1
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Eade L, Sullivan MP, Allison TM, Goldstone DC, Hartinger CG. Not All Binding Sites Are Equal: Site Determination and Folding State Analysis of Gas-Phase Protein-Metallodrug Adducts. Chemistry 2024; 30:e202400268. [PMID: 38472116 DOI: 10.1002/chem.202400268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 03/08/2024] [Accepted: 03/11/2024] [Indexed: 03/14/2024]
Abstract
Modern approaches in metallodrug research focus on compounds that bind protein targets rather than DNA. However, the identification of protein targets and binding sites is challenging. Using intact mass spectrometry and proteomics, we investigated the binding of the antimetastatic agent RAPTA-C to the model proteins ubiquitin, cytochrome c, lysozyme, and myoglobin. Binding to cytochrome c and lysozyme was negligible. However, ubiquitin bound up to three Ru moieties, two of which were localized at Met1 and His68 as [Ru(cym)], and [Ru(cym)] or [Ru(cym)(PTA)] adducts, respectively. Myoglobin bound up to four [Ru(cym)(PTA)] moieties and five sites were identified at His24, His36, His64, His81/82 and His113. Collision-induced unfolding (CIU) studies via ion-mobility mass spectrometry allowed measuring protein folding as a function of collisional activation. CIU of protein-RAPTA-C adducts showed binding of [Ru(cym)] to Met1 caused a significant compaction of ubiquitin, likely from N-terminal S-Ru-N chelation, while binding of [Ru(cym)(PTA)] to His residues of ubiquitin or myoglobin induced a smaller effect. Interestingly, the folded state of ubiquitin formed by His functionalization was more stable than Met1 metalation. The data suggests that selective metalation of amino acids at different positions on the protein impacts the conformation and potentially the biological activity of anticancer compounds.
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Affiliation(s)
- Liam Eade
- School of Chemical Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Matthew P Sullivan
- School of Chemical Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Timothy M Allison
- Biomolecular Interaction Centre, School of Physical and Chemical Sciences, University of Canterbury, Christchurch, New Zealand
| | - David C Goldstone
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Christian G Hartinger
- School of Chemical Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
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2
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Dafun AS, Marcoux J. Structural mass spectrometry of membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2022; 1870:140813. [PMID: 35750312 DOI: 10.1016/j.bbapap.2022.140813] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 06/10/2022] [Accepted: 06/17/2022] [Indexed: 06/15/2023]
Abstract
The analysis of proteins and protein complexes by mass spectrometry (MS) has come a long way since the invention of electrospray ionization (ESI) in the mid 80s. Originally used to characterize small soluble polypeptide chains, MS has progressively evolved over the past 3 decades towards the analysis of samples of ever increasing heterogeneity and complexity, while the instruments have become more and more sensitive and resolutive. The proofs of concepts and first examples of most structural MS methods appeared in the early 90s. However, their application to membrane proteins, key targets in the biopharma industry, is more recent. Nowadays, a wealth of information can be gathered from such MS-based methods, on all aspects of membrane protein structure: sequencing (and more precisely proteoform characterization), but also stoichiometry, non-covalent ligand binding (metals, drug, lipids, carbohydrates), conformations, dynamics and distance restraints for modelling. In this review, we present the concept and some historical and more recent applications on membrane proteins, for the major structural MS methods.
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Affiliation(s)
- Angelique Sanchez Dafun
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Julien Marcoux
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France.
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3
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Skeene K, Khatri K, Soloviev Z, Lapthorn C. Current status and future prospects for ion-mobility mass spectrometry in the biopharmaceutical industry. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2021; 1869:140697. [PMID: 34246790 DOI: 10.1016/j.bbapap.2021.140697] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 06/11/2021] [Accepted: 07/06/2021] [Indexed: 12/12/2022]
Abstract
Detailed characterization of protein reagents and biopharmaceuticals is key in defining successful drug discovery campaigns, aimed at bringing molecules through different discovery stages up to development and commercialization. There are many challenges in this process, with complex and detailed analyses playing paramount roles in modern industry. Mass spectrometry (MS) has become an essential tool for characterization of proteins ever since the onset of soft ionization techniques and has taken the lead in quality assessment of biopharmaceutical molecules, and protein reagents, used in the drug discovery pipeline. MS use spans from identification of correct sequences, to intact molecule analyses, protein complexes and more recently epitope and paratope identification. MS toolkits could be incredibly diverse and with ever evolving instrumentation, increasingly novel MS-based techniques are becoming indispensable tools in the biopharmaceutical industry. Here we discuss application of Ion Mobility MS (IMMS) in an industrial setting, and what the current applications and outlook are for making IMMS more mainstream.
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Affiliation(s)
- Kirsty Skeene
- Biopharm Process Research, Medicinal Science and Technology, GlaxoSmithKline, Stevenage SG1 2NY, UK.
| | - Kshitij Khatri
- Structure and Function Characterization, CMC-Analytical, GlaxoSmithKline, Collegeville, PA 19406, USA.
| | - Zoja Soloviev
- Protein, Cellular and Structural Sciences, Medicinal Science and Technology, GlaxoSmithKline, Stevenage SG1 2NY, UK.
| | - Cris Lapthorn
- Structure and Function Characterization, CMC-Analytical, GlaxoSmithKline, Stevenage SG1 2NY, UK.
