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Kumar S, Stover L, Wang L, Bahramimoghaddam H, Zhou M, Russell DH, Laganowsky A. Native mass spectrometry of membrane protein-lipid interactions in different detergent environments. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.27.601044. [PMID: 38979331 PMCID: PMC11230385 DOI: 10.1101/2024.06.27.601044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Native mass spectrometry (MS) is revealing the role of specific lipids in modulating membrane protein structure and function. Membrane proteins solubilized in detergents are often introduced into the mass spectrometer; however, commonly used detergents for structural studies, such as dodecylmaltoside, tend to generate highly charged ions, leading to protein unfolding, thereby diminishing their utility for characterizing protein-lipid interactions. Thus, there is a critical need to develop approaches to investigate protein-lipid interactions in different detergents. Here, we demonstrate how charge-reducing molecules, such as spermine and trimethylamine-N-oxide, enable characterization of lipid binding to the bacterial water channel (AqpZ) and ammonia channel (AmtB) in complex with regulatory protein GlnK in different detergent environments. We find protein-lipid interactions are not only protein-dependent but can also be influenced by the detergent and type of charge-reducing molecule. AqpZ-lipid interactions are enhanced in LDAO (n-dodecyl-N,N-dimethylamine-N-oxide), whereas the interaction of AmtB-GlnK with lipids is comparable among different detergents. A fluorescent lipid binding assay also shows detergent dependence for AqpZ-lipid interactions, consistent with results from native MS. Taken together, native MS will play a pivotal role in establishing optimal experimental parameters that will be invaluable for various applications, such as drug discovery, as well as biochemical and structural investigations.
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Affiliation(s)
- Smriti Kumar
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Lauren Stover
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Lie Wang
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, United States
| | | | - Ming Zhou
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - David H. Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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2
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Gozzo TA, Bush MF. Effects of charge on protein ion structure: Lessons from cation-to-anion, proton-transfer reactions. MASS SPECTROMETRY REVIEWS 2024; 43:500-525. [PMID: 37129026 DOI: 10.1002/mas.21847] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/10/2023] [Accepted: 04/11/2023] [Indexed: 05/03/2023]
Abstract
Collision cross-section values, which can be determined using ion mobility experiments, are sensitive to the structures of protein ions and useful for applications to structural biology and biophysics. Protein ions with different charge states can exhibit very different collision cross-section values, but a comprehensive understanding of this relationship remains elusive. Here, we review cation-to-anion, proton-transfer reactions (CAPTR), a method for generating a series of charge-reduced protein cations by reacting quadrupole-selected cations with even-electron monoanions. The resulting CAPTR products are analyzed using a combination of ion mobility, mass spectrometry, and collisional activation. We compare CAPTR to other charge-manipulation strategies and review the results of various CAPTR-based experiments, exploring their contribution to a deeper understanding of the relationship between protein ion structure and charge state.
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Affiliation(s)
- Theresa A Gozzo
- Department of Chemistry, University of Washington, Seattle, Washington, USA
| | - Matthew F Bush
- Department of Chemistry, University of Washington, Seattle, Washington, USA
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3
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Townsend JA, Marty MT. What's the defect? Using mass defects to study oligomerization of membrane proteins and peptides in nanodiscs with native mass spectrometry. Methods 2023; 218:1-13. [PMID: 37482149 PMCID: PMC10529358 DOI: 10.1016/j.ymeth.2023.07.004] [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: 04/21/2023] [Revised: 06/20/2023] [Accepted: 07/03/2023] [Indexed: 07/25/2023] Open
Abstract
Many membrane proteins form functional complexes that are either homo- or hetero-oligomeric. However, it is challenging to characterize membrane protein oligomerization in intact lipid bilayers, especially for polydisperse mixtures. Native mass spectrometry of membrane proteins and peptides inserted in lipid nanodiscs provides a unique method to study the oligomeric state distribution and lipid preferences of oligomeric assemblies. To interpret these complex spectra, we developed novel data analysis methods using macromolecular mass defect analysis. Here, we provide an overview of how mass defect analysis can be used to study oligomerization in nanodiscs, discuss potential limitations in interpretation, and explore strategies to resolve these ambiguities. Finally, we review recent work applying this technique to studying formation of antimicrobial peptide, amyloid protein, and viroporin complexes with lipid membranes.
