave velocities are very similar to those obtained using static drift (average difference = 0.3%) for ions formed from both denaturing and buffered aqueous solutions. In contrast, the cross-sections obtained with high wave velocities are significantly greater, especially for ions formed from buffered aqueous solutions. These higher cross-sections at high wave velocities may result from high-order factors not accounted for in the model presented here or from the protein ions unfolding during TWIMS. Results from this study demonstrate that collisional cross-sections can be obtained from single TWIMS drift time measurements, but that low wave velocities and gentle instrument conditions should be used in order to minimize any uncertainties resulting from high-order effects not accounted for in the present model and from any protein unfolding that might occur. Thus, the method presented here eliminates the need to calibrate TWIMS drift times with collisional cross-sections measured using other ion mobility devices. Graphical Abstract ᅟ.
Collapse
Affiliation(s)
- Daniel N Mortensen
- Department of Chemistry, University of California, Berkeley, CA, 94720-1460, USA
| | - Anna C Susa
- Department of Chemistry, University of California, Berkeley, CA, 94720-1460, USA
| | - Evan R Williams
- Department of Chemistry, University of California, Berkeley, CA, 94720-1460, USA.
| |
Collapse
|
14
|
López A, Vilaseca M, Madurga S, Varese M, Tarragó T, Giralt E. Analyzing slowly exchanging protein conformations by ion mobility mass spectrometry: study of the dynamic equilibrium of prolyl oligopeptidase. JOURNAL OF MASS SPECTROMETRY : JMS 2016; 51:504-511. [PMID: 27434808 DOI: 10.1002/jms.3777] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 03/29/2016] [Accepted: 04/20/2016] [Indexed: 06/06/2023]
Abstract
Ion mobility mass spectrometry (IMMS) is a biophysical technique that allows the separation of isobaric species on the basis of their size and shape. The high separation capacity, sensitivity and relatively fast time scale measurements confer IMMS great potential for the study of proteins in slow (µs-ms) conformational equilibrium in solution. However, the use of this technique for examining dynamic proteins is still not generalized. One of the major limitations is the instability of protein ions in the gas phase, which raises the question as to what extent the structures detected reflect those in solution. Here, we addressed this issue by analyzing the conformational landscape of prolyl oligopeptidase (POP) - a model of a large dynamic enzyme in the µs-ms range - by native IMMS and compared the results obtained in the gas phase with those obtained in solution. In order to interpret the experimental results, we used theoretical simulations. In addition, the stability of POP gaseous ions was explored by charge reduction and collision-induced unfolding experiments. Our experiments disclosed two species of POP in the gas phase, which correlated well with the open and closed conformations in equilibrium in solution; moreover, a gas-phase collapsed form of POP was also detected. Therefore, our findings not only support the potential of IMMS for the study of multiple co-existing conformations of large proteins in slow dynamic equilibrium in solution but also stress the need for careful data analysis to avoid artifacts. Copyright © 2016 John Wiley & Sons, Ltd.
