1
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Han Z, Hishida S, Chen LC. Formation of Alternating Surfactant-Enriched and Surfactant-Depleted Phases in the Taylor Cone of a Nanoelectrospray. Anal Chem 2024; 96:7297-7303. [PMID: 38682329 DOI: 10.1021/acs.analchem.4c01379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
The electrospray ionization of highly conductive solutions containing Triton X-100, a nonionic surfactant, is found to induce alternating periods of surfactant enrichment and depletion when the concentration of the surfactant is near the critical micelle concentration (CMC) and when the flow rate is on the order of 10 nL/min. Analyzing the surfactant-protein mixture shows that the protein is partially denatured during the surfactant enrichment. The measurement of the phospholipid and oligosaccharide mixture prepared in the surfactant solution shows that the ion signal of the lipid is in phase with, and the hydrophilic oligosaccharide is out of phase with the surfactant signal. The results suggest that this novel phenomenon can be exploited for in situ separation of compounds in ESI-MS. Besides the ion signal, the condition of the alternating phase is also reflected in the spray current and Taylor cone's apex angle. The phase separation is likely related to the formation of a micelle in the Taylor cone and can be selectively triggered by tuning the flow rate with emitter voltage for an on-demand application.
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Affiliation(s)
- Zhongbao Han
- College of Chemistry and Chemical Engineering, Shenyang Normal University, Shenyang 110034, China
| | - Shoki Hishida
- Faculty of Engineering, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Lee Chuin Chen
- Faculty of Engineering, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
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2
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Smeriglio N, Li H, Mazli WNAB, Bendel K, Hao L. Contaminant Spot Check and Removal Assay (ContamSPOT) for Mass Spectrometry Analysis. Anal Chem 2024; 96:2574-2581. [PMID: 38291764 DOI: 10.1021/acs.analchem.3c05020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Mass spectrometry (MS) analysis is often challenged by contaminations from detergents, salts, and polymers that compromise data quality and can damage the chromatography and MS instruments. However, researchers often discover contamination issues only after they acquire the data. There is no existing contaminant assay that is sensitive enough to detect trace amounts of contaminants from a few microliters of samples prior to MS analysis. To address this crucial need in the field, we developed a sensitive, rapid, and cost-effective contaminant spot check and removal assay (ContamSPOT) to detect and quantify trace amounts of contaminants, such as detergents, salts, and other chemicals commonly used in the MS sample preparation workflow. Only 1 μL of the sample was used prior to MS injection to quantify contaminants by ContamSPOT colorimetric or fluorometric assay on a thin layer chromatography (TLC) plate. We also optimized contaminant removal methods to salvage samples with minimal loss when ContamSPOT showed a positive result. ContamSPOT was then successfully applied to evaluate commonly used bottom-up proteomic methods regarding the effectiveness of removing detergent, peptide recovery, reproducibility, and proteome coverage. We expect ContamSPOT to be widely adopted by MS laboratories as a last-step quality checkpoint prior to MS injection. We provided a practical decision tree and a step-by-step protocol with a troubleshooting guide to facilitate the use of ContamSPOT by other researchers. ContamSPOT can also provide a unique readout of sample cleanliness for developing new MS-based sample preparation methods in the future.
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Affiliation(s)
- Noah Smeriglio
- Department of Chemistry, The George Washington University, Science and Engineering Hall 4000, 800 22nd St., NW, Washington, D.C. 20052, United States
| | - Haorong Li
- Department of Chemistry, The George Washington University, Science and Engineering Hall 4000, 800 22nd St., NW, Washington, D.C. 20052, United States
| | - Wan Nur Atiqah Binti Mazli
- Department of Chemistry, The George Washington University, Science and Engineering Hall 4000, 800 22nd St., NW, Washington, D.C. 20052, United States
| | - Katharine Bendel
- Department of Chemistry, The George Washington University, Science and Engineering Hall 4000, 800 22nd St., NW, Washington, D.C. 20052, United States
| | - Ling Hao
- Department of Chemistry, The George Washington University, Science and Engineering Hall 4000, 800 22nd St., NW, Washington, D.C. 20052, United States
- Department of Biochemistry and Molecular Medicine, The George Washington University, Science and Engineering Hall 4000, 800 22nd St., NW, Washington, D.C. 20052, United States
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3
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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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4
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Hammerschmid D, Calvaresi V, Bailey C, Russell Lewis B, Politis A, Morris M, Denbigh L, Anderson M, Reading E. Chromatographic Phospholipid Trapping for Automated H/D Exchange Mass Spectrometry of Membrane Protein-Lipid Assemblies. Anal Chem 2023; 95:3002-3011. [PMID: 36706021 PMCID: PMC9909672 DOI: 10.1021/acs.analchem.2c04876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Lipid interactions modulate the function, folding, structure, and organization of membrane proteins. Hydrogen/deuterium exchange mass spectrometry (HDX-MS) has emerged as a useful tool to understand the structural dynamics of these proteins within lipid environments. Lipids, however, have proven problematic for HDX-MS analysis of membrane-embedded proteins due to their presence of impairing proteolytic digestion, causing liquid chromatography column fouling, ion suppression, and/or mass spectral overlap. Herein, we describe the integration of a chromatographic phospholipid trap column into the HDX-MS apparatus to enable online sample delipidation prior to protease digestion of deuterium-labeled protein-lipid assemblies. We demonstrate the utility of this method on membrane scaffold protein-lipid nanodisc─both empty and loaded with the ∼115 kDa transmembrane protein AcrB─proving efficient and automated phospholipid capture with minimal D-to-H back-exchange, peptide carry-over, and protein loss. Our results provide insights into the efficiency of phospholipid capture by ZrO2-coated and TiO2 beads and describe how solution conditions can be optimized to maximize not only the performance of our online but also the existing offline, delipidation workflows for HDX-MS. We envision that this HDX-MS method will significantly ease membrane protein analysis, allowing to better interrogate their dynamics in artificial lipid bilayers or even native cell membranes.