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4
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Ion mobility-mass spectrometry reveals the role of peripheral myelin protein dimers in peripheral neuropathy. Proc Natl Acad Sci U S A 2021; 118:2015331118. [PMID: 33893233 DOI: 10.1073/pnas.2015331118] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Peripheral myelin protein (PMP22) is an integral membrane protein that traffics inefficiently even in wild-type (WT) form, with only 20% of the WT protein reaching its final plasma membrane destination in myelinating Schwann cells. Misfolding of PMP22 has been identified as a key factor in multiple peripheral neuropathies, including Charcot-Marie-Tooth disease and Dejerine-Sottas syndrome. While biophysical analyses of disease-associated PMP22 mutants show altered protein stabilities, leading to reduced surface trafficking and loss of PMP22 function, it remains unclear how destabilization of PMP22 mutations causes mistrafficking. Here, native ion mobility-mass spectrometry (IM-MS) is used to compare the gas phase stabilities and abundances for an array of mutant PM22 complexes. We find key differences in the PMP22 mutant stabilities and propensities to form homodimeric complexes. Of particular note, we observe that severely destabilized forms of PMP22 exhibit a higher propensity to dimerize than WT PMP22. Furthermore, we employ lipid raft-mimicking SCOR bicelles to study PMP22 mutants, and find that the differences in dimer abundances are amplified in this medium when compared to micelle-based data, with disease mutants exhibiting up to 4 times more dimer than WT when liberated from SCOR bicelles. We combine our findings with previous cellular data to propose that the formation of PMP22 dimers from destabilized monomers is a key element of PMP22 mistrafficking.
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5
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Hammerschmid D, van Dyck JF, Sobott F, Calabrese AN. Interrogating Membrane Protein Structure and Lipid Interactions by Native Mass Spectrometry. Methods Mol Biol 2021; 2168:233-261. [PMID: 33582995 DOI: 10.1007/978-1-0716-0724-4_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Native mass spectrometry and native ion mobility mass spectrometry are now established techniques in structural biology, with recent work developing these methods for the study of integral membrane proteins reconstituted in both lipid bilayer and detergent environments. Here we show how native mass spectrometry can be used to interrogate integral membrane proteins, providing insights into conformation, oligomerization, subunit composition/stoichiometry, and interactions with detergents/lipids/drugs. Furthermore, we discuss the sample requirements and experimental considerations unique to integral membrane protein native mass spectrometry research.
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Affiliation(s)
- Dietmar Hammerschmid
- Protein Chemistry, Proteomics and Epigenetic Signalling (PPES), Department of Biomedical Sciences, University of Antwerp, Wilrijk, Belgium.,Biomolecular & Analytical Mass Spectrometry Group, Chemistry Department, University of Antwerp, Antwerp, Belgium
| | - Jeroen F van Dyck
- Biomolecular & Analytical Mass Spectrometry Group, Chemistry Department, University of Antwerp, Antwerp, Belgium
| | - Frank Sobott
- Biomolecular & Analytical Mass Spectrometry Group, Chemistry Department, University of Antwerp, Antwerp, Belgium.,Faculty of Biological Sciences, School of Molecular and Cellular Biology, University of Leeds, Leeds, UK.,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Antonio N Calabrese
- Faculty of Biological Sciences, School of Molecular and Cellular Biology, University of Leeds, Leeds, UK. .,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK.
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6
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Landreh M, Sahin C, Gault J, Sadeghi S, Drum CL, Uzdavinys P, Drew D, Allison TM, Degiacomi MT, Marklund EG. Predicting the Shapes of Protein Complexes through Collision Cross Section Measurements and Database Searches. Anal Chem 2020; 92:12297-12303. [PMID: 32660238 DOI: 10.1021/acs.analchem.0c01940] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
In structural biology, collision cross sections (CCSs) from ion mobility mass spectrometry (IM-MS) measurements are routinely compared to computationally or experimentally derived protein structures. Here, we investigate whether CCS data can inform about the shape of a protein in the absence of specific reference structures. Analysis of the proteins in the CCS database shows that protein complexes with low apparent densities are structurally more diverse than those with a high apparent density. Although assigning protein shapes purely on CCS data is not possible, we find that we can distinguish oblate- and prolate-shaped protein complexes by using the CCS, molecular weight, and oligomeric states to mine the Protein Data Bank (PDB) for potentially similar protein structures. Furthermore, comparing the CCS of a ferritin cage to the solution structures in the PDB reveals significant deviations caused by structural collapse in the gas phase. We then apply the strategy to an integral membrane protein by comparing the shapes of a prokaryotic and a eukaryotic sodium/proton antiporter homologue. We conclude that mining the PDB with IM-MS data is a time-effective way to derive low-resolution structural models.
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Affiliation(s)
- Michael Landreh
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solnavägen 9, 171 65, Stockholm, Sweden
| | - Cagla Sahin
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solnavägen 9, 171 65, Stockholm, Sweden.,Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Joseph Gault
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Samira Sadeghi
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 10 Medical Dr, Singapore 119228, Singapore
| | - Chester L Drum
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 10 Medical Dr, Singapore 119228, Singapore
| | - Povilas Uzdavinys
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm 114 19, Sweden
| | - David Drew
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm 114 19, Sweden
| | - Timothy M Allison
- Biomolecular Interaction Centre and School of Physical and Chemical Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Matteo T Degiacomi
- Department of Physics, Durham University, South Road, Durham DH1 3LE, United Kingdom
| | - Erik G Marklund
- Department of Chemistry - BMC, Uppsala University, Box 576, Uppsala 751 23, Sweden
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7
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Petroff JT, Tong A, Chen LJ, Dekoster GT, Khan F, Abramson J, Frieden C, Cheng WWL. Charge Reduction of Membrane Proteins in Native Mass Spectrometry Using Alkali Metal Acetate Salts. Anal Chem 2020; 92:6622-6630. [PMID: 32250604 DOI: 10.1021/acs.analchem.0c00454] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Native mass spectrometry (MS) provides the capacity to monitor membrane protein complexes and noncovalent binding of ligands and lipids to membrane proteins. The charge states produced by native MS of membrane proteins often result in gas-phase protein unfolding or loss of noncovalent interactions. In an effort to reduce the charge of membrane proteins, we examined the utility of alkali metal salts as a charge-reducing agent. Low concentrations of alkali metal salts caused marked charge reduction in the membrane protein, Erwinia ligand-gated ion channel (ELIC). The charge-reducing effect only occurred for membrane proteins and was detergent-dependent, being most pronounced in long polyethylene glycol (PEG)-based detergents such as C10E5 and C12E8. On the basis of these results, we propose a mechanism for alkali metal charge reduction of membrane proteins. Addition of low concentrations of alkali metals may provide an advantageous approach for charge reduction of detergent-solubilized membrane proteins by native MS.