Collapse
Affiliation(s)
- Abraham López
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain
- Department of Organic Chemistry, University of Barcelona, Martí i Franquès 1, 08028, Barcelona, Spain
| | - Marta Vilaseca
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Sergio Madurga
- Department of Physical Chemistry and Research Institute of Theoretical and Computational Chemistry (IQTCUB), University of Barcelona, Martí i Franquès 1, 08028, Barcelona, Spain
| | - Monica Varese
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Teresa Tarragó
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain
- Iproteos, S.L., Barcelona Science Park, Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Ernest Giralt
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain
- Department of Organic Chemistry, University of Barcelona, Martí i Franquès 1, 08028, Barcelona, Spain
| |
Collapse
|
15
|
Ewing MA, Glover MS, Clemmer DE. Hybrid ion mobility and mass spectrometry as a separation tool. J Chromatogr A 2016; 1439:3-25. [DOI: 10.1016/j.chroma.2015.10.080] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 10/05/2015] [Accepted: 10/21/2015] [Indexed: 11/29/2022]
|
16
|
Sun Y, Vahidi S, Sowole MA, Konermann L. Protein Structural Studies by Traveling Wave Ion Mobility Spectrometry: A Critical Look at Electrospray Sources and Calibration Issues. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:31-40. [PMID: 26369778 DOI: 10.1007/s13361-015-1244-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Revised: 07/27/2015] [Accepted: 07/29/2015] [Indexed: 06/05/2023]
Abstract
The question whether electrosprayed protein ions retain solution-like conformations continues to be a matter of debate. One way to address this issue involves comparisons of collision cross sections (Ω) measured by ion mobility spectrometry (IMS) with Ω values calculated for candidate structures. Many investigations in this area employ traveling wave IMS (TWIMS). It is often implied that nanoESI is more conducive for the retention of solution structure than regular ESI. Focusing on ubiquitin, cytochrome c, myoglobin, and hemoglobin, we demonstrate that Ω values and collisional unfolding profiles are virtually indistinguishable under both conditions. These findings suggest that gas-phase structures and ion internal energies are independent of the type of electrospray source. We also note that TWIMS calibration can be challenging because differences in the extent of collisional activation relative to drift tube reference data may lead to ambiguous peak assignments. It is demonstrated that this problem can be circumvented by employing collisionally heated calibrant ions. Overall, our data are consistent with the view that exposure of native proteins to electrospray conditions can generate kinetically trapped ions that retain solution-like structures on the millisecond time scale of TWIMS experiments. ᅟ
Collapse
Affiliation(s)
- Yu Sun
- Department of Chemistry, The University of Western Ontario, London, ON, N6A 5B7, Canada
| | - Siavash Vahidi
- Department of Chemistry, The University of Western Ontario, London, ON, N6A 5B7, Canada
| | - Modupeola A Sowole
- Department of Chemistry, The University of Western Ontario, London, ON, N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, ON, N6A 5B7, Canada.
| |
Collapse
|
17
|
Thevis M, Dib J, Thomas A, Höppner S, Lagojda A, Kuehne D, Sander M, Opfermann G, Schänzer W. Complementing the characterization ofin vivogeneratedN-glucuronic acid conjugates of stanozolol by collision cross section computation and analysis. Drug Test Anal 2015; 7:1050-6. [DOI: 10.1002/dta.1907] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 09/25/2015] [Accepted: 09/25/2015] [Indexed: 02/06/2023]
Affiliation(s)
- Mario Thevis
- Center for Preventive Doping Research - Institute of Biochemistry; German Sport University Cologne; Am Sportpark Müngersdorf 6 50933 Cologne Germany
- European Monitoring Center for Emerging Doping Agents (EuMoCEDA); Cologne/Bonn Germany
| | - Josef Dib
- Center for Preventive Doping Research - Institute of Biochemistry; German Sport University Cologne; Am Sportpark Müngersdorf 6 50933 Cologne Germany
| | - Andreas Thomas
- Center for Preventive Doping Research - Institute of Biochemistry; German Sport University Cologne; Am Sportpark Müngersdorf 6 50933 Cologne Germany
| | - Sebastian Höppner
- Center for Preventive Doping Research - Institute of Biochemistry; German Sport University Cologne; Am Sportpark Müngersdorf 6 50933 Cologne Germany
| | - Andreas Lagojda
- Bayer CropScience AG; Alfred-Nobel-Str. 50 40789 Monheim Germany
| | - Dirk Kuehne
- Bayer CropScience AG; Alfred-Nobel-Str. 50 40789 Monheim Germany
| | - Mark Sander
- Center for Preventive Doping Research - Institute of Biochemistry; German Sport University Cologne; Am Sportpark Müngersdorf 6 50933 Cologne Germany
| | - Georg Opfermann
- Center for Preventive Doping Research - Institute of Biochemistry; German Sport University Cologne; Am Sportpark Müngersdorf 6 50933 Cologne Germany
| | - Wilhelm Schänzer
- Center for Preventive Doping Research - Institute of Biochemistry; German Sport University Cologne; Am Sportpark Müngersdorf 6 50933 Cologne Germany
| |
Collapse
|
18
|