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Affiliation(s)
- Dietmar Hammerschmid
- Department
of Chemistry, King’s College London, 7 Trinity Street, SE1 1DB London, U.K.
| | - Valeria Calvaresi
- Department
of Chemistry, King’s College London, 7 Trinity Street, SE1 1DB London, U.K.
| | - Chloe Bailey
- Department
of Chemistry, King’s College London, 7 Trinity Street, SE1 1DB London, U.K.
| | | | - Argyris Politis
- Department
of Chemistry, King’s College London, 7 Trinity Street, SE1 1DB London, U.K.
| | - Michael Morris
- Waters
Corporation, Stamford Avenue, Altrincham Road, SK9
4AX Wilmslow, U.K.
| | - Laetitia Denbigh
- Waters
Corporation, Stamford Avenue, Altrincham Road, SK9
4AX Wilmslow, U.K.
| | - Malcolm Anderson
- Waters
Corporation, Stamford Avenue, Altrincham Road, SK9
4AX Wilmslow, U.K.
| | - Eamonn Reading
- Department
of Chemistry, King’s College London, 7 Trinity Street, SE1 1DB London, U.K.
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5
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Structural Analyses of the Glycolipids in Lipid Rafts. Methods Mol Biol 2023; 2613:145-152. [PMID: 36587077 DOI: 10.1007/978-1-0716-2910-9_12] [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: 01/02/2023]
Abstract
Lipid rafts are usually isolated from cells or tissues using sucrose gradient ultracentrifugation in the presence of detergents such as Triton X-100 at 4 °C. Although detergents should be removed for further structural characterization following fractionation, these compounds are often difficult to completely remove, especially from the glycolipids. In this chapter, we describe a novel method for the fast and convenient removal of detergents from lipid raft glycolipids following fraction and describe the application of this method.
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6
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Kalaninová Z, Fojtík L, Chmelík J, Novák P, Volný M, Man P. Probing Antibody Structures by Hydrogen/Deuterium Exchange Mass Spectrometry. Methods Mol Biol 2023; 2718:303-334. [PMID: 37665467 DOI: 10.1007/978-1-0716-3457-8_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Hydrogen/deuterium exchange (HDX) followed by mass spectrometry detection (MS) provides a fast, reliable, and detailed solution for the assessment of a protein structure. It has been widely recognized as an indispensable tool and already approved by several regulatory agencies as a structural technique for the validation of protein biopharmaceuticals, including antibody-based drugs. Antibodies are of a key importance in life and medical sciences but considered to be challenging analytical targets because of their compact structure stabilized by disulfide bonds and due to the presence of glycosylation. Despite these difficulties, there are already numerous excellent studies describing MS-based antibody structure characterization. In this chapter, we describe a universal HDX-MS workflow. Deeper attention is paid to sample handling, optimization procedures, and feasibility stages, as these elements of the HDX experiment are crucial for obtaining reliable detailed and spatially well-resolved information.
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Affiliation(s)
- Zuzana Kalaninová
- BioCeV - Institute of Microbiology of the Czech Academy of Sciences, Vestec, Czech Republic
- Department of Biochemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - Lukáš Fojtík
- BioCeV - Institute of Microbiology of the Czech Academy of Sciences, Vestec, Czech Republic
- Department of Biochemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - Josef Chmelík
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Petr Novák
- BioCeV - Institute of Microbiology of the Czech Academy of Sciences, Vestec, Czech Republic
| | - Michael Volný
- BioCeV - Institute of Microbiology of the Czech Academy of Sciences, Vestec, Czech Republic
| | - Petr Man
- BioCeV - Institute of Microbiology of the Czech Academy of Sciences, Vestec, Czech Republic.
