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Hellwig N, Martin J, Morgner N. LILBID-MS: using lasers to shed light on biomolecular architectures. Biochem Soc Trans 2022; 50:1057-1067. [PMID: 35695670 PMCID: PMC9317959 DOI: 10.1042/bst20190881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 05/15/2022] [Accepted: 05/20/2022] [Indexed: 11/17/2022]
Abstract
Structural Biology has moved beyond the aim of simply identifying the components of a cellular subsystem towards analysing the dynamics and interactions of multiple players within a cell. This focal shift comes with additional requirements for the analytical tools used to investigate these systems of increased size and complexity, such as Native Mass Spectrometry, which has always been an important tool for structural biology. Scientific advance and recent developments, such as new ways to mimic a cell membrane for a membrane protein, have caused established methods to struggle to keep up with the increased demands. In this review, we summarize the possibilities, which Laser Induced Liquid Bead Ion Desorption (LILBID) mass spectrometry offers with regard to the challenges of modern structural biology, like increasingly complex sample composition, novel membrane mimics and advanced structural analysis, including next neighbor relations and the dynamics of complex formation.
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Affiliation(s)
- Nils Hellwig
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt/Main, Max-von-Laue-Str. 9, 60438 Frankfurt/Main, Germany
| | - Janosch Martin
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt/Main, Max-von-Laue-Str. 9, 60438 Frankfurt/Main, Germany
| | - Nina Morgner
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt/Main, Max-von-Laue-Str. 9, 60438 Frankfurt/Main, Germany
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2
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Reid DJ, Rohrbough JG, Kostelic MM, Marty MT. Investigating Antimicrobial Peptide-Membrane Interactions Using Fast Photochemical Oxidation of Peptides in Nanodiscs. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:62-67. [PMID: 34866389 PMCID: PMC8732327 DOI: 10.1021/jasms.1c00252] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Antimicrobial peptides (AMPs) are an important part of the innate immune system and demonstrate promising applications in the fight against antibiotic-resistant infections due to their unique mechanism of targeting bacterial membranes. However, it is challenging to study the interactions of these peptides within lipid bilayers, making it difficult to understand their mechanisms of toxicity and selectivity. Here, we used fast photochemical oxidation of peptides, an irreversible footprinting technique that labels solvent accessible residues, and native charge detection-mass spectrometry to study AMP-lipid interactions with different lipid bilayer nanodiscs. We observed differences in the oxidation of two peptides, indolicidin and LL-37, in three distinct lipid environments, which reveal their affinity for lipid bilayers. Our findings suggest that indolicidin interacts with lipid head groups via a simple charge-driven mechanism, but LL-37 is more specific for Escherichia coli nanodiscs. These results provide complementary information on the potential modes of action and lipid selectivity of AMPs.
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Affiliation(s)
- Deseree J. Reid
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
| | - James G. Rohrbough
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
| | - Marius M. Kostelic
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
| | - Michael T. Marty
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
- Bio5 Institute, University of Arizona, Tucson, AZ 85721, USA
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3
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Scratching the surface: native mass spectrometry of peripheral membrane protein complexes. Biochem Soc Trans 2021; 48:547-558. [PMID: 32129823 PMCID: PMC7192793 DOI: 10.1042/bst20190787] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 02/09/2020] [Accepted: 02/11/2020] [Indexed: 02/06/2023]
Abstract
A growing number of integral membrane proteins have been shown to tune their activity by selectively interacting with specific lipids. The ability to regulate biological functions via lipid interactions extends to the diverse group of proteins that associate only peripherally with the lipid bilayer. However, the structural basis of these interactions remains challenging to study due to their transient and promiscuous nature. Recently, native mass spectrometry has come into focus as a new tool to investigate lipid interactions in membrane proteins. Here, we outline how the native MS strategies developed for integral membrane proteins can be applied to generate insights into the structure and function of peripheral membrane proteins. Specifically, native MS studies of proteins in complex with detergent-solubilized lipids, bound to lipid nanodiscs, and released from native-like lipid vesicles all shed new light on the role of lipid interactions. The unique ability of native MS to capture and interrogate protein–protein, protein–ligand, and protein–lipid interactions opens exciting new avenues for the study of peripheral membrane protein biology.
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Marty MT. Nanodiscs and Mass Spectrometry: Making Membranes Fly. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2020; 458:116436. [PMID: 33100891 PMCID: PMC7584149 DOI: 10.1016/j.ijms.2020.116436] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Cells are surrounded by a protective lipid bilayer membrane, and membrane proteins in the bilayer control the flow of chemicals, information, and energy across this barrier. Many therapeutics target membrane proteins, and some directly target the lipid membrane itself. However, interactions within biological membranes are challenging to study due to their heterogeneity and insolubility. Mass spectrometry (MS) has become a powerful technique for studying membrane proteins, especially how membrane proteins interact with their surrounding lipid environment. Although detergent micelles are the most common membrane mimetic, nanodiscs are emerging as a promising platform for MS. Nanodiscs, nanoscale lipid bilayers encircled by two scaffold proteins, provide a controllable lipid bilayer for solubilizing membrane proteins. This Young Scientist Perspective focuses on native MS of intact nanodiscs and highlights the unique experiments enabled by making membranes fly, including studying membrane protein-lipid interactions and exploring the specificity of fragile transmembrane peptide complexes. It will also explore current challenges and future perspectives for interfacing nanodiscs with MS.
