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Russell Lewis B, Lawrence R, Hammerschmid D, Reading E. Structural mass spectrometry approaches to understand multidrug efflux systems. Essays Biochem 2022; 67:255-267. [PMID: 36504255 PMCID: PMC10070475 DOI: 10.1042/ebc20220190] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/23/2022] [Accepted: 11/23/2022] [Indexed: 12/14/2022]
Abstract
Multidrug efflux pumps are ubiquitous across both eukaryotes and prokaryotes, and have major implications in antimicrobial and multidrug resistance. They reside within cellular membranes and have proven difficult to study owing to their hydrophobic character and relationship with their compositionally complex lipid environment. Advances in structural mass spectrometry (MS) techniques have made it possible to study these systems to elucidate critical information on their structure-function relationships. For example, MS techniques can report on protein structural dynamics, stoichiometry, connectivity, solvent accessibility, and binding interactions with ligands, lipids, and other proteins. This information proving powerful when used in conjunction with complementary structural biology methods and molecular dynamics (MD) simulations. In the present review, aimed at those not experts in MS techniques, we report on the current uses of MS in studying multidrug efflux systems, practical considerations to consider, and the future direction of the field. In the first section, we highlight the importance of studying multidrug efflux proteins, and introduce a range of different MS techniques and explain what information they yield. In the second section, we review recent studies that have utilised MS techniques to study and characterise a range of different multidrug efflux systems.
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Affiliation(s)
- Benjamin Russell Lewis
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, U.K
| | - Ryan Lawrence
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, U.K
| | - Dietmar Hammerschmid
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, U.K
| | - Eamonn Reading
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, U.K
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Pan X, Vachet RW. MEMBRANE PROTEIN STRUCTURES AND INTERACTIONS FROM COVALENT LABELING COUPLED WITH MASS SPECTROMETRY. MASS SPECTROMETRY REVIEWS 2022; 41:51-69. [PMID: 33145813 PMCID: PMC8093322 DOI: 10.1002/mas.21667] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 05/31/2023]
Abstract
Membrane proteins are incredibly important biomolecules because they mediate interactions between a cell's external and internal environment. Obtaining information about membrane protein structure and interactions is thus important for understanding these essential biomolecules. Compared with the analyses of water-soluble proteins, the structural analysis of membrane proteins is more challenging owing to their unique chemical properties and the presence of lipid components that are necessary to solubilize them. The combination of covalent labeling (CL) and mass spectrometry (MS) has recently been applied with great success to study membrane protein structure and interactions. These studies have demonstrated the many advantages that CL-MS methods have over other traditional biophysical techniques. In this review, we discuss both amino acid-specific and non-specific labeling approaches and the special considerations needed to address the unique challenges associated with interrogating membrane proteins. This review highlights the aspects of this approach that require special care to be applied correctly and provides a comprehensive review of the membrane protein systems that have been studied by CL-MS. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.
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Cheng M, Guo C, Li W, Gross ML. Free‐Radical Membrane Protein Footprinting by Photolysis of Perfluoroisopropyl Iodide Partitioned to Detergent Micelle by Sonication. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202014096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Ming Cheng
- Department of Chemistry Washington University in St. Louis One Brookings Drive Saint Louis MO 63130 USA
- Current address: Department of Molecular Medicine The Scripps Research Institute La Jolla CA 92037 USA
| | - Chunyang Guo
- Department of Chemistry Washington University in St. Louis One Brookings Drive Saint Louis MO 63130 USA
| | - Weikai Li
- Department of Biochemistry and Molecular Biophysics Washington University School of Medicine St. Louis MO 63130 USA
| | - Michael L. Gross
- Department of Chemistry Washington University in St. Louis One Brookings Drive Saint Louis MO 63130 USA
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Cheng M, Guo C, Li W, Gross ML. Free-Radical Membrane Protein Footprinting by Photolysis of Perfluoroisopropyl Iodide Partitioned to Detergent Micelle by Sonication. Angew Chem Int Ed Engl 2021; 60:8867-8873. [PMID: 33751812 PMCID: PMC8083173 DOI: 10.1002/anie.202014096] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/29/2020] [Indexed: 12/14/2022]
Abstract
A free-radical footprinting approach is described for integral membrane protein (IMP) that extends, significantly, the "fast photochemical oxidation of proteins" (FPOP) platform. This new approach exploits highly hydrophobic perfluoroisopropyl iodide (PFIPI) together with tip sonication to ensure efficient transport into the micelle interior, allowing laser dissociation and footprinting of the transmembrane domains. In contrast to water soluble footprinters, PFIPI footprints both the hydrophobic intramembrane and the hydrophilic extramembrane domains of the IMP vitamin K epoxide reductase (VKOR). The footprinting is fast, giving high coverage for Tyr (100 %) and Trp. The incorporation of the reagent with sonication does not significantly affect VKOR's enzymatic function, and tyrosine iodination does not compromise protease digestion and the subsequent analysis. The locations for the modifications are largely consistent with the corresponding solvent accessibilities, recommending this approach for future membrane protein footprinting.