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7
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Aerts J, Andrén PE, Jansson ET. Zero-Degree Celsius Capillary Electrophoresis Electrospray Ionization for Hydrogen Exchange Mass Spectrometry. Anal Chem 2022; 95:1149-1158. [PMID: 36546842 PMCID: PMC9850406 DOI: 10.1021/acs.analchem.2c03893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Currently, fast liquid chromatographic separations at low temperatures are exclusively used for the separation of peptides generated in hydrogen deuterium exchange (HDX) workflows. However, it has been suggested that capillary electrophoresis may be a better option for use with HDX. We performed in solution HDX on peptides and bovine hemoglobin (Hb) followed by quenching, pepsin digestion, and cold capillary electrophoretic separation coupled with mass spectrometry (MS) detection for benchmarking a laboratory-built HDX-MS platform. We found that capillaries with a neutral coating to eliminate electroosmotic flow and adsorptive processes provided fast separations with upper limit peak capacities surpassing 170. In contrast, uncoated capillaries achieved 30% higher deuterium retention for an angiotensin II peptide standard owing to faster separations but with only half the peak capacity of coated capillaries. Data obtained using two different separation conditions on peptic digests of Hb showed strong agreement of the relative deuterium uptake between methods. Processed data for denatured versus native Hb after deuterium labeling for the longest timepoint in this study (50,000 s) also showed agreement with subunit interaction sites determined by crystallographic methods. All proteomic data are available under DOI: 10.6019/PXD034245.
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Affiliation(s)
- Jordan
T. Aerts
- Department
of Pharmaceutical Biosciences, Uppsala University, Uppsala751 24, Sweden
| | - Per E. Andrén
- Department
of Pharmaceutical Biosciences, Uppsala University, Uppsala751 24, Sweden,Science
for Life Laboratory, Spatial Mass Spectrometry, Uppsala University, Uppsala751 24, Sweden
| | - Erik T. Jansson
- Department
of Pharmaceutical Biosciences, Uppsala University, Uppsala751 24, Sweden,
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8
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Anderson KW, Hudgens JW. Chromatography at -30 °C for Reduced Back-Exchange, Reduced Carryover, and Improved Dynamic Range for Hydrogen-Deuterium Exchange Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1282-1292. [PMID: 35732031 PMCID: PMC9264389 DOI: 10.1021/jasms.2c00096] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
For hydrogen-deuterium exchange mass spectrometry (HDX-MS) to have an increased role in quality control of biopharmaceuticals, H for D back-exchange occurring during protein analyses should be minimized to promote greater reproducibility. Standard HDX-MS analysis systems that digest proteins and separate peptides at pH 2.7 and 0 °C can lose >30% of the deuterium marker within 15 min of sample injection. This report describes the architecture and performance of a dual-enzyme, HDX-MS instrument that conducts liquid chromatography (LC) separations at subzero temperature, thereby reducing back-exchange and supporting longer LC separations with improved chromatographic resolution. LC separations of perdeuterated, fully reduced, iodoacetamide-treated BSA protein digest standard peptides were performed at 0, -10, -20, and -30 °C in ethylene glycol (EG)/H2O mixtures. Analyses conducted at -20 and -30 °C produced similar results. After subtracting for deuterium retained in arginine side chains, the average peptide eluted during a 40 min gradient contained ≈16% more deuterium than peptides eluted with a conventional 8 min gradient at 0 °C. A subset of peptides exhibited ≈26% more deuterium. Although chromatographic peaks shift with EG concentration and temperature, the apparatus elutes unbroadened LC peaks. Electrospray ion intensity does not decline with increasing EG fraction. To minimize bias from sample carryover, the fluidic circuits allow flush and backflush cleaning of all enzyme and LC columns. The system can perform LC separations and clean enzyme columns simultaneously. Temperature zones are controlled ±0.058 °C. The potential of increased sensitivity by mixing acetonitrile with the analytical column effluent was also examined.
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Affiliation(s)
- Kyle W. Anderson
- National
Institute of Standards and Technology, Bioprocess
Measurement Group, Biomolecular Measurements Division, Rockville, Maryland 20850, United States
- Institute
for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, Maryland 20850, United States
| | - Jeffrey W. Hudgens
- National
Institute of Standards and Technology, Bioprocess
Measurement Group, Biomolecular Measurements Division, Rockville, Maryland 20850, United States
- Institute
for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, Maryland 20850, United States
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9
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Rapid removal of detergent in glycolipids using ionic liquids. ANAL SCI 2022; 38:1115-1121. [PMID: 35718829 DOI: 10.1007/s44211-022-00139-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 05/24/2022] [Indexed: 11/01/2022]
Abstract
Detergent removal in glycolipid after sample preparation, such as enzymatic reaction or isolation of detergent-resistant membrane microdomain, is indispensable for further structural characterization. We previously established the rapid and effective method of detergent removal in glycolipid samples from glass test tube using 1,2-dichloroethane (DCE) washing. However, the use of DCE has several drawbacks, such as environmental risks, harmful effects (potentially carcinogenic), and high vaporability and flammability. To solve the issue, we used ionic liquids to remove detergents from glycolipid samples, and found 1-butyl-3-methylimidazolium iodide was a suitable alternative for DCE.