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Affiliation(s)
| | | | | | | | - Farha Khan
- Department of Physiology, David Geffen School of Medicine at UCLA, 310833 Le Conte Avenue, Los Angeles, California 90095, United States
| | - Jeff Abramson
- Department of Physiology, David Geffen School of Medicine at UCLA, 310833 Le Conte Avenue, Los Angeles, California 90095, United States
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8
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Stiving AQ, Jones BJ, Ujma J, Giles K, Wysocki VH. Collision Cross Sections of Charge-Reduced Proteins and Protein Complexes: A Database for Collision Cross Section Calibration. Anal Chem 2020; 92:4475-4483. [PMID: 32048834 PMCID: PMC7170229 DOI: 10.1021/acs.analchem.9b05519] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The use of charge-reducing reagents to generate lower-charge ions has gained popularity in the field of native mass spectrometry (MS) and ion mobility mass spectrometry (IM-MS). This is because the lower number of charged sites decreases the propensity for Coulombic repulsions and unfolding/restructuring, helping to preserve the native-like structure. Furthermore, lowering the charge state consequently increases the mass-to-charge values (m/z), effectively increasing spacing between signals originating from small mass differences, such as different proteoforms or protein-drug complexes. IM-MS yields collision cross section (CCS, Ω) values that provide information about the three-dimensional structure of the ion. Traveling wave IM (TWIM) is an established and expanding technique within the native MS field. TWIM measurements require CCS calibration, which is achieved via the use of standard species of known CCS. Current databases for native-like proteins and protein complexes provide CCS values obtained using normal (i.e., non-charge-reducing) conditions. Herein, we explored the validity of using "normal" charge calibrants to calibrate for charge-reduced proteins and show cases where it is not appropriate. Using a custom linear field drift cell that enables the determination of ion mobilities from "first principles", we directly determined CCS values for 19 protein calibrant species under three solution conditions (yielding a broad range of charge states) and two drift gases. This has established a database of CCS and reduced-mobility (K0) values, along with their associated uncertainties, for proteins and protein complexes over a large m/z range. TWIM validation of this database shows improved accuracy over existing methods in calibrating CCS values for charge-reduced proteins.
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Affiliation(s)
- Alyssa Q. Stiving
- Department of Chemistry and Biochemistry
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH, USA
| | - Benjamin J. Jones
- Department of Chemistry and Biochemistry
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH, USA
| | - Jakub Ujma
- Waters Corporation, Wilmslow, SK9 4AX, United Kingdom
| | - Kevin Giles
- Waters Corporation, Wilmslow, SK9 4AX, United Kingdom
| | - Vicki H. Wysocki
- Department of Chemistry and Biochemistry
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH, USA
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9
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Poltash ML, McCabe JW, Shirzadeh M, Laganowsky A, Russell DH. Native IM-Orbitrap MS: Resolving What Was Hidden. Trends Analyt Chem 2020; 124:115533. [PMID: 32189816 PMCID: PMC7079669 DOI: 10.1016/j.trac.2019.05.035] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Native ion mobility-mass spectrometry (IM-MS) is an emerging biophysical approach to probe the intricate details of protein structure and function. The instrument design enables measurements of accurate first-principle determinations of rotationally-averaged ion-neutral collision cross sections coupled with high-mass, high-resolution mass measurement capabilities of Orbitrap MS. The inherent duty-cycle mismatch between drift tube IM and Orbitrap MS is alleviated by operating the drift tube in a frequency modulated mode while continuously acquiring mass spectra with the Orbitrap MS. Fourier transform of the resulting time-domain signal, i.e., ion abundances as a function of the modulation frequency, yields a frequency domain spectrum that is then converted (s-1 to s) to IM drift time. This multiplexed approach allows for a duty-cycle of 25% compared to <1% for traditional "pulse-and-wait" IM-ToF-MS. Improvements in mobility and mass resolution of the IM-Orbitrap allows for accurate analysis of intact protein complexes and the possibility of capturing protein dynamics.