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Affiliation(s)
- Ming Cheng
- Department of Chemistry, Washington University in St. Louis, One Brookings Drive, Saint Louis, MO, 63130, USA
- Current address: Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Chunyang Guo
- Department of Chemistry, Washington University in St. Louis, One Brookings Drive, Saint Louis, MO, 63130, USA
| | - Weikai Li
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, 63130, USA
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, One Brookings Drive, Saint Louis, MO, 63130, USA
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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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Calabrese AN, Jackson SM, Jones LN, Beckstein O, Heinkel F, Gsponer J, Sharples D, Sans M, Kokkinidou M, Pearson AR, Radford SE, Ashcroft AE, Henderson PJF. Topological Dissection of the Membrane Transport Protein Mhp1 Derived from Cysteine Accessibility and Mass Spectrometry. Anal Chem 2017; 89:8844-8852. [PMID: 28726379 PMCID: PMC5588088 DOI: 10.1021/acs.analchem.7b01310] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Accepted: 07/20/2017] [Indexed: 01/01/2023]
Abstract
Cys accessibility and quantitative intact mass spectrometry (MS) analyses have been devised to study the topological transitions of Mhp1, the membrane protein for sodium-linked transport of hydantoins from Microbacterium liquefaciens. Mhp1 has been crystallized in three forms (outward-facing open, outward-facing occluded with substrate bound, and inward-facing open). We show that one natural cysteine residue, Cys327, out of three, has an enhanced solvent accessibility in the inward-facing (relative to the outward-facing) form. Reaction of the purified protein, in detergent, with the thiol-reactive N-ethylmalemide (NEM), results in modification of Cys327, suggesting that Mhp1 adopts predominantly inward-facing conformations. Addition of either sodium ions or the substrate 5-benzyl-l-hydantoin (L-BH) does not shift this conformational equilibrium, but systematic co-addition of the two results in an attenuation of labeling, indicating a shift toward outward-facing conformations that can be interpreted using conventional enzyme kinetic analyses. Such measurements can afford the Km for each ligand as well as the stoichiometry of ion-substrate-coupled conformational changes. Mutations that perturb the substrate binding site either result in the protein being unable to adopt outward-facing conformations or in a global destabilization of structure. The methodology combines covalent labeling, mass spectrometry, and kinetic analyses in a straightforward workflow applicable to a range of systems, enabling the interrogation of changes in a protein's conformation required for function at varied concentrations of substrates, and the consequences of mutations on these conformational transitions.