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10
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The changing face of SDS denaturation: Complexes of Thermomyces lanuginosus lipase with SDS at pH 4.0, 6.0 and 8.0. J Colloid Interface Sci 2022; 614:214-232. [DOI: 10.1016/j.jcis.2021.12.188] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/16/2021] [Accepted: 12/29/2021] [Indexed: 12/15/2022]
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11
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Bang G, Lee H, Kim H, Han EH, Park YH, Kim JY. Comparison of protein characterization using In solution and S-Trap digestion methods for proteomics. Biochem Biophys Res Commun 2021; 589:197-203. [PMID: 34922203 DOI: 10.1016/j.bbrc.2021.12.026] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 12/08/2021] [Indexed: 11/02/2022]
Abstract
Protein extraction and digestion are important analytical steps in the study of proteomics. The use of sodium dodecyl sulfate (SDS) buffer makes it possible to effectively analyze various proteins. Its use was evaluated using the S-Trap digestion method and compared to the traditional In solution digestion method. Differences in protein composition were examined for each protein preparation method. S-Trap digestion followed by SDS buffer extraction clearly increased the number of identified proteins, including more mitochondrial and membrane-related proteins. The S-Trap digestion method with 5% SDS buffer was applied to the pellet remaining from the removal of RIPA buffer-soluble proteins, which identified more extracellular space proteins than the conventional S-Trap digestion method. S-Trap digestion of the pellet was particularly advantageous for identifying proteins located inside multilayer membranes.
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Affiliation(s)
- Geul Bang
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Chungbuk, 28119, Republic of Korea; Metabolomics Laboratory, College of Pharmacy, Korea University, Sejong, 30019, Republic of Korea
| | - Hayoung Lee
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Chungbuk, 28119, Republic of Korea; Department of Bio-Analytical Science, University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Hyejin Kim
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Chungbuk, 28119, Republic of Korea
| | - Eun Hee Han
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Chungbuk, 28119, Republic of Korea
| | - Youngja Hwang Park
- Metabolomics Laboratory, College of Pharmacy, Korea University, Sejong, 30019, Republic of Korea.
| | - Jin Young Kim
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Chungbuk, 28119, Republic of Korea.
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12
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Deep Membrane Proteome Profiling Reveals Overexpression of Prostate-Specific Membrane Antigen (PSMA) in High-Risk Human Paraganglioma and Pheochromocytoma, Suggesting New Theranostic Opportunity. Molecules 2021; 26:molecules26216567. [PMID: 34770976 PMCID: PMC8587166 DOI: 10.3390/molecules26216567] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 10/27/2021] [Accepted: 10/28/2021] [Indexed: 11/17/2022] Open
Abstract
Pheochromocytomas and paragangliomas (PPGLs) are rare neuroendocrine tumors arising from chromaffin cells of adrenal medulla or sympathetic or parasympathetic paraganglia, respectively. To identify new therapeutic targets, we performed a detailed membrane-focused proteomic analysis of five human paraganglioma (PGL) samples. Using the Pitchfork strategy, which combines specific enrichments of glycopeptides, hydrophobic transmembrane segments, and non-glycosylated extra-membrane peptides, we identified over 1800 integral membrane proteins (IMPs). We found 45 “tumor enriched” proteins, i.e., proteins identified in all five PGLs but not found in control chromaffin tissue. Among them, 18 IMPs were predicted to be localized on the cell surface, a preferred drug targeting site, including prostate-specific membrane antigen (PSMA), a well-established target for nuclear imaging and therapy of advanced prostate cancer. Using specific antibodies, we verified PSMA expression in 22 well-characterized human PPGL samples. Compared to control chromaffin tissue, PSMA was markedly overexpressed in high-risk PPGLs belonging to the established Cluster 1, which is characterized by worse clinical outcomes, pseudohypoxia, multiplicity, recurrence, and metastasis, specifically including SDHB, VHL, and EPAS1 mutations. Using immunohistochemistry, we localized PSMA expression to tumor vasculature. Our study provides the first direct evidence of PSMA overexpression in PPGLs which could translate to therapeutic and diagnostic applications of anti-PSMA radio-conjugates in high-risk PPGLs.
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13
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James EI, Murphree TA, Vorauer C, Engen JR, Guttman M. Advances in Hydrogen/Deuterium Exchange Mass Spectrometry and the Pursuit of Challenging Biological Systems. Chem Rev 2021; 122:7562-7623. [PMID: 34493042 PMCID: PMC9053315 DOI: 10.1021/acs.chemrev.1c00279] [Citation(s) in RCA: 95] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
Solution-phase hydrogen/deuterium
exchange (HDX) coupled to mass
spectrometry (MS) is a widespread tool for structural analysis across
academia and the biopharmaceutical industry. By monitoring the exchangeability
of backbone amide protons, HDX-MS can reveal information about higher-order
structure and dynamics throughout a protein, can track protein folding
pathways, map interaction sites, and assess conformational states
of protein samples. The combination of the versatility of the hydrogen/deuterium
exchange reaction with the sensitivity of mass spectrometry has enabled
the study of extremely challenging protein systems, some of which
cannot be suitably studied using other techniques. Improvements over
the past three decades have continually increased throughput, robustness,
and expanded the limits of what is feasible for HDX-MS investigations.