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Affiliation(s)
- Michael L. Poltash
- Department of Chemistry, Texas A&M University, 3255 TAMU, College Station, Texas 77843
| | - Jacob W. McCabe
- Department of Chemistry, Texas A&M University, 3255 TAMU, College Station, Texas 77843
| | - Mehdi Shirzadeh
- Department of Chemistry, Texas A&M University, 3255 TAMU, College Station, Texas 77843
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, 3255 TAMU, College Station, Texas 77843
| | - David H. Russell
- Department of Chemistry, Texas A&M University, 3255 TAMU, College Station, Texas 77843
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10
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McAlary L, Harrison JA, Aquilina JA, Fitzgerald SP, Kelso C, Benesch JL, Yerbury JJ. Trajectory Taken by Dimeric Cu/Zn Superoxide Dismutase through the Protein Unfolding and Dissociation Landscape Is Modulated by Salt Bridge Formation. Anal Chem 2019; 92:1702-1711. [DOI: 10.1021/acs.analchem.9b01699] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Luke McAlary
- Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
- Molecular Horizons and School of Chemistry and Molecular Bioscience, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Julian A. Harrison
- Molecular Horizons and School of Chemistry and Molecular Bioscience, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - J. Andrew Aquilina
- Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
- Molecular Horizons and School of Chemistry and Molecular Bioscience, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | | | - Celine Kelso
- Molecular Horizons and School of Chemistry and Molecular Bioscience, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Justin L.P. Benesch
- Department of Chemistry, Physical and Theoretical Chemistry Department, University of Oxford, Oxford OX1 3QZ, U.K
| | - Justin J. Yerbury
- Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
- Molecular Horizons and School of Chemistry and Molecular Bioscience, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, New South Wales 2522, Australia
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11
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Fantin SM, Parson KF, Niu S, Liu J, Polasky DA, Dixit SM, Ferguson-Miller SM, Ruotolo BT. Collision Induced Unfolding Classifies Ligands Bound to the Integral Membrane Translocator Protein. Anal Chem 2019; 91:15469-15476. [PMID: 31743004 DOI: 10.1021/acs.analchem.9b03208] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Membrane proteins represent most current therapeutic targets, yet remain understudied due to their insolubility in aqueous solvents and generally low yields during purification and expression. Ion mobility-mass spectrometry and collision induced unfolding experiments have recently garnered attention as methods capable of directly detecting and quantifying ligand binding within a wide range of membrane protein systems. Despite prior success, ionized surfactant often creates chemical noise patterns resulting in significant challenges surrounding the study of small membrane protein-ligand complexes. Here, we present a new data analysis workflow that overcomes such chemical noise and then utilize this approach to quantify and classify ligand binding associated with the 36 kDa dimer of translocator protein (TSPO). Following our denoising protocol, we detect separate gas-phase unfolding signatures for lipid and protoporphyrin TSPO binders, molecular classes that likely interact with separate regions of the protein surface. Further, a detailed classification analysis reveals that lipid alkyl chain saturation levels can be detected within our gas-phase protein unfolding data. We combine these data and classification schemes with mass spectra acquired directly from liquid-liquid extracts to propose an identity for a previously unknown endogenous TSPO ligand.
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Affiliation(s)
- Sarah M Fantin
- Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Kristine F Parson
- Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Shuai Niu
- Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Jian Liu
- Department of Biochemistry and Molecular Biology , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Daniel A Polasky
- Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Sugyan M Dixit
- Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Shelagh M Ferguson-Miller
- Department of Biochemistry and Molecular Biology , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Brandon T Ruotolo
- Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
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12
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Kaldmäe M, Österlund N, Lianoudaki D, Sahin C, Bergman P, Nyman T, Kronqvist N, Ilag LL, Allison TM, Marklund EG, Landreh M. Gas-Phase Collisions with Trimethylamine-N-Oxide Enable Activation-Controlled Protein Ion Charge Reduction. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:1385-1388. [PMID: 31286443 PMCID: PMC6669196 DOI: 10.1007/s13361-019-02177-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 02/20/2019] [Accepted: 03/01/2019] [Indexed: 05/19/2023]
Abstract
Modulating protein ion charge is a useful tool for the study of protein folding and interactions by electrospray ionization mass spectrometry. Here, we investigate activation-dependent charge reduction of protein ions with the chemical chaperone trimethylamine-N-oxide (TMAO). Based on experiments carried out on proteins ranging from 4.5 to 35 kDa, we find that when combined with collisional activation, TMAO removes approximately 60% of the charges acquired under native conditions. Ion mobility measurements furthermore show that TMAO-mediated charge reduction produces the same end charge state and arrival time distributions for native-like and denatured protein ions. Our results suggest that gas-phase collisions between the protein ions and TMAO result in proton transfer, in line with previous findings for dimethyl- and trimethylamine. By adjusting the energy of the collisions experienced by the ions, it is possible to control the degree of charge reduction, making TMAO a highly dynamic charge reducer that opens new avenues for manipulating protein charge states in ESI-MS and for investigating the relationship between protein charge and conformation. ᅟ.
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Affiliation(s)
- Margit Kaldmäe
- Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 65, Stockholm, Sweden
| | - Nicklas Österlund
- Department of Biochemistry and Biophysics, Stockholm University, 106 91, Stockholm, Sweden
- Department of Environmental Science and Analytical Chemistry, Stockholm University, 106 91, Stockholm, Sweden
| | - Danai Lianoudaki
- Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 65, Stockholm, Sweden
| | - Cagla Sahin
- Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 65, Stockholm, Sweden
| | - Peter Bergman
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, 141 86, Huddinge, Sweden
| | - Tomas Nyman
- Protein Science Facility, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 65, Stockholm, Sweden
| | - Nina Kronqvist
- Division for Neurogeriatrics, Department of Neurobiology, Care Sciences and Society (NVS), Karolinska Institutet, 141 83, Huddinge, Sweden
| | - Leopold L Ilag
- Department of Environmental Science and Analytical Chemistry, Stockholm University, 106 91, Stockholm, Sweden
| | - Timothy M Allison
- Biomolecular Interaction Centre and School of Physical and Chemical Sciences, University of Canterbury, Christchurch, 8140, New Zealand
| | - Erik G Marklund
- Department of Chemistry - BMC, Uppsala University, Box 576, 751 23, Uppsala, Sweden
| | - Michael Landreh
- Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 65, Stockholm, Sweden.