Chendo C, Moreira G, Tintaru A, Posocco P, Laurini E, Lefay C, Gigmes D, Viel S, Pricl S, Charles L. Anomerization of Acrylated Glucose During Traveling Wave Ion Mobility Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:1483-1493. [PMID: 26041082 DOI: 10.1007/s13361-015-1170-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 04/16/2015] [Accepted: 04/18/2015] [Indexed: 06/04/2023]
Abstract
Anomerization of simple sugars in the liquid phase is known as an acid- and base-catalyzed process, which highly depends on solvent polarity. This reaction is reported here to occur in the gas phase, during traveling wave ion mobility spectrometry (TWIMS) experiments aimed at separating α- and β-anomers of penta-acrylated glucose generated as ammonium adducts in electrospray ionization. This compound was available in two samples prepared from glucose dissolved in solvents of different polarity, namely tetrahydrofuran (THF) and N,N-dimethylacetamide (DMAC), and analyzed by electrospray tandem mass spectrometry (ESI-MS/MS) as well as traveling wave ion mobility (ESI-TWIMS-MS). In MS/MS, an anchimerically-assisted process was found to be unique to the electrosprayed α-anomer, and was only observed for the THF sample. In ESI-TWIMS-MS, a signal was measured at the drift time expected for the α-anomer for both the THF and DMAC samples, in apparent contradiction to the MS/MS results, which indicated that the α-anomer was not present in the DMAC sample. However, MS/MS experiments performed after TWIMS separation revealed that ammonium adducts of the α-anomer produced from each sample, although exhibiting the same collision cross section, were clearly different. Indeed, while the α-anomer actually present in the THF sample was electrosprayed with the ammonium adducted at the C2 acrylate, its homologue only observed when the DMAC sample was subjected to TWIMS hold the adducted ammonium at the C1 acrylate. These findings were explained by a β/α inter-conversion upon injection in the TWIMS cell, as supported by theoretical calculation and dynamic molecular modeling.
Collapse
Affiliation(s)
- Christophe Chendo
- Aix-Marseille Université - CNRS, UMR 7273, Institut de Chimie Radicalaire, Marseille, France
| | | | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Sinz A, Arlt C, Chorev D, Sharon M. Chemical cross-linking and native mass spectrometry: A fruitful combination for structural biology. Protein Sci 2015; 24:1193-209. [PMID: 25970732 PMCID: PMC4534171 DOI: 10.1002/pro.2696] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 04/14/2015] [Accepted: 04/29/2015] [Indexed: 12/31/2022]
Abstract
Mass spectrometry (MS) is becoming increasingly popular in the field of structural biology for analyzing protein three-dimensional-structures and for mapping protein-protein interactions. In this review, the specific contributions of chemical crosslinking and native MS are outlined to reveal the structural features of proteins and protein assemblies. Both strategies are illustrated based on the examples of the tetrameric tumor suppressor protein p53 and multisubunit vinculin-Arp2/3 hybrid complexes. We describe the distinct advantages and limitations of each technique and highlight synergistic effects when both techniques are combined. Integrating both methods is especially useful for characterizing large protein assemblies and for capturing transient interactions. We also point out the future directions we foresee for a combination of in vivo crosslinking and native MS for structural investigation of intact protein assemblies.
Collapse
Affiliation(s)
- Andrea Sinz
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-WittenbergD-06120, Halle, Germany
| | - Christian Arlt
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-WittenbergD-06120, Halle, Germany
| | - Dror Chorev
- Department of Biological Chemistry, Weizmann Institute of ScienceRehovot, 76100, Israel
| | - Michal Sharon
- Department of Biological Chemistry, Weizmann Institute of ScienceRehovot, 76100, Israel
| |
Collapse
|
20
|
Morsa D, Gabelica V, De Pauw E. Fragmentation and isomerization due to field heating in traveling wave ion mobility spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:1384-1393. [PMID: 24845353 DOI: 10.1007/s13361-014-0909-9] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 04/08/2014] [Accepted: 04/08/2014] [Indexed: 06/03/2023]
Abstract
During their travel inside a traveling wave ion mobility cell (TW IMS), ions are susceptible to heating because of the presence of high intensity electric fields. Here, we report effective temperatures Teff,vib obtained at the injection and inside the mobility cell of a SYNAPT G2 HDMS spectrometer for different probe ions: benzylpyridinium ions and leucine enkephalin. Using standard parameter sets, we obtained a temperature of ~800 K at injection and 728 ± 2 K into the IMS cell for p-methoxybenzylpyridinium. We found that Teff,vib inside the cell was dependent on the separation parameters and on the nature of the analyte. While the mean energy of the Boltzmann distributions increases with ion size, the corresponding temperature decreases because of increasing numbers of vibrational normal modes. We also investigated conformational rearrangements of 7+ ions of cytochrome c and reveal isomerization of the most compact structure, therefore highlighting the effects of weak heating on the gas-phase structure of biologically relevant ions.