To provide an overview for researchers seeking to utilize and derive
the most from HDX-MS for protein structural analysis, we summarize
the fundamental principles, basic methodology, strengths and weaknesses,
and the established applications of HDX-MS while highlighting new
developments and applications.
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Affiliation(s)
- Ellie I James
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Taylor A Murphree
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Clint Vorauer
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - John R Engen
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
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14
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Filandrova R, Kavan D, Kadek A, Novak P, Man P. Studying Protein-DNA Interactions by Hydrogen/Deuterium Exchange Mass Spectrometry. Methods Mol Biol 2021; 2247:193-219. [PMID: 33301119 DOI: 10.1007/978-1-0716-1126-5_11] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Protein hydrogen/deuterium exchange (HDX) coupled to mass spectrometry (MS) can be used to study interactions of proteins with various ligands, to describe the effects of mutations, or to reveal structural responses of proteins to different experimental conditions. It is often described as a method with virtually no limitations in terms of protein size or sample composition. While this is generally true, there are, however, ligands or buffer components that can significantly complicate the analysis. One such compound, that can make HDX-MS troublesome, is DNA. In this chapter, we will focus on the analysis of protein-DNA interactions, describe the detailed protocol, and point out ways to overcome the complications arising from the presence of DNA.
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Affiliation(s)
- Ruzena Filandrova
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
- Faculty of Sciences, Charles University, Prague, Czech Republic
| | - Daniel Kavan
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Alan Kadek
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Petr Novak
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Petr Man
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic.
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15
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Lenčo J, Šemlej T, Khalikova MA, Fabrik I, Švec F. Sense and Nonsense of Elevated Column Temperature in Proteomic Bottom-up LC-MS Analyses. J Proteome Res 2020; 20:420-432. [PMID: 33085896 DOI: 10.1021/acs.jproteome.0c00479] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Elevated column temperature represents a simple means for improving chromatographic separation of peptides. Here, we demonstrated the advantages of the column temperature in peptide separation using state-of-the-art columns. More importantly, we also determined how temperature can impair proteomic bottom-up analyses. We found that an elevated temperature in combination with the acidic pH of the mobile phase induced in-column peptide hydrolysis with high specificity to Asp and accelerated five modification reactions of amino acids. The positive effects of temperature dominated in the 30 min long gradients since the column operated at 90 °C provided the largest number of identified peptides and proteins. However, the adverse effects of temperature on peptide integrity in longer liquid chromatography-mass spectrometry (LC-MS) analyses required its reduction to obtain optimum results. The largest number of peptides was identified using the column maintained at 75 °C in 60 min long gradients, at 60 °C in 120 min long gradients, and at 45 °C in 240 min long gradients. Our results indicate that no universal column temperature exists for bottom-up LC-MS analyses. Quite the contrary, the temperature setting must be selected rationally to exploit the full capabilities of the state-of-the-art mass spectrometers in proteomic LC-MS analyses, with the gradient time being a critical factor.
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Affiliation(s)
- Juraj Lenčo
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05 Hradec Králové, Czech Republic
| | - Tomáš Šemlej
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05 Hradec Králové, Czech Republic
| | - Maria A Khalikova
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05 Hradec Králové, Czech Republic
| | - Ivo Fabrik
- Biomedical Research Center, University Hospital Hradec Králové, Sokolská 581, 500 05 Hradec Králové, Czech Republic
| | - František Švec
- Department of Analytical Chemistry, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203/8, 500 05 Hradec Králové, Czech Republic
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16
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Liu XR, Zhang MM, Gross ML. Mass Spectrometry-Based Protein Footprinting for Higher-Order Structure Analysis: Fundamentals and Applications. Chem Rev 2020; 120:4355-4454. [PMID: 32319757 PMCID: PMC7531764 DOI: 10.1021/acs.chemrev.9b00815] [Citation(s) in RCA: 130] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Proteins adopt different higher-order structures (HOS) to enable their unique biological functions. Understanding the complexities of protein higher-order structures and dynamics requires integrated approaches, where mass spectrometry (MS) is now positioned to play a key role. One of those approaches is protein footprinting. Although the initial demonstration of footprinting was for the HOS determination of protein/nucleic acid binding, the concept was later adapted to MS-based protein HOS analysis, through which different covalent labeling approaches "mark" the solvent accessible surface area (SASA) of proteins to reflect protein HOS. Hydrogen-deuterium exchange (HDX), where deuterium in D2O replaces hydrogen of the backbone amides, is the most common example of footprinting. Its advantage is that the footprint reflects SASA and hydrogen bonding, whereas one drawback is the labeling is reversible. Another example of footprinting is slow irreversible labeling of functional groups on amino acid side chains by targeted reagents with high specificity, probing structural changes at selected sites. A third footprinting approach is by reactions with fast, irreversible labeling species that are highly reactive and footprint broadly several amino acid residue side chains on the time scale of submilliseconds. All of these covalent labeling approaches combine to constitute a problem-solving toolbox that enables mass spectrometry as a valuable tool for HOS elucidation. As there has been a growing need for MS-based protein footprinting in both academia and industry owing to its high throughput capability, prompt availability, and high spatial resolution, we present a summary of the history, descriptions, principles, mechanisms, and applications of these covalent labeling approaches. Moreover, their applications are highlighted according to the biological questions they can answer. This review is intended as a tutorial for MS-based protein HOS elucidation and as a reference for investigators seeking a MS-based tool to address structural questions in protein science.