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13
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Rolland AD, Prell JS. Computational Insights into Compaction of Gas-Phase Protein and Protein Complex Ions in Native Ion Mobility-Mass Spectrometry. Trends Analyt Chem 2019; 116:282-291. [PMID: 31983791 PMCID: PMC6979403 DOI: 10.1016/j.trac.2019.04.023] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Native ion mobility-mass spectrometry (IM-MS) is a rapidly growing field for studying the composition and structure of biomolecules and biomolecular complexes using gas-phase methods. Typically, ions are formed in native IM-MS using gentle nanoelectrospray ionization conditions, which in many cases can preserve condensed-phase stoichiometry. Although much evidence shows that large-scale condensed-phase structure, such as quaternary structure and topology, can also be preserved, it is less clear to what extent smaller-scale structure is preserved in native IM-MS. This review surveys computational and experimental efforts aimed at characterizing compaction and structural rearrangements of protein and protein complex ions upon transfer to the gas phase. A brief summary of gas-phase compaction results from molecular dynamics simulations using multiple common force fields and a wide variety of protein ions is presented and compared to literature IM-MS data.
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Affiliation(s)
- Amber D. Rolland
- Department of Chemistry and Biochemistry, 1253 University
of Oregon, Eugene, OR, USA, 97403-1253
| | - James S. Prell
- Department of Chemistry and Biochemistry, 1253 University
of Oregon, Eugene, OR, USA, 97403-1253
- Materials Science Institute, 1252 University of Oregon,
Eugene, OR, USA 97403-1252
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14
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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: 19] [Impact Index Per Article: 3.8] [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.
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Affiliation(s)
- Tara Pukala
- Discipline of Chemistry, University of Adelaide, North Terrace, Adelaide, South Australia, 5005
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15
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Österlund N, Moons R, Ilag LL, Sobott F, Gräslund A. Native Ion Mobility-Mass Spectrometry Reveals the Formation of β-Barrel Shaped Amyloid-β Hexamers in a Membrane-Mimicking Environment. J Am Chem Soc 2019; 141:10440-10450. [DOI: 10.1021/jacs.9b04596] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Nicklas Österlund
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Rani Moons
- Department of Chemistry, University of Antwerp, Antwerp, Belgium
| | - Leopold L. Ilag
- Department of Environmental Science and Analytical Chemistry, Stockholm University, Stockholm, Sweden
| | - Frank Sobott
- Department of Chemistry, University of Antwerp, Antwerp, Belgium
- The Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, The United Kingdom
- School of Molecular and Cellular Biology, University of Leeds, Leeds, The United Kingdom
| | - Astrid Gräslund
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
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16
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Harrison JA, Kelso C, Pukala TL, Beck JL. Conditions for Analysis of Native Protein Structures Using Uniform Field Drift Tube Ion Mobility Mass Spectrometry and Characterization of Stable Calibrants for TWIM-MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:256-267. [PMID: 30324262 DOI: 10.1007/s13361-018-2074-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Revised: 09/14/2018] [Accepted: 09/20/2018] [Indexed: 06/08/2023]
Abstract
Determination of collisional cross sections (CCS) by travelling wave ion mobility mass spectrometry (TWIM-MS) requires calibration against standards for which the CCS has been measured previously by drift tube ion mobility mass spectrometry (DTIM-MS). The different extents of collisional activation in TWIM-MS and DTIM-MS can give rise to discrepancies in the CCS of calibrants across the two platforms. Furthermore, the conditions required to ionize and transmit large, folded proteins and assemblies may variably affect the structure of the calibrants and analytes. Stable hetero-oligomeric phospholipase A2 (PDx) and its subunits were characterized as calibrants for TWIM-MS. Conditions for acquisition of native-like TWIM (Synapt G1 HDMS) and DTIM (Agilent 6560 IM-Q-TOF) mass spectra were optimized to ensure the spectra exhibited similar charge state distributions. CCS measurements (DTIM-MS) for ubiquitin, cytochrome c, holo-myoglobin, serum albumin and glutamate dehydrogenase were in good agreement with other recent results determined using this and other DTIM-MS instruments. PDx and its β and γ subunits were stable across a wide range of cone and trap voltages in TWIM-MS and were stable in the presence of organic solvents. The CCS of PDx and its subunits were determined by DTIM-MS and were used as calibrants in determination of CCS of native-like cytochrome c, holo-myoglobin, carbonic anhydrase, serum albumin and haemoglobin in TWIM-MS. The CCS values were in good agreement with those measured by DTIM-MS where available. These experiments demonstrate conditions for analysis of native-like proteins using a commercially available DTIM-MS instrument, characterize robust calibrants for TWIM-MS, and present CCS values determined by DTIM-MS and TWIM-MS for native proteins to add to the current literature database. Graphical Abstract ᅟ.
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Affiliation(s)
- Julian A Harrison
- School of Chemistry, University of Wollongong, Wollongong, NSW, 2522, Australia
- Molecular Horizons, University of Wollongong, Wollongong, NSW, 2522, Australia
| | - Celine Kelso
- School of Chemistry, University of Wollongong, Wollongong, NSW, 2522, Australia
- Molecular Horizons, University of Wollongong, Wollongong, NSW, 2522, Australia
| | - Tara L Pukala
- Discipline of Chemistry, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Jennifer L Beck
- School of Chemistry, University of Wollongong, Wollongong, NSW, 2522, Australia.
- Molecular Horizons, University of Wollongong, Wollongong, NSW, 2522, Australia.