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Affiliation(s)
- Julia A Townsend
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, AZ 85721, USA
| | - Michael T Marty
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, AZ 85721, USA.
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4
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Emergence of mass spectrometry detergents for membrane proteomics. Anal Bioanal Chem 2023:10.1007/s00216-023-04584-z. [PMID: 36808272 PMCID: PMC10328889 DOI: 10.1007/s00216-023-04584-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 01/25/2023] [Accepted: 02/02/2023] [Indexed: 02/21/2023]
Abstract
Detergents enable the investigation of membrane proteins by mass spectrometry. Detergent designers aim to improve underlying methodologies and are confronted with the challenge to design detergents with optimal solution and gas-phase properties. Herein, we review literature related to the optimization of detergent chemistry and handling and identify an emerging research direction: the optimization of mass spectrometry detergents for individual applications in mass spectrometry-based membrane proteomics. We provide an overview about qualitative design aspects including their relevance for the optimization of detergents in bottom-up proteomics, top-down proteomics, native mass spectrometry, and Nativeomics. In addition to established design aspects, such as charge, concentration, degradability, detergent removal, and detergent exchange, it becomes apparent that detergent heterogeneity is a promising key driver for innovation. We anticipate that rationalizing the role of detergent structures in membrane proteomics will serve as an enabling step for the analysis of challenging biological systems.
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5
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Yen HY, Abramsson ML, Agasid MT, Lama D, Gault J, Liko I, Kaldmäe M, Saluri M, Qureshi AA, Suades A, Drew D, Degiacomi MT, Marklund EG, Allison TM, Robinson CV, Landreh M. Electrospray ionization of native membrane proteins proceeds via a charge equilibration step. RSC Adv 2022; 12:9671-9680. [PMID: 35424940 PMCID: PMC8972943 DOI: 10.1039/d2ra01282k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 03/21/2022] [Indexed: 11/21/2022] Open
Abstract
Electrospray ionization mass spectrometry is increasingly applied to study the structures and interactions of membrane protein complexes. However, the charging mechanism is complicated by the presence of detergent micelles during ionization. Here, we show that the final charge of membrane proteins can be predicted by their molecular weight when released from the non-charge reducing saccharide detergents. Our data indicate that PEG detergents lower the charge depending on the number of detergent molecules in the surrounding micelle, whereas fos-choline detergents may additionally participate in ion–ion reactions after desolvation. The supercharging reagent sulfolane, on the other hand, has no discernible effect on the charge of detergent-free membrane proteins. Taking our observations into the context of protein-detergent interactions in the gas phase, we propose a charge equilibration model for the generation of native-like membrane protein ions. During ionization of the protein-detergent complex, the ESI charges are distributed between detergent and protein according to proton affinity of the detergent, number of detergent molecules, and surface area of the protein. Charge equilibration influenced by detergents determines the final charge state of membrane proteins. This process likely contributes to maintaining a native-like fold after detergent release and can be harnessed to stabilize particularly labile membrane protein complexes in the gas phase. The electrospray ionization mechanism contributes to preserving the structures and interactions of membrane protein complexes in native mass spectrometry.![]()
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Affiliation(s)
- Hsin-Yung Yen
- Department of Chemistry, University of Oxford South Parks Road Oxford OX1 3QZ UK .,Institute of Biological Chemistry, Academia Sinica 128, Academia Road Sec. 2, Nankang Taipei 115 Taiwan
| | - Mia L Abramsson
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet Tomtebodavägen 23A 17165 Stockholm Sweden
| | - Mark T Agasid
- Department of Chemistry, University of Oxford South Parks Road Oxford OX1 3QZ UK
| | - Dilraj Lama
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet Tomtebodavägen 23A 17165 Stockholm Sweden
| | - Joseph Gault
- Department of Chemistry, University of Oxford South Parks Road Oxford OX1 3QZ UK
| | - Idlir Liko
- Department of Chemistry, University of Oxford South Parks Road Oxford OX1 3QZ UK
| | - Margit Kaldmäe
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet Tomtebodavägen 23A 17165 Stockholm Sweden
| | - Mihkel Saluri
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet Tomtebodavägen 23A 17165 Stockholm Sweden
| | - Abdul Aziz Qureshi
- Department of Chemistry, University of Oxford South Parks Road Oxford OX1 3QZ UK .,Department of Biochemistry and Biophysics, Stockholm University 10691 Stockholm Sweden