Collapse
Affiliation(s)
- Denis Morsa
- Mass Spectrometry Laboratory, University of Liège, Institut de Chimie Bat. B6c, 4000, Liège, Belgium
| | | | | |
Collapse
|
21
|
Lavanant H, Tognetti V, Afonso C. Traveling wave ion mobility mass spectrometry and ab initio calculations of phosphoric acid clusters. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:572-580. [PMID: 24500700 DOI: 10.1007/s13361-013-0818-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Revised: 12/20/2013] [Accepted: 12/21/2013] [Indexed: 06/03/2023]
Abstract
Positive and negative ion electrospray mass spectra obtained from 50 mM phosphoric acid solutions presented a large number of phosphoric acid clusters: [(H3PO4)n + zH](z+) or [(H3PO4)n - zH](z-), with n up to 200 and z up to 4 for positively charged clusters, and n up to 270 and z up to 7 for negatively charged cluster ions. Ion mobility experiments allowed very explicit separation of the different charge states. Because of the increased pressures involved in ion mobility experiments, dissociation to smaller clusters was observed both in the trap and transfer areas. Voltages along the ion path could be optimized so as to minimize this effect, which can be directly associated with the cleavage of hydrogen bonds. Having excluded the ion mobility times that resulted from dissociated ions, each cluster ion appeared at a single drift time. These drift times showed a linear progression with the number of phosphoric atoms for cluster ions of the same charge state. Cross section calculations were carried out with MOBCAL on DFT optimized geometries with different hydrogen locations and with three types of atomic charges. DFT geometry optimizations yielded roughly spherical structures. Our results for nitrogen gas interaction cross sections showed that values were dependent on the atomic charges definition used in the MOBCAL calculation. This pinpointed the necessity to define a clear theoretical framework before any comparative interpretations can be attempted with uncharacterized compounds.
Collapse
Affiliation(s)
- Hélène Lavanant
- Normandie Université, COBRA, UMR 6014 et FR 3038, Université de Rouen; INSA de Rouen; CNRS, IRCOF, 1 rue Tesnière, 76821, Mont-Saint-Aignan Cedex, France,
| | | | | |
Collapse
|
22
|
Saikusa K, Kuwabara N, Kokabu Y, Inoue Y, Sato M, Iwasaki H, Shimizu T, Ikeguchi M, Akashi S. Characterisation of an intrinsically disordered protein complex of Swi5-Sfr1 by ion mobility mass spectrometry and small-angle X-ray scattering. Analyst 2013; 138:1441-9. [PMID: 23324799 DOI: 10.1039/c2an35878f] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
It is now recognized that intrinsically disordered proteins (IDPs) play important roles as hubs in intracellular networks, and their structural characterisation is of significance. However, due to their highly dynamic features, it is challenging to investigate the structures of IDPs solely by conventional methods. In the present study, we demonstrate a novel method to characterise protein complexes using electrospray ionization ion mobility mass spectrometry (ESI-IM-MS) in combination with small-angle X-ray scattering (SAXS). This method enables structural characterisation even of proteins that have difficulties in crystallisation. With this method, we have characterised the Schizosaccharomyces pombe Swi5-Sfr1 complex, which is expected to have a long disordered region at the N-terminal portion of Sfr1. ESI-IM-MS analysis of the Swi5-Sfr1 complex revealed that its experimental collision cross-section (CCS) had a wide distribution, and the CCS values of the most dominant ions were ∼56% of the theoretically calculated value based on the SAXS low-resolution model, suggesting a significant size reduction in the gas phase. The present study demonstrates that the newly developed method for calculation of the theoretical CCSs of the SAXS low-resolution models of proteins allows accurate evaluation of the experimental CCS values of IDPs provided by ESI-IM-MS by comparing with the low-resolution solution structures. Furthermore, it was revealed that the combination of ESI-IM-MS and SAXS is a promising method for structural characterisation of protein complexes that are unable to crystallise.