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Affiliation(s)
| | | | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA, 63130
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Lenčo J, Khalikova MA, Švec F. Dissolving Peptides in 0.1% Formic Acid Brings Risk of Artificial Formylation. J Proteome Res 2020; 19:993-999. [DOI: 10.1021/acs.jproteome.9b00823] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Juraj Lenčo
- Department of Analytical Chemistry, Faculty of Pharmacy, Charles University, Heyrovského 1203/8, 500 05 Hradec Králové, Czech Republic
| | - Maria A. Khalikova
- Department of Analytical Chemistry, Faculty of Pharmacy, Charles University, Heyrovského 1203/8, 500 05 Hradec Králové, Czech Republic
| | - František Švec
- Department of Analytical Chemistry, Faculty of Pharmacy, Charles University, Heyrovského 1203/8, 500 05 Hradec Králové, Czech Republic
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Vit O, Harant K, Klener P, Man P, Petrak J. A three-pronged "Pitchfork" strategy enables an extensive description of the human membrane proteome and the identification of missing proteins. J Proteomics 2019; 204:103411. [PMID: 31176011 DOI: 10.1016/j.jprot.2019.103411] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 05/14/2019] [Accepted: 06/03/2019] [Indexed: 11/28/2022]
Abstract
Integral membrane proteins are under-represented in standard proteomic analyses, mostly because of their low expression and absence of trypsin-cleavage sites in their hydrophobic transmembrane segments. Novel and effective strategies for membrane proteomic analysis aim at soluble N-glycosylated segments of integral membrane proteins (CSC, SPEG, N-glyco-FASP) or selectively target the hydrophobic transmembrane alpha-helical segments employing chemical peptide cleavage by CNBr (hpTC). We combined a solid phase enrichment of glycopeptides (SPEG) with a transmembrane segment-oriented hpTC method and a standard "detergent and trypsin" approach into a three-pronged "Pitchfork" strategy to maximize the membrane proteome coverage in human lymphoma cells. This strategy enabled the identification of >1200 integral membrane proteins from all cellular compartments, including 105 CD antigens, 24 G protein-coupled receptors, and 141 solute carrier transporters. The advantage of the combination lies in the complementarity of the methods. SPEG and hpTC target different sets of membrane proteins. HpTC provided identifications of proteins and peptides with significantly higher hydrophobicity compared to SPEG and detergent-trypsin approaches. Among all identified proteins, we observed 32 so-called "missing proteins". The Pitchfork strategy presented here is universally applicable and enables deep and fast description of membrane proteomes in only 3 LC-MS/MS runs per replicate. SIGNIFICANCE: Integral membrane proteins (IMPs) are encoded by roughly a quarter of human coding genes. Their functions and their specific localization makes IMPs highly attractive drug targets. In fact, roughly half of the currently approved drugs in medicine target IMPs. Our knowledge of membrane proteomes is, however, limited. We present a new strategy for the membrane proteome analysis that combines three complementary methods targeting different features of IMPs. Using the combined strategy, we identified over 1200 IMPs in human lymphoma tissue from all sub-cellular compartments in only 3 LC-MS/MS runs per replicate. The three-pronged "Pitchfork" strategy is universally applicable, and offers a fast way toward a reasonably concise description of membrane proteomes in multiple samples.
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Affiliation(s)
- Ondrej Vit
- BIOCEV, First Faculty of Medicine, Charles University, Czech Republic
| | - Karel Harant
- Laboratory of Mass Spectrometry - Service Laboratory of Biology Section, BIOCEV, Faculty of Science, Charles University, Prague, Czech Republic
| | - Pavel Klener
- Institute of Pathological Physiology, First Faculty of Medicine, Charles University, Czech Republic
| | - Petr Man
- BIOCEV, Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic; Department of Biochemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jiri Petrak
- BIOCEV, First Faculty of Medicine, Charles University, Czech Republic.