| | - Albert Suades
- Department of Biochemistry and Biophysics, Stockholm University 10691 Stockholm Sweden
| | - David Drew
- Department of Biochemistry and Biophysics, Stockholm University 10691 Stockholm Sweden
| | | | - Erik G Marklund
- Department of Chemistry - BMC, Uppsala University Box 576 75123 Uppsala Sweden
| | - Timothy M Allison
- Biomolecular Interaction Centre, School of Physical and Chemical Sciences, University of Canterbury Christchurch 8140 New Zealand
| | - Carol V Robinson
- Department of Chemistry, University of Oxford South Parks Road Oxford OX1 3QZ UK
| | - Michael Landreh
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet Tomtebodavägen 23A 17165 Stockholm Sweden
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6
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Bailey AO, Huguet R, Mullen C, Syka JEP, Russell WK. Ion-Ion Charge Reduction Addresses Multiple Challenges Common to Denaturing Intact Mass Analysis. Anal Chem 2022; 94:3930-3938. [PMID: 35189062 DOI: 10.1021/acs.analchem.1c04973] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Complete LC-MS-based protein primary sequence characterization requires measurement of intact protein profiles under denaturing and/or reducing conditions. To address issues of protein overcharging of unstructured proteins under acidic, denaturing conditions and sample heterogeneity (macro- and micro-scales) which often confound denaturing intact mass analysis of a wide variety of protein samples, we propose the use of broadband isolation of entire charge state distributions of intact proteins followed by ion-ion proton transfer charge reduction, which we have termed "full scan PTCR" (fsPTCR). Using rapid denaturing size exclusion chromatography coupled to fsPTCR-Orbitrap MS and time-resolved deconvolution data analysis, we demonstrate a strategy for method optimization, leading to significant analytical advantages over conventional MS1. Denaturing analysis of the flexible bacterial translation initiation factor 2 (91 kDa) using fsPTCR reduced overcharging and showed an 11-fold gain in S/N compared to conventional MS1. Analysis by fsPTCR-MS of the microheterogeneous glycoprotein fetuin revealed twice as many proteoforms as MS1 (112 vs 56). In a macroheterogeneous mixture of proteins ranging from 14 to 148 kDa, fsPTCR provided more than 10-fold increased sensitivity and quantitative accuracy for diluted bovine serum albumin (66 kDa). Finally, our analysis shows that collisional gas pressure is a key parameter which can be utilized during fsPTCR to retain or remove larger proteins from acquired spectra.
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Affiliation(s)
- Aaron O Bailey
- University of Texas Medical Branch, 301 University Drive, Galveston, Texas 77551, United States
| | - Romain Huguet
- Thermo Fisher Scientific, 355 River Oaks Pkwy, San Jose, California 95134, United States
| | - Christopher Mullen
- Thermo Fisher Scientific, 355 River Oaks Pkwy, San Jose, California 95134, United States
| | - John E P Syka
- Thermo Fisher Scientific, 355 River Oaks Pkwy, San Jose, California 95134, United States
| | - William K Russell
- University of Texas Medical Branch, 301 University Drive, Galveston, Texas 77551, United States
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7
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Abramsson ML, Sahin C, Hopper JTS, Branca RMM, Danielsson J, Xu M, Chandler SA, Österlund N, Ilag LL, Leppert A, Costeira-Paulo J, Lang L, Teilum K, Laganowsky A, Benesch JLP, Oliveberg M, Robinson CV, Marklund EG, Allison TM, Winther JR, Landreh M. Charge Engineering Reveals the Roles of Ionizable Side Chains in Electrospray Ionization Mass Spectrometry. JACS AU 2021; 1:2385-2393. [PMID: 34977906 PMCID: PMC8717373 DOI: 10.1021/jacsau.1c00458] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Indexed: 05/03/2023]
Abstract
In solution, the charge of a protein is intricately linked to its stability, but electrospray ionization distorts this connection, potentially limiting the ability of native mass spectrometry to inform about protein structure and dynamics. How the behavior of intact proteins in the gas phase depends on the presence and distribution of ionizable surface residues has been difficult to answer because multiple chargeable sites are present in virtually all proteins. Turning to protein engineering, we show that ionizable side chains are completely dispensable for charging under native conditions, but if present, they are preferential protonation sites. The absence of ionizable side chains results in identical charge state distributions under native-like and denaturing conditions, while coexisting conformers can be distinguished using ion mobility separation. An excess of ionizable side chains, on the other hand, effectively modulates protein ion stability. In fact, moving a single ionizable group can dramatically alter the gas-phase conformation of a protein ion. We conclude that although the sum of the charges is governed solely by Coulombic terms, their locations affect the stability of the protein in the gas phase.