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17
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Ion Mobility in Structural Biology. ADVANCES IN ION MOBILITY-MASS SPECTROMETRY: FUNDAMENTALS, INSTRUMENTATION AND APPLICATIONS 2019. [DOI: 10.1016/bs.coac.2018.10.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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18
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Hinnenkamp V, Klein J, Meckelmann SW, Balsaa P, Schmidt TC, Schmitz OJ. Comparison of CCS Values Determined by Traveling Wave Ion Mobility Mass Spectrometry and Drift Tube Ion Mobility Mass Spectrometry. Anal Chem 2018; 90:12042-12050. [DOI: 10.1021/acs.analchem.8b02711] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Vanessa Hinnenkamp
- IWW Water Centre, Moritzstraße 26, 45476 Muelheim an der Ruhr, Germany
- Instrumental Analytical Chemistry and Centre for Water and Environmental Research, Universitaetsstrasse 5, 45141 Essen, Germany
| | | | | | - Peter Balsaa
- IWW Water Centre, Moritzstraße 26, 45476 Muelheim an der Ruhr, Germany
| | - Torsten C. Schmidt
- IWW Water Centre, Moritzstraße 26, 45476 Muelheim an der Ruhr, Germany
- Instrumental Analytical Chemistry and Centre for Water and Environmental Research, Universitaetsstrasse 5, 45141 Essen, Germany
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19
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Calabrese AN, Radford SE. Mass spectrometry-enabled structural biology of membrane proteins. Methods 2018; 147:187-205. [DOI: 10.1016/j.ymeth.2018.02.020] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 01/30/2018] [Accepted: 02/21/2018] [Indexed: 01/01/2023] Open
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20
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Abstract
Membrane proteins interact with a myriad of lipid species in the biological membrane, leading to a bewildering number of possible protein-lipid assemblies. Despite this inherent complexity, the identification of specific protein-lipid interactions and the crucial role of lipids in the folding, structure, and function of membrane proteins is emerging from an increasing number of reports. Fundamental questions remain, however, regarding the ability of specific lipid binding events to membrane proteins to alter remote binding sites for lipids of a different type, a property referred to as allostery [Monod J, Wyman J, Changeux JP (1965) J Mol Biol 12:88-118]. Here, we use native mass spectrometry to determine the allosteric nature of heterogeneous lipid binding events to membrane proteins. We monitored individual lipid binding events to the ammonia channel (AmtB) from Escherichia coli, enabling determination of their equilibrium binding constants. We found that different lipid pairs display a range of allosteric modulation. In particular, the binding of phosphatidylethanolamine and cardiolipin-like molecules to AmtB exhibited the largest degree of allosteric modulation, inspiring us to determine the cocrystal structure of AmtB in this lipid environment. The 2.45-Å resolution structure reveals a cardiolipin-like molecule bound to each subunit of the trimeric complex. Mutation of a single residue in AmtB abolishes the positive allosteric modulation observed for binding phosphatidylethanolamine and cardiolipin-like molecules. Our results demonstrate that specific lipid-protein interactions can act as allosteric modulators for the binding of different lipid types to integral membrane proteins.
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21
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Eyers CE, Vonderach M, Ferries S, Jeacock K, Eyers PA. Understanding protein–drug interactions using ion mobility–mass spectrometry. Curr Opin Chem Biol 2018; 42:167-176. [DOI: 10.1016/j.cbpa.2017.12.013] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 12/08/2017] [Accepted: 12/22/2017] [Indexed: 01/23/2023]
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22
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Fundamentals of ion mobility spectrometry. Curr Opin Chem Biol 2018; 42:51-59. [DOI: 10.1016/j.cbpa.2017.10.022] [Citation(s) in RCA: 186] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 10/13/2017] [Accepted: 10/17/2017] [Indexed: 12/13/2022]
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23
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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.
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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.
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24
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D'Atri V, Causon T, Hernandez-Alba O, Mutabazi A, Veuthey JL, Cianferani S, Guillarme D. Adding a new separation dimension to MS and LC-MS: What is the utility of ion mobility spectrometry? J Sep Sci 2017; 41:20-67. [PMID: 29024509 DOI: 10.1002/jssc.201700919] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 09/19/2017] [Accepted: 09/19/2017] [Indexed: 12/12/2022]
Abstract
Ion mobility spectrometry is an analytical technique known for more than 100 years, which entails separating ions in the gas phase based on their size, shape, and charge. While ion mobility spectrometry alone can be useful for some applications (mostly security analysis for detecting certain classes of narcotics and explosives), it becomes even more powerful in combination with mass spectrometry and high-performance liquid chromatography. Indeed, the limited resolving power of ion mobility spectrometry alone can be tackled when combining this analytical strategy with mass spectrometry or liquid chromatography with mass spectrometry. Over the last few years, the hyphenation of ion mobility spectrometry to mass spectrometry or liquid chromatography with mass spectrometry has attracted more and more interest, with significant progresses in both technical advances and pioneering applications. This review describes the theoretical background, available technologies, and future capabilities of these techniques. It also highlights a wide range of applications, from small molecules (natural products, metabolites, glycans, lipids) to large biomolecules (proteins, protein complexes, biopharmaceuticals, oligonucleotides).