Collapse
Affiliation(s)
- Kazumi Saikusa
- Graduate School of Nanobioscience, Yokohama City University, Yokohama, Kanagawa 230-0045, Japan
| | | | | | | | | | | | | | | | | |
Collapse
|
23
|
Saikusa K, Fuchigami S, Takahashi K, Asano Y, Nagadoi A, Tachiwana H, Kurumizaka H, Ikeguchi M, Nishimura Y, Akashi S. Gas-Phase Structure of the Histone Multimers Characterized by Ion Mobility Mass Spectrometry and Molecular Dynamics Simulation. Anal Chem 2013; 85:4165-71. [DOI: 10.1021/ac400395j] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Kazumi Saikusa
- Department of Supramolecular
Biology, Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama,
Kanagawa 230-0045, Japan
| | - Sotaro Fuchigami
- Department of Supramolecular
Biology, Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama,
Kanagawa 230-0045, Japan
| | - Kyohei Takahashi
- Department of Supramolecular
Biology, Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama,
Kanagawa 230-0045, Japan
| | - Yuuki Asano
- Department of Supramolecular
Biology, Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama,
Kanagawa 230-0045, Japan
| | - Aritaka Nagadoi
- Department of Supramolecular
Biology, Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama,
Kanagawa 230-0045, Japan
| | - Hiroaki Tachiwana
- Graduate School of Advanced
Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Hitoshi Kurumizaka
- Graduate School of Advanced
Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Mitsunori Ikeguchi
- Department of Supramolecular
Biology, Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama,
Kanagawa 230-0045, Japan
| | - Yoshifumi Nishimura
- Department of Supramolecular
Biology, Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama,
Kanagawa 230-0045, Japan
| | - Satoko Akashi
- Department of Supramolecular
Biology, Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama,
Kanagawa 230-0045, Japan
| |
Collapse
|
24
|
Wright VE, Castro-Gómez F, Jurneczko E, Reynolds JC, Poulton A, Christie SDR, Barran P, Bo C, Creaser CS. Structural studies of metal ligand complexes by ion mobility-mass spectrometry. ACTA ACUST UNITED AC 2013. [DOI: 10.1007/s12127-013-0122-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|
25
|
Salbo R, Bush MF, Naver H, Campuzano I, Robinson CV, Pettersson I, Jørgensen TJD, Haselmann KF. Traveling-wave ion mobility mass spectrometry of protein complexes: accurate calibrated collision cross-sections of human insulin oligomers. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2012; 26:1181-1193. [PMID: 22499193 DOI: 10.1002/rcm.6211] [Citation(s) in RCA: 127] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
RATIONALE The collision cross-section (Ω) of a protein or protein complex ion can be measured using traveling-wave (T-wave) ion mobility (IM) mass spectrometry (MS) via calibration with compounds of known Ω. The T-wave Ω-values depend strongly on instrument parameters and calibrant selection. Optimization of instrument parameters and calibration standards are crucial for obtaining accurate T-wave Ω-values. METHODS Human insulin and the fast-acting insulin aspart under native-like conditions (ammonium acetate, physiological pH) were analyzed on Waters SYNAPT G1 and G2 HDMS instruments. The calibrated T-wave Ω-values of insulin monomer, dimer, and hexamer ions were measured using many different combinations of denatured and native-like calibrants (masses between 2.85 and 256 kDa) and T-wave conditions. Drift-tube Ω-values were obtained on a modified SYNAPT G1. RESULTS Insulin T-wave Ω-values were measured at 26 combinations of T-wave velocity and amplitude. Optimal sets of calibrants were identified that yield Ω-values with minimal dependence on T-wave conditions and calibration plots with high R(2)-values. The T-wave Ω-values determined under conditions satisfying these criteria had absolute errors <2%. Structural differences between human insulin and fast-acting insulin aspart were probed with IM-MS. Insulin aspart monomers have increased flexibility, while hexamers are more compact than human insulin. CONCLUSIONS Accurate T-wave Ω-values that are indistinguishable from drift-tube values are obtained when using (1) native-like calibrants with masses that closely bracket that of the analyte, (2) T-wave velocities that maximize the R(2) of the calibration plot for those calibrants, and (3) at least three replicates at T-wave velocities that yield calibration plots with high R(2).