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Affiliation(s)
- Mia L. Abramsson
- Department
of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Tomtebodavägen 23A, 171 65 Stockholm, Sweden
| | - Cagla Sahin
- Department
of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Tomtebodavägen 23A, 171 65 Stockholm, Sweden
- Linderstrøm-Lang
Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes vej 5, 2200 Copenhagen, Denmark
| | - Jonathan T. S. Hopper
- Department
of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K.
| | - Rui M. M. Branca
- Department
of Oncology-Pathology, Science for Life
Laboratory and Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Jens Danielsson
- Department
of Biochemistry and Biophysics, Stockholm
University, 106 91 Stockholm, Sweden
| | - Mingming Xu
- Department
of Biochemistry and Biophysics, Stockholm
University, 106 91 Stockholm, Sweden
| | - Shane A. Chandler
- Department
of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K.
| | - Nicklas Österlund
- Department
of Biochemistry and Biophysics, Stockholm
University, 106 91 Stockholm, Sweden
| | - Leopold L. Ilag
- Department
of Material and Environmental Chemistry, Stockholm University, 106 91 Stockholm, Sweden
| | - Axel Leppert
- Department
of Biosciences and Nutrition, Karolinska
Institutet, Neo, 141 83 Huddinge, Sweden
| | - Joana Costeira-Paulo
- Department
of Chemistry−BMC, Uppsala University, Box 576, 751 23 Uppsala, Sweden
| | - Lisa Lang
- Department
of Biochemistry and Biophysics, Stockholm
University, 106 91 Stockholm, Sweden
| | - Kaare Teilum
- Linderstrøm-Lang
Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes vej 5, 2200 Copenhagen, Denmark
| | - Arthur Laganowsky
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Justin L. P. Benesch
- Department
of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K.
| | - Mikael Oliveberg
- Department
of Biochemistry and Biophysics, Stockholm
University, 106 91 Stockholm, Sweden
| | - Carol V. Robinson
- Department
of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K.
| | - Erik G. Marklund
- Department
of Chemistry−BMC, Uppsala University, Box 576, 751 23 Uppsala, Sweden
| | - Timothy M. Allison
- Biomolecular
Interaction Centre, School of Physical and Chemical Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Jakob R. Winther
- Linderstrøm-Lang
Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes vej 5, 2200 Copenhagen, Denmark
| | - Michael Landreh
- Department
of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Tomtebodavägen 23A, 171 65 Stockholm, Sweden
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8
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Donor MT, Wilson JW, Shepherd SO, Prell JS. Lipid Head Group Adduction to Soluble Proteins Follows Gas-Phase Basicity Predictions: Dissociation Barriers and Charge Abstraction. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2021; 469:116670. [PMID: 34421332 PMCID: PMC8372978 DOI: 10.1016/j.ijms.2021.116670] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Native mass spectrometry analysis of membrane proteins has yielded many useful insights in recent years with respect to membrane protein-lipid interactions, including identifying specific interactions and even measuring binding affinities based on observed abundances of lipid-bound ions after collision-induced dissociation (CID). However, the behavior of non-covalent complexes subjected to extensive CID can in principle be affected by numerous factors related to gas-phase chemistry, including gas-phase basicity (GB) and acidity, shared-proton bonds, and other factors. A recent report from our group showed that common lipids span a wide range of GB values. Notably, phosphatidylcholine (PC) and sphingomyelin lipids are more basic than arginine, suggesting they may strip charge upon dissociation in positive ion mode, while phosphoserine lipids are slightly less basic than arginine and may form especially strong shared-proton bonds. Here, we use CID to probe the strength of non-specific gas-phase interactions between lipid head groups and several soluble proteins, used to deliberately avoid possible physiological protein-lipid interactions. The strengths of the protein-head group interactions follow the trend predicted based solely on lipid and amino acid GBs: phosphoserine (PS) head group forms the strongest bonds with these proteins and out-competes the other head groups studied, while glycerophosphocholine (GPC) head groups form the weakest interactions and dissociate carrying away a positive charge. These results indicate that gas-phase thermochemistry can play an important role in determining which head groups remain bound to protein ions with native-like structures and charge states in positive ion mode upon extensive collisional activation.