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Li Y, Lee JS. Staring at protein-surfactant interactions: Fundamental approaches and comparative evaluation of their combinations - A review. Anal Chim Acta 2019; 1063:18-39. [DOI: 10.1016/j.aca.2019.02.024] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Revised: 02/15/2019] [Accepted: 02/18/2019] [Indexed: 02/07/2023]
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20
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Möller IR, Slivacka M, Hausner J, Nielsen AK, Pospíšilová E, Merkle PS, Lišková R, Polák M, Loland CJ, Kádek A, Man P, Rand KD. Improving the Sequence Coverage of Integral Membrane Proteins during Hydrogen/Deuterium Exchange Mass Spectrometry Experiments. Anal Chem 2019; 91:10970-10978. [DOI: 10.1021/acs.analchem.9b00973] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Ingvar R. Möller
- Department of Pharmacy, University of Copenhagen, Universitetsparken 2, Copenhagen E DK-2100, Denmark
| | - Marika Slivacka
- Department of Pharmacy, University of Copenhagen, Universitetsparken 2, Copenhagen E DK-2100, Denmark
| | - Jiří Hausner
- BioCeV - Institute of Microbiology of the CAS, Prumyslova 595, CZ-252 50 Vestec, Czech Republic
- Faculty of Science, Charles University, Hlavova 8, CZ-128 20 Prague, Czech Republic
| | - Anne Kathrine Nielsen
- Laboratory for Membrane Protein Dynamics, Department of Neuroscience, University of Copenhagen, Blegdamsvej 3, Copenhagen N DK-2200, Denmark
| | - Eliška Pospíšilová
- BioCeV - Institute of Microbiology of the CAS, Prumyslova 595, CZ-252 50 Vestec, Czech Republic
- Faculty of Science, Charles University, Hlavova 8, CZ-128 20 Prague, Czech Republic
| | - Patrick S. Merkle
- Department of Pharmacy, University of Copenhagen, Universitetsparken 2, Copenhagen E DK-2100, Denmark
| | - Růžena Lišková
- BioCeV - Institute of Microbiology of the CAS, Prumyslova 595, CZ-252 50 Vestec, Czech Republic
- Faculty of Science, Charles University, Hlavova 8, CZ-128 20 Prague, Czech Republic
| | - Marek Polák
- BioCeV - Institute of Microbiology of the CAS, Prumyslova 595, CZ-252 50 Vestec, Czech Republic
- Faculty of Science, Charles University, Hlavova 8, CZ-128 20 Prague, Czech Republic
| | - Claus J. Loland
- Laboratory for Membrane Protein Dynamics, Department of Neuroscience, University of Copenhagen, Blegdamsvej 3, Copenhagen N DK-2200, Denmark
| | - Alan Kádek
- BioCeV - Institute of Microbiology of the CAS, Prumyslova 595, CZ-252 50 Vestec, Czech Republic
- Faculty of Science, Charles University, Hlavova 8, CZ-128 20 Prague, Czech Republic
| | - Petr Man
- BioCeV - Institute of Microbiology of the CAS, Prumyslova 595, CZ-252 50 Vestec, Czech Republic
- Faculty of Science, Charles University, Hlavova 8, CZ-128 20 Prague, Czech Republic
| | - Kasper D. Rand
- Department of Pharmacy, University of Copenhagen, Universitetsparken 2, Copenhagen E DK-2100, Denmark
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Elinger D, Gabashvili A, Levin Y. Suspension Trapping (S-Trap) Is Compatible with Typical Protein Extraction Buffers and Detergents for Bottom-Up Proteomics. J Proteome Res 2019; 18:1441-1445. [DOI: 10.1021/acs.jproteome.8b00891] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Dalia Elinger
- de Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Alexandra Gabashvili
- de Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yishai Levin
- de Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 76100, Israel
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22
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Benhaim M, Lee KK, Guttman M. Tracking Higher Order Protein Structure by Hydrogen-Deuterium Exchange Mass Spectrometry. Protein Pept Lett 2019; 26:16-26. [PMID: 30543159 PMCID: PMC6386625 DOI: 10.2174/0929866526666181212165037] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 08/30/2018] [Accepted: 11/17/2018] [Indexed: 12/27/2022]
Abstract
BACKGROUND Structural biology has provided a fundamental understanding of protein structure and mechanistic insight into their function. However, high-resolution structures alone are insufficient for a complete understanding of protein behavior. Higher energy conformations, conformational changes, and subtle structural fluctuations that underlie the proper function of proteins are often difficult to probe using traditional structural approaches. Hydrogen/Deuterium Exchange with Mass Spectrometry (HDX-MS) provides a way to probe the accessibility of backbone amide protons under native conditions, which reports on local structural dynamics of solution protein structure that can be used to track complex structural rearrangements that occur in the course of a protein's function. CONCLUSION In the last 20 years the advances in labeling techniques, sample preparation, instrumentation, and data analysis have enabled HDX to gain insights into very complex biological systems. Analysis of challenging targets such as membrane protein complexes is now feasible and the field is paving the way to the analysis of more and more complex systems.