Collapse
Affiliation(s)
- Rune Salbo
- Diabetes Protein Engineering, Novo Nordisk A/S, Novo Nordisk Park, Måløv, Denmark
| | | | | | | | | | | | | | | |
Collapse
|
26
|
Zhong Y, Hyung SJ, Ruotolo BT. Ion mobility-mass spectrometry for structural proteomics. Expert Rev Proteomics 2012; 9:47-58. [PMID: 22292823 DOI: 10.1586/epr.11.75] [Citation(s) in RCA: 134] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Ion mobility coupled to mass spectrometry has been an important tool in the fields of chemical physics and analytical chemistry for decades, but its potential for interrogating the structure of proteins and multiprotein complexes has only recently begun to be realized. Today, ion mobility-mass spectrometry is often applied to the structural elucidation of protein assemblies that have failed high-throughput crystallization or NMR spectroscopy screens. Here, we highlight the technology, approaches and data that have led to this dramatic shift in use, including emerging trends such as the integration of ion mobility-mass spectrometry data with more classical (e.g., 'bottom-up') proteomics approaches for the rapid structural characterization of protein networks.
Collapse
Affiliation(s)
- Yueyang Zhong
- Department of Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, MI 48109, USA
| | | | | |
Collapse
|
27
|
Merenbloom SI, Flick TG, Williams ER. How hot are your ions in TWAVE ion mobility spectrometry? JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:553-62. [PMID: 22203576 PMCID: PMC3296450 DOI: 10.1007/s13361-011-0313-7] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2011] [Revised: 11/30/2011] [Accepted: 12/02/2011] [Indexed: 05/04/2023]
Abstract
Effective temperatures of ions during traveling wave ion mobility spectrometry (TWIMS) analysis were measured using singly protonated leucine enkephalin dimer as a chemical thermometer by monitoring dissociation of the dimer into monomer, as well as the subsequent dissociation of monomer into a-, b-, and y-ions, as a function of instrumental parameters. At fixed helium cell and TWIMS cell gas flow rates, the extent of dissociation does not vary significantly with either the wave velocity or wave height, except at low (<500 m/s) wave velocities that are not commonly used. Increasing the flow rate of nitrogen gas into the TWIMS cell and decreasing the flow rate of helium gas into the helium cell resulted in greater dissociation. However, the mobility distributions of the fragment ions formed by dissociation of the dimer upon injection into the TWIMS cell are nearly indistinguishable from those of fragment ions formed in the collision cell prior to TWIMS analysis for all TWIMS experiments. These results indicate that heating and dissociation occur when ions are injected into the TWIMS cell, and that the effective temperature subsequently decreases to a point at which no further dissociation is observed during the TWIMS analysis. An upper limit to the effective ion temperature of 449 K during TWIMS analysis is obtained at a helium flow rate of 180 mL/min, TWIMS flow rate of 80 mL/min, and traveling wave height of 40 V, which is well below previously reported values. Effects of ion heating in TWIMS on gas-phase protein conformation are presented.