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Affiliation(s)
| | | | | | - Oliver Beckstein
- Department of Physics, Arizona State University , Tempe, Arizona 85287-1504, United States
| | - Florian Heinkel
- Centre for High-Throughput Biology, University of British Columbia , Vancouver, British Columbia, Canada V6T 1Z4
| | - Joerg Gsponer
- Centre for High-Throughput Biology, University of British Columbia , Vancouver, British Columbia, Canada V6T 1Z4
| | | | - Marta Sans
- Hamburg Centre for Ultrafast Imaging, Institute for Nanostructure and Solid State Physics, Universität Hamburg , Hamburg 22761, Germany
| | - Maria Kokkinidou
- Hamburg Centre for Ultrafast Imaging, Institute for Nanostructure and Solid State Physics, Universität Hamburg , Hamburg 22761, Germany
| | - Arwen R Pearson
- Hamburg Centre for Ultrafast Imaging, Institute for Nanostructure and Solid State Physics, Universität Hamburg , Hamburg 22761, Germany
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Calabrese AN, Watkinson TG, Henderson PJF, Radford SE, Ashcroft AE. Amphipols outperform dodecylmaltoside micelles in stabilizing membrane protein structure in the gas phase. Anal Chem 2014; 87:1118-26. [PMID: 25495802 PMCID: PMC4636139 DOI: 10.1021/ac5037022] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Noncovalent mass spectrometry (MS) is emerging as an invaluable technique to probe the structure, interactions, and dynamics of membrane proteins (MPs). However, maintaining native-like MP conformations in the gas phase using detergent solubilized proteins is often challenging and may limit structural analysis. Amphipols, such as the well characterized A8-35, are alternative reagents able to maintain the solubility of MPs in detergent-free solution. In this work, the ability of A8-35 to retain the structural integrity of MPs for interrogation by electrospray ionization-ion mobility spectrometry-mass spectrometry (ESI-IMS-MS) is compared systematically with the commonly used detergent dodecylmaltoside. MPs from the two major structural classes were selected for analysis, including two β-barrel outer MPs, PagP and OmpT (20.2 and 33.5 kDa, respectively), and two α-helical proteins, Mhp1 and GalP (54.6 and 51.7 kDa, respectively). Evaluation of the rotationally averaged collision cross sections of the observed ions revealed that the native structures of detergent solubilized MPs were not always retained in the gas phase, with both collapsed and unfolded species being detected. In contrast, ESI-IMS-MS analysis of the amphipol solubilized MPs studied resulted in charge state distributions consistent with less gas phase induced unfolding, and the presence of lowly charged ions which exhibit collision cross sections comparable with those calculated from high resolution structural data. The data demonstrate that A8-35 can be more effective than dodecylmaltoside at maintaining native MP structure and interactions in the gas phase, permitting noncovalent ESI-IMS-MS analysis of MPs from the two major structural classes, while gas phase dissociation from dodecylmaltoside micelles leads to significant gas phase unfolding, especially for the α-helical MPs studied.
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Affiliation(s)
- Antonio N Calabrese
- School of Molecular and Cellular Biology and ‡School of Biomedical Sciences, Astbury Centre for Structural Molecular Biology, University of Leeds , Leeds, LS2 9JT, United Kingdom
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Barrera NP, Robinson CV. Advances in the mass spectrometry of membrane proteins: from individual proteins to intact complexes. Annu Rev Biochem 2011; 80:247-71. [PMID: 21548785 DOI: 10.1146/annurev-biochem-062309-093307] [Citation(s) in RCA: 127] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Rapid advances in structural genomics and in large-scale proteomic projects have yielded vast amounts of data on soluble proteins and their complexes. Despite these advances, progress in studying membrane proteins using mass spectrometry (MS) has been slow. This is due in part to the inherent solubility and dynamic properties of these proteins, but also to their low abundance and the absence of polar side chains in amino acid residues. Considerable progress in overcoming these challenges is, however, now being made for all levels of structural characterization. This progress includes MS studies of the primary structure of membrane proteins, wherein sophisticated enrichment and trapping procedures are allowing multiple posttranslational modifications to be defined through to the secondary structure level in which proteins and peptides have been probed using hydrogen exchange, covalent, or radiolytic labeling methods. Exciting possibilities now exist to go beyond primary and secondary structure to reveal the tertiary and quaternary interactions of soluble and membrane subunits within intact assemblies of more than 700 kDa.
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Affiliation(s)
- Nelson P Barrera
- Department of Physiology, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile.
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Berridge G, Chalk R, D’Avanzo N, Dong L, Doyle D, Kim JI, Xia X, Burgess-Brown N, deRiso A, Carpenter EP, Gileadi O. High-performance liquid chromatography separation and intact mass analysis of detergent-solubilized integral membrane proteins. Anal Biochem 2011; 410:272-80. [PMID: 21093405 PMCID: PMC3041925 DOI: 10.1016/j.ab.2010.11.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2010] [Revised: 11/04/2010] [Accepted: 11/05/2010] [Indexed: 11/17/2022]
Abstract
We have developed a method for intact mass analysis of detergent-solubilized and purified integral membrane proteins using liquid chromatography-mass spectrometry (LC-MS) with methanol as the organic mobile phase. Membrane proteins and detergents are separated chromatographically during the isocratic stage of the gradient profile from a 150-mm C3 reversed-phase column. The mass accuracy is comparable to standard methods employed for soluble proteins; the sensitivity is 10-fold lower, requiring 0.2-5 μg of protein. The method is also compatible with our standard LC-MS method used for intact mass analysis of soluble proteins and may therefore be applied on a multiuser instrument or in a high-throughput environment.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Opher Gileadi
- Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, UK
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