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Affiliation(s)
- Micah T. Donor
- Department of Chemistry and Biochemistry, 1253 University of Oregon, Eugene OR 97403-1253
| | - Jesse W. Wilson
- Department of Chemistry and Biochemistry, 1253 University of Oregon, Eugene OR 97403-1253
| | - Samantha O. Shepherd
- Department of Chemistry and Biochemistry, 1253 University of Oregon, Eugene OR 97403-1253
| | - James S. Prell
- Department of Chemistry and Biochemistry, 1253 University of Oregon, Eugene OR 97403-1253
- Materials Science Institute, University of Oregon, 1252 University of Oregon, Eugene, OR 97403-1252
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9
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Ieritano C, Rickert D, Featherstone J, Honek JF, Campbell JL, Blanc JCYL, Schneider BB, Hopkins WS. The Charge-State and Structural Stability of Peptides Conferred by Microsolvating Environments in Differential Mobility Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:956-968. [PMID: 33733774 DOI: 10.1021/jasms.0c00469] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The presence of solvent vapor in a differential mobility spectrometry (DMS) cell creates a microsolvating environment that can mitigate complications associated with field-induced heating. In the case of peptides, the microsolvation of protonation sites results in a stabilization of charge density through localized solvent clustering, sheltering the ion from collisional activation. Seeding the DMS carrier gas (N2) with a solvent vapor prevented nearly all field-induced fragmentation of the protonated peptides GGG, AAA, and the Lys-rich Polybia-MP1 (IDWKKLLDAAKQIL-NH2). Modeling the microsolvation propensity of protonated n-propylamine [PrNH3]+, a mimic of the Lys side chain and N-terminus, with common gas-phase modifiers (H2O, MeOH, EtOH, iPrOH, acetone, and MeCN) confirms that all solvent molecules form stable clusters at the site of protonation. Moreover, modeling populations of microsolvated clusters indicates that species containing protonated amine moieties exist as microsolvated species with one to six solvent ligands at all effective ion temperatures (Teff) accessible during a DMS experiment (ca. 375-600 K). Calculated Teff of protonated GGG, AAA, and Polybia-MPI using a modified two-temperature theory approach were up to 86 K cooler in DMS environments seeded with solvent vapor compared to pure N2 environments. Stabilizing effects were largely driven by an increase in the ion's apparent collision cross section and by evaporative cooling processes induced by the dynamic evaporation/condensation cycles incurred in the presence of an oscillating electric separation field. When the microsolvating partner was a protic solvent, abstraction of a proton from [MP1 + 3H]3+ to yield [MP1 + 2H]2+ was observed. This result was attributed to the proclivity of protic solvents to form hydrogen-bond networks with enhanced gas-phase basicity. Collectively, microsolvation provides analytes with a solvent "air bag," whereby charge reduction and microsolvation-induced stabilization were shown to shelter peptides from the fragmentation induced by field heating and may play a role in preserving native-like ion configurations.
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Affiliation(s)
- Christian Ieritano
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo N2L 3G1, Ontario, Canada
| | - Daniel Rickert
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo N2L 3G1, Ontario, Canada
| | - Joshua Featherstone
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo N2L 3G1, Ontario, Canada
| | - John F Honek
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo N2L 3G1, Ontario, Canada
| | - J Larry Campbell
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo N2L 3G1, Ontario, Canada
- Watermine Innovation, Waterloo N0B 2T0, Ontario, Canada
- Bedrock Scientific, Milton L6T 6J9, Ontario, Canada
| | | | | | - W Scott Hopkins
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo N2L 3G1, Ontario, Canada
- Watermine Innovation, Waterloo N0B 2T0, Ontario, Canada
- Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo N2L 3G1, Ontario, Canada
- Centre for Eye and Vision Research, Hong Kong Science Park, New Territories 999077, Hong Kong
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10
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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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11
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Lyu J, Liu Y, McCabe JW, Schrecke S, Fang L, Russell DH, Laganowsky A. Discovery of Potent Charge-Reducing Molecules for Native Ion Mobility Mass Spectrometry Studies. Anal Chem 2020; 92:11242-11249. [PMID: 32672445 DOI: 10.1021/acs.analchem.0c01826] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
There is growing interest in the characterization of protein complexes and their interactions with ligands using native ion mobility mass spectrometry. A particular challenge, especially for membrane proteins, is preserving noncovalent interactions and maintaining native-like structures. Different approaches have been developed to minimize activation of protein complexes by manipulating charge on protein complexes in solution and the gas-phase. Here, we report the utility of polyamines that have exceptionally high charge-reducing potencies with some molecules requiring 5-fold less than trimethylamine oxide to elicit the same effect. The charge-reducing molecules do not adduct to membrane protein complexes and are also compatible with ion-mobility mass spectrometry, paving the way for improved methods of charge reduction.