Collapse
Affiliation(s)
- Samuel I Merenbloom
- Department of Chemistry, University of California, Berkeley, CA 94720-1460, USA
| | | | | |
Collapse
|
28
|
Hall Z, Politis A, Bush MF, Smith LJ, Robinson CV. Charge-State Dependent Compaction and Dissociation of Protein Complexes: Insights from Ion Mobility and Molecular Dynamics. J Am Chem Soc 2012; 134:3429-38. [DOI: 10.1021/ja2096859] [Citation(s) in RCA: 206] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Zoe Hall
- Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry
Laboratory, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Argyris Politis
- Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry
Laboratory, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Matthew F. Bush
- Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry
Laboratory, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Lorna J. Smith
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory,
South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Carol V. Robinson
- Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry
Laboratory, South Parks Road, Oxford OX1 3QZ, United Kingdom
| |
Collapse
|
29
|
Merenbloom SI, Flick TG, Daly MP, Williams ER. Effects of select anions from the Hofmeister series on the gas-phase conformations of protein ions measured with traveling-wave ion mobility spectrometry/mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:1978-90. [PMID: 21952780 PMCID: PMC3212098 DOI: 10.1007/s13361-011-0238-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Revised: 08/19/2011] [Accepted: 08/19/2011] [Indexed: 05/10/2023]
Abstract
The gas-phase conformations of ubiquitin, cytochrome c, lysozyme, and α-lactalbumin ions, formed by electrospray ionization (ESI) from aqueous solutions containing 5 mM ammonium perchlorate, ammonium iodide, ammonium sulfate, ammonium chloride, ammonium thiocyanate, or guanidinium chloride, are examined using traveling-wave ion mobility spectrometry (TWIMS) coupled to time-of-flight (TOF) mass spectrometry (MS). For ubiquitin, cytochrome c, and α-lactalbumin, adduction of multiple acid molecules results in no significant conformational changes to the highest and lowest charge states formed from aqueous solutions, whereas the intermediate charge states become more compact. The transition to more compact conformers for the intermediate charge states occurs with fewer bound H(2)SO(4) molecules than HClO(4) or HI molecules, suggesting ion-ion or salt-bridge interactions are stabilizing more compact forms of the gaseous protein. However, the drift time distributions for protein ions of the same net charge with the highest levels of adduction of each acid are comparable, indicating that these protein ions all adopt similarly compact conformations or families of conformers. No significant change in conformation is observed upon the adduction of multiple acid molecules to charge states of lysozyme. These results show that the attachment of HClO(4), HI, or H(2)SO(4) to multiply protonated proteins can induce compact conformations in the resulting gas-phase protein ions. In contrast, differing Hofmeister effects are observed for the corresponding anions in solution at higher concentrations.
Collapse
Affiliation(s)
- Samuel I. Merenbloom
- Department of Chemistry, University of California-Berkeley, Berkeley, California, USA
| | - Tawnya G. Flick
- Department of Chemistry, University of California-Berkeley, Berkeley, California, USA
| | | | - Evan R. Williams
- Department of Chemistry, University of California-Berkeley, Berkeley, California, USA
| |
Collapse
|
30
|
Morsa D, Gabelica V, De Pauw E. Effective Temperature of Ions in Traveling Wave Ion Mobility Spectrometry. Anal Chem 2011; 83:5775-82. [DOI: 10.1021/ac201509p] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Denis Morsa
- Physical Chemistry and Mass Spectrometry Laboratory, Department of Chemistry, University of Liège, Institut de Chimie Bat. B6c, B-4000 Liège, Belgium
| | - Valérie Gabelica
- Physical Chemistry and Mass Spectrometry Laboratory, Department of Chemistry, University of Liège, Institut de Chimie Bat. B6c, B-4000 Liège, Belgium
| | - Edwin De Pauw
- Physical Chemistry and Mass Spectrometry Laboratory, Department of Chemistry, University of Liège, Institut de Chimie Bat. B6c, B-4000 Liège, Belgium
| |
Collapse
|
31
|
Zhong Y, Hyung SJ, Ruotolo BT. Characterizing the resolution and accuracy of a second-generation traveling-wave ion mobility separator for biomolecular ions. Analyst 2011; 136:3534-41. [DOI: 10.1039/c0an00987c] [Citation(s) in RCA: 120] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|