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Affiliation(s)
- Valentina D'Atri
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
| | - Tim Causon
- Division of Analytical Chemistry, Department of Chemistry, University of Natural Resources and Life Sciences (BOKU Vienna), Vienna, Austria
| | - Oscar Hernandez-Alba
- BioOrganic Mass Spectrometry Laboratory (LSMBO), IPHC, Université de Strasbourg, CNRS, Strasbourg, France
| | - Aline Mutabazi
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
| | - Jean-Luc Veuthey
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
| | - Sarah Cianferani
- BioOrganic Mass Spectrometry Laboratory (LSMBO), IPHC, Université de Strasbourg, CNRS, Strasbourg, France
| | - Davy Guillarme
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
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25
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Haler JRN, Kune C, Massonnet P, Comby-Zerbino C, Jordens J, Honing M, Mengerink Y, Far J, De Pauw E. Comprehensive Ion Mobility Calibration: Poly(ethylene oxide) Polymer Calibrants and General Strategies. Anal Chem 2017; 89:12076-12086. [DOI: 10.1021/acs.analchem.7b02564] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jean R. N. Haler
- Mass
Spectrometry Laboratory, University of Liège, Quartier Agora, Allée du
Six Aout 11, B-4000 Liège, Belgium
| | - Christopher Kune
- Mass
Spectrometry Laboratory, University of Liège, Quartier Agora, Allée du
Six Aout 11, B-4000 Liège, Belgium
| | - Philippe Massonnet
- Mass
Spectrometry Laboratory, University of Liège, Quartier Agora, Allée du
Six Aout 11, B-4000 Liège, Belgium
| | - Clothilde Comby-Zerbino
- Institut
Lumière Matière, Université de Lyon, Université Lyon 1, CNRS, 69100 Villeurbanne, France
| | | | | | | | - Johann Far
- Mass
Spectrometry Laboratory, University of Liège, Quartier Agora, Allée du
Six Aout 11, B-4000 Liège, Belgium
| | - Edwin De Pauw
- Mass
Spectrometry Laboratory, University of Liège, Quartier Agora, Allée du
Six Aout 11, B-4000 Liège, Belgium
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26
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Duez Q, Chirot F, Liénard R, Josse T, Choi C, Coulembier O, Dugourd P, Cornil J, Gerbaux P, De Winter J. Polymers for Traveling Wave Ion Mobility Spectrometry Calibration. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:2483-2491. [PMID: 28762031 DOI: 10.1007/s13361-017-1762-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 06/30/2017] [Accepted: 07/09/2017] [Indexed: 06/07/2023]
Abstract
One of the main issues when using traveling wave ion mobility spectrometry (TWIMS) for the determination of collisional cross-section (CCS) concerns the need for a robust calibration procedure built from referent ions of known CCS. Here, we implement synthetic polymer ions as CCS calibrants in positive ion mode. Based on their intrinsic polydispersities, polymers offer in a single sample the opportunity to generate, upon electrospray ionization, numerous ions covering a broad mass range and a large CCS window for different charge states at a time. In addition, the key advantage of polymer ions as CCS calibrants lies in the robustness of their gas-phase structure with respect to the instrumental conditions, making them less prone to collisional-induced unfolding (CIU) than protein ions. In this paper, we present a CCS calibration procedure using sodium cationized polylactide and polyethylene glycol, PLA and PEG, as calibrants with reference CCS determined on a home-made drift tube. Our calibration procedure is further validated by testing the polymer calibration to determine CCS of numerous different ions for which CCS are reported in the literature. Graphical Abstract ᅟ.
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Affiliation(s)
- Quentin Duez
- Organic Synthesis and Mass Spectrometry Laboratory, Interdisciplinary Center for Mass Spectrometry (CISMa), University of Mons (UMons), Place du Parc, 23, Mons, 7000, Belgium
- Laboratory for Chemistry of Novel Materials, Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons (UMons), Place du Parc, 23, Mons, 7000, Belgium
| | - Fabien Chirot
- Université Lyon, Université Claude Bernard Lyon 1, ENS de Lyon, CNRS, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100, Villeurbanne, France
| | - Romain Liénard
- Organic Synthesis and Mass Spectrometry Laboratory, Interdisciplinary Center for Mass Spectrometry (CISMa), University of Mons (UMons), Place du Parc, 23, Mons, 7000, Belgium
- Laboratory of Polymeric and Composite Materials, Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons, UMons, 23 Place du Parc, 7000, Mons, Belgium
| | - Thomas Josse
- Organic Synthesis and Mass Spectrometry Laboratory, Interdisciplinary Center for Mass Spectrometry (CISMa), University of Mons (UMons), Place du Parc, 23, Mons, 7000, Belgium
- Laboratory of Polymeric and Composite Materials, Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons, UMons, 23 Place du Parc, 7000, Mons, Belgium
| | - ChangMin Choi
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622, Lyon, France
| | - Olivier Coulembier
- Laboratory of Polymeric and Composite Materials, Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons, UMons, 23 Place du Parc, 7000, Mons, Belgium
| | - Philippe Dugourd
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622, Lyon, France
| | - Jérôme Cornil
- Laboratory for Chemistry of Novel Materials, Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons (UMons), Place du Parc, 23, Mons, 7000, Belgium
| | - Pascal Gerbaux
- Organic Synthesis and Mass Spectrometry Laboratory, Interdisciplinary Center for Mass Spectrometry (CISMa), University of Mons (UMons), Place du Parc, 23, Mons, 7000, Belgium
| | - Julien De Winter
- Organic Synthesis and Mass Spectrometry Laboratory, Interdisciplinary Center for Mass Spectrometry (CISMa), University of Mons (UMons), Place du Parc, 23, Mons, 7000, Belgium.
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27
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Van der Rest G, Halgand F. Size Exclusion Chromatography-Ion Mobility-Mass Spectrometry Coupling: a Step Toward Structural Biology. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:2519-2522. [PMID: 28933014 DOI: 10.1007/s13361-017-1810-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 09/04/2017] [Accepted: 09/04/2017] [Indexed: 06/07/2023]
Abstract
Noncovalent interactions are essential for the structural organization of biomacromolecules in cells. For this reason, the study of the biophysical, dynamic, and architectural interactions among biomacromolecules is essential. Since mass spectrometry requires compatible solutions while preserving the noncovalent bonding network, we envisioned that size exclusion chromatography coupled with ion mobility and mass spectrometry would be a valuable technique to desalt the initial sample and provide solution and gas-phase structural information in a single stage experiment. Such coupling allowed obtaining information on solution protein complex composition with SEC separation and on authenticity and purity with IMS-MS. Our study demonstrated that such coupling is compatible, useful, as well as suitable for a routine analysis, in pharmaceutical industry, for example. Mobility data were reliable and injected standards allowed calibrating the collision cross-section scale. Graphical Abstract ᅟ.