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Affiliation(s)
- Jixing Lyu
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Yang Liu
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Jacob W McCabe
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Samantha Schrecke
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Lei Fang
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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12
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Zheng X, Kurulugama RT, Laganowsky A, Russell DH. Collision-Induced Unfolding Studies of Proteins and Protein Complexes using Drift Tube Ion Mobility-Mass Spectrometer. Anal Chem 2020; 92:7218-7225. [PMID: 32338885 DOI: 10.1021/acs.analchem.0c00772] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Elucidating the structures and stabilities of proteins and their complexes is paramount to understanding their biological functions in cellular processes. Native mass spectrometry (MS) coupled with ion mobility spectrometry (IMS) is emerging as an important biophysical technique owing to its high sensitivity, rapid analysis time, and ability to interrogate sample complexity or heterogeneity and the ability to probe protein structure dynamics. Here, a commercial IMS-MS platform has been modified for static native ESI emitters and an extended mass-to-charge range (20 kDa m/z) and its performance capabilities and limits were explored for a range of protein and protein complexes. The results show new potential for this instrument platform for studies of large protein and protein complexes and provides a roadmap for extending the performance metrics for studies of even larger, more complex systems, namely, membrane protein complexes and their interactions with ligands.
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Affiliation(s)
- Xueyun Zheng
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | | | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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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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Townsend JA, Keener JE, Miller ZM, Prell JS, Marty MT. Imidazole Derivatives Improve Charge Reduction and Stabilization for Native Mass Spectrometry. Anal Chem 2019; 91:14765-14772. [PMID: 31638377 DOI: 10.1021/acs.analchem.9b04263] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Noncovalent interactions between biomolecules are critical to their activity. Native mass spectrometry (MS) has enabled characterization of these interactions by preserving noncovalent assemblies for mass analysis, including protein-ligand and protein-protein complexes for a wide range of soluble and membrane proteins. Recent advances in native MS of lipoprotein nanodiscs have also allowed characterization of antimicrobial peptides and membrane proteins embedded in intact lipid bilayers. However, conventional native electrospray ionization (ESI) can disrupt labile interactions. To stabilize macromolecular complexes for native MS, charge reducing reagents can be added to the solution prior to ESI, such as triethylamine, trimethylamine oxide, and imidazole. Lowering the charge acquired during ESI reduces Coulombic repulsion that leads to dissociation, and charge reduction reagents may also lower the internal energy of the ions through evaporative cooling. Here, we tested a range of imidazole derivatives to discover improved charge reducing reagents and to determine how their chemical properties influence charge reduction efficacy. We measured their effects on a soluble protein complex, a membrane protein complex in detergent, and lipoprotein nanodiscs with and without embedded peptides, and used computational chemistry to understand the observed charge-reduction behavior. Together, our data revealed that hydrophobic substituents at the 2 position on imidazole can significantly improve both charge reduction and gas-phase stability over existing reagents. These new imidazole derivatives will be immediately beneficial for a range of native MS applications and provide chemical principles to guide development of novel charge reducing reagents.
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Affiliation(s)
- Julia A Townsend
- 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
| | - Zachary M Miller
- Department of Chemistry and Biochemistry , University of Oregon , Eugene , Oregon 97403 , United States
| | - James S Prell
- Department of Chemistry and Biochemistry , University of Oregon , Eugene , Oregon 97403 , United States.,Materials Science Institute , University of Oregon , Eugene , Oregon 97403 , United States
| | - Michael T Marty
- Department of Chemistry and Biochemistry , University of Arizona , Tucson , Arizona 85721 , United States
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