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Affiliation(s)
- Mark Benhaim
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195 USA
| | - Kelly K. Lee
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195 USA
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195 USA
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23
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Cell Separation and Disruption, Product Recovery, and Purification. ESSENTIALS IN FERMENTATION TECHNOLOGY 2019. [DOI: 10.1007/978-3-030-16230-6_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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24
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Gan V. Remembering Eric Forest (1957-2017). From analytical chemistry to the rise of HDXMS for structural biology of complex protein systems. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2017; 31:978-982. [PMID: 28345278 DOI: 10.1002/rcm.7858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
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25
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Vadas O, Jenkins ML, Dornan GL, Burke JE. Using Hydrogen-Deuterium Exchange Mass Spectrometry to Examine Protein-Membrane Interactions. Methods Enzymol 2016; 583:143-172. [PMID: 28063489 DOI: 10.1016/bs.mie.2016.09.008] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Many fundamental cellular processes are controlled via assembly of a network of proteins at membrane surfaces. The proper recruitment of proteins to membranes can be controlled by a wide variety of mechanisms, including protein lipidation, protein-protein interactions, posttranslational modifications, and binding to specific lipid species present in membranes. There are, however, only a limited number of analytical techniques that can study the assembly of protein-membrane complexes at the molecular level. A relatively new addition to the set of techniques available to study these protein-membrane systems is the use of hydrogen-deuterium exchange mass spectrometry (HDX-MS). HDX-MS experiments measure protein conformational dynamics in their native state, based on the rate of exchange of amide hydrogens with solvent. This review discusses the use of HDX-MS as a tool to identify the interfaces of proteins with membranes and membrane-associated proteins, as well as define conformational changes elicited by membrane recruitment. Specific examples will focus on the use of HDX-MS to examine how large macromolecular protein complexes are recruited and activated on membranes, and how both posttranslational modifications and cancer-linked oncogenic mutations affect these processes.
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Affiliation(s)
- O Vadas
- Pharmaceutical Sciences Section, University of Geneva, Geneva, Switzerland
| | | | - G L Dornan
- University of Victoria, Victoria BC, Canada
| | - J E Burke
- University of Victoria, Victoria BC, Canada.
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26
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Vit O, Man P, Kadek A, Hausner J, Sklenar J, Harant K, Novak P, Scigelova M, Woffendin G, Petrak J. Large-scale identification of membrane proteins based on analysis of trypsin-protected transmembrane segments. J Proteomics 2016; 149:15-22. [DOI: 10.1016/j.jprot.2016.03.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 02/03/2016] [Accepted: 03/04/2016] [Indexed: 01/06/2023]
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27
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Vit O, Petrak J. Integral membrane proteins in proteomics. How to break open the black box? J Proteomics 2016; 153:8-20. [PMID: 27530594 DOI: 10.1016/j.jprot.2016.08.006] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 06/30/2016] [Accepted: 08/09/2016] [Indexed: 12/22/2022]
Abstract
Integral membrane proteins (IMPs) are coded by 20-30% of human genes and execute important functions - transmembrane transport, signal transduction, cell-cell communication, cell adhesion to the extracellular matrix, and many other processes. Due to their hydrophobicity, low expression and lack of trypsin cleavage sites in their transmembrane segments, IMPs have been generally under-represented in routine proteomic analyses. However, the field of membrane proteomics has changed markedly in the past decade, namely due to the introduction of filter assisted sample preparation (FASP), the establishment of cell surface capture (CSC) protocols, and the development of methods that enable analysis of the hydrophobic transmembrane segments. This review will summarize the recent developments in the field and outline the most successful strategies for the analysis of integral membrane proteins. SIGNIFICANCE Integral membrane proteins (IMPs) are attractive therapeutic targets mostly due to their many important functions. However, our knowledge of the membrane proteome is severely limited to effectively exploit their potential. This is mostly due to the lack of appropriate techniques or methods compatible with the typical features of IMPs, namely hydrophobicity, low expression and lack of trypsin cleavage sites. This review summarizes the most recent development in membrane proteomics and outlines the most successful strategies for their large-scale analysis.
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Affiliation(s)
- O Vit
- BIOCEV, First Faculty of Medicine, Charles University in Prague, Czech Republic.
| | - J Petrak
- BIOCEV, First Faculty of Medicine, Charles University in Prague, Czech Republic
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28
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SUZUKI Y, OKANO A, KABAYAMA K, NISHINA A, TANIGAWA M, NISHIMURA K, KUSHI Y. Purification of Pyridylaminated Oligosaccharides Using 1,2-Dichloroethane Extraction. ANAL SCI 2016; 32:487-90. [DOI: 10.2116/analsci.32.487] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
| | - Aya OKANO
- College of Science and Technology, Nihon University
| | - Kazuya KABAYAMA
- Department of Chemistry, Graduate School of Science, Osaka University
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29
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Forest E, Man P. Conformational Dynamics and Interactions of Membrane Proteins by Hydrogen/Deuterium Mass Spectrometry. Methods Mol Biol 2016; 1432:269-79. [PMID: 27485342 DOI: 10.1007/978-1-4939-3637-3_17] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Hydrogen/deuterium exchange associated with mass spectrometry has been recently used to characterize the dynamics and the interactions of membrane proteins. Here we describe experimental workflow enabling localization of the regions involved in conformational changes or interactions.
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Affiliation(s)
- Eric Forest
- Univ. Grenoble Alpes, IBS, Grenoble, France. .,CNRS, IBS, Grenoble, France. .,CEA, IBS, Grenoble, France. .,Institut de Biologie Structurale, CNRS (UMR 5075)/CEA/UGA, EPN Campus, 71 avenue des Martyrs, CS 10090, 38044, Grenoble Cedex 9, France