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Affiliation(s)
- Guillaume Van der Rest
- Université Paris Sud-CNRS, UMR 8000, Rue Henri Becquerel, Bâtiment 201 P 2, 91405, Orsay, France
| | - Frédéric Halgand
- Université Paris Sud-CNRS, UMR 8000, Rue Henri Becquerel, Bâtiment 201 P 2, 91405, Orsay, France.
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28
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Kar UK, Simonian M, Whitelegge JP. Integral membrane proteins: bottom-up, top-down and structural proteomics. Expert Rev Proteomics 2017; 14:715-723. [PMID: 28737967 DOI: 10.1080/14789450.2017.1359545] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
INTRODUCTION Integral membrane proteins and lipids constitute the bilayer membranes that surround cells and sub-cellular compartments, and modulate movements of molecules and information between them. Since membrane protein drug targets represent a disproportionately large segment of the proteome, technical developments need timely review. Areas covered: Publically available resources such as Pubmed were surveyed. Bottom-up proteomics analyses now allow efficient extraction and digestion such that membrane protein coverage is essentially complete, making up around one third of the proteome. However, this coverage relies upon hydrophilic loop regions while transmembrane domains are generally poorly covered in peptide-based strategies. Top-down mass spectrometry where the intact membrane protein is fragmented in the gas phase gives good coverage in transmembrane regions, and membrane fractions are yielding to high-throughput top-down proteomics. Exciting progress in native mass spectrometry of membrane protein complexes is providing insights into subunit stoichiometry and lipid binding, and cross-linking strategies are contributing critical in-vivo information. Expert commentary: It is clear from the literature that integral membrane proteins have yielded to advanced techniques in protein chemistry and mass spectrometry, with applications limited only by the imagination of investigators. Key advances toward translation to the clinic are emphasized.
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Affiliation(s)
- Upendra K Kar
- a Department of Pharmaceutical Sciences, College of Pharmacy , University of Arkansas for Medical Sciences , Little Rock , AR , USA
| | - Margaret Simonian
- b NPI-Semel Institute , University of California Los Angeles , Los Angeles , CA , USA
| | - Julian P Whitelegge
- b NPI-Semel Institute , University of California Los Angeles , Los Angeles , CA , USA
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29
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Landreh M, Marklund EG, Uzdavinys P, Degiacomi MT, Coincon M, Gault J, Gupta K, Liko I, Benesch JLP, Drew D, Robinson CV. Integrating mass spectrometry with MD simulations reveals the role of lipids in Na +/H + antiporters. Nat Commun 2017; 8:13993. [PMID: 28071645 PMCID: PMC5234078 DOI: 10.1038/ncomms13993] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 11/18/2016] [Indexed: 12/15/2022] Open
Abstract
Na+/H+ antiporters are found in all kingdoms of life and exhibit catalysis rates that are among the fastest of all known secondary-active transporters. Here we combine ion mobility mass spectrometry and molecular dynamics simulations to study the conformational stability and lipid-binding properties of the Na+/H+ exchanger NapA from Thermus thermophilus and compare this to the prototypical antiporter NhaA from Escherichia coli and the human homologue NHA2. We find that NapA and NHA2, but not NhaA, form stable dimers and do not selectively retain membrane lipids. By comparing wild-type NapA with engineered variants, we show that the unfolding of the protein in the gas phase involves the disruption of inter-domain contacts. Lipids around the domain interface protect the native fold in the gas phase by mediating contacts between the mobile protein segments. We speculate that elevator-type antiporters such as NapA, and likely NHA2, use a subset of annular lipids as structural support to facilitate large-scale conformational changes within the membrane.
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Affiliation(s)
- Michael Landreh
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, Oxfordshire OX1 3QZ, UK
| | - Erik G. Marklund
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, Oxfordshire OX1 3QZ, UK
- Department of Chemistry–BMC, Uppsala University, Box 576, Uppsala SE-751 23, Sweden
| | - Povilas Uzdavinys
- Centre for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Stockholm SE-106 91, Sweden
| | - Matteo T. Degiacomi
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, Oxfordshire OX1 3QZ, UK
| | - Mathieu Coincon
- Centre for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Stockholm SE-106 91, Sweden
| | - Joseph Gault
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, Oxfordshire OX1 3QZ, UK
| | - Kallol Gupta
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, Oxfordshire OX1 3QZ, UK
| | - Idlir Liko
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, Oxfordshire OX1 3QZ, UK
| | - Justin L. P. Benesch
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, Oxfordshire OX1 3QZ, UK
| | - David Drew
- Centre for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Stockholm SE-106 91, Sweden
| | - Carol V. Robinson
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, Oxfordshire OX1 3QZ, UK
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30
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Allen SJ, Eaton RM, Bush MF. Analysis of Native-Like Ions Using Structures for Lossless Ion Manipulations. Anal Chem 2016; 88:9118-26. [DOI: 10.1021/acs.analchem.6b02089] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Samuel J. Allen
- University of Washington, Department of Chemistry, Box 351700, Seattle, Washington 98195-1700, United States
| | - Rachel M. Eaton
- University of Washington, Department of Chemistry, Box 351700, Seattle, Washington 98195-1700, United States
| | - Matthew F. Bush
- University of Washington, Department of Chemistry, Box 351700, Seattle, Washington 98195-1700, United States
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