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Affiliation(s)
- Michael T Marty
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, AZ 85721
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5
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Kostelic MM, Ryan AM, Reid DJ, Noun JM, Marty MT. Expanding the Types of Lipids Amenable to Native Mass Spectrometry of Lipoprotein Complexes. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:1416-1425. [PMID: 30972726 PMCID: PMC6675625 DOI: 10.1007/s13361-019-02174-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 02/25/2019] [Accepted: 02/25/2019] [Indexed: 05/12/2023]
Abstract
Native mass spectrometry (MS) has become an important tool for the analysis of membrane proteins. Although detergent micelles are the most commonly used method for solubilizing membrane proteins for native MS, nanoscale lipoprotein complexes such as nanodiscs are emerging as a promising complementary approach because they solubilize membrane proteins in a lipid bilayer environment. However, prior native MS studies of intact nanodiscs have employed only a limited set of phospholipids that are similar in mass. Here, we extend the range of lipids that are amenable to native MS of nanodiscs by combining lipids with masses that are simple integer multiples of each other. Although these lipid combinations create complex distributions, overlap between resonant peak series allows interpretation of nanodisc spectra containing glycolipids, sterols, and cardiolipin. We also investigate the gas-phase stability of nanodiscs with these new lipids towards collisional activation. We observe that negative ionization mode or charge reduction stabilizes nanodiscs and is essential to preserving labile lipids such as sterols. These new approaches to native MS of nanodiscs will enable future studies of membrane proteins embedded in model membranes that more accurately mimic natural bilayers. Graphical Abstract.
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Affiliation(s)
- Marius M Kostelic
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E University Blvd, Tucson, AZ, 85721, USA
| | - Alex M Ryan
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E University Blvd, Tucson, AZ, 85721, USA
| | - Deseree J Reid
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E University Blvd, Tucson, AZ, 85721, USA
| | - Jibriel M Noun
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E University Blvd, Tucson, AZ, 85721, USA
| | - Michael T Marty
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E University Blvd, Tucson, AZ, 85721, USA.
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Walker LR, Marzluff EM, Townsend JA, Resager WC, Marty MT. Native Mass Spectrometry of Antimicrobial Peptides in Lipid Nanodiscs Elucidates Complex Assembly. Anal Chem 2019; 91:9284-9291. [PMID: 31251560 PMCID: PMC6635019 DOI: 10.1021/acs.analchem.9b02261] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Antimicrobial peptides (AMPs) are generally cationic and amphipathic peptides that show potential applications to combat the growing threat of antibiotic resistant infections. AMPs are known to interact with bacterial membranes, but their mechanisms of toxicity and selectivity are poorly understood, in part because it is challenging to characterize AMP oligomeric complexes within lipid bilayers. Here, we used native mass spectrometry to measure the stoichiometry of AMPs inserted into lipoprotein nanodiscs with different lipid components. Titrations of increasing peptide concentration and collisional activation experiments reveal that AMPs can exhibit a range of behaviors from nonspecific incorporation into the nanodisc to formation of specific complexes. This new approach to characterizing formation of AMP complexes within lipid membranes will provide unique insights into AMP mechanisms.
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Affiliation(s)
- Lawrence R. Walker
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, AZ 85721
| | | | - Julia A. Townsend
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, AZ 85721
| | - William C. Resager
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, AZ 85721
| | - Michael T. Marty
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, AZ 85721
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Reid DJ, Keener JE, Wheeler AP, Zambrano DE, Diesing JM, Reinhardt-Szyba M, Makarov A, Marty MT. Engineering Nanodisc Scaffold Proteins for Native Mass Spectrometry. Anal Chem 2017; 89:11189-11192. [PMID: 29048874 DOI: 10.1021/acs.analchem.7b03569] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Lipoprotein nanodiscs are ideally suited for native mass spectrometry because they provide a relatively monodisperse nanoscale lipid bilayer environment for delivering membrane proteins into the gas phase. However, native mass spectrometry of nanodiscs produces complex spectra that can be challenging to assign unambiguously. To simplify interpretation of nanodisc spectra, we engineered a series of mutant membrane scaffold proteins (MSP) that do not affect nanodisc formation but shift the masses of nanodiscs in a controllable way, eliminating isobaric interference from the lipids. Moreover, by mixing two different belts before assembly, the stoichiometry of MSP is encoded in the peak shape, which allows the stoichiometry to be assigned unambiguously from a single spectrum. Finally, we demonstrate the use of mixed belt nanodiscs with embedded membrane proteins to confirm the dissociation of MSP prior to desolvation.
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Affiliation(s)
- Deseree J Reid
- Department of Chemistry and Biochemistry, University of Arizona , Tucson, Arizona 85721, United States
| | - James E Keener
- Department of Chemistry and Biochemistry, University of Arizona , Tucson, Arizona 85721, United States
| | - Andrew P Wheeler
- Department of Chemistry and Biochemistry, University of Arizona , Tucson, Arizona 85721, United States
| | - Dane Evan Zambrano
- Department of Chemistry and Biochemistry, University of Arizona , Tucson, Arizona 85721, United States
| | - Jessica M Diesing
- Department of Chemistry and Biochemistry, University of Arizona , Tucson, Arizona 85721, United States
| | | | | | - Michael T Marty
- Department of Chemistry and Biochemistry, University of Arizona , Tucson, Arizona 85721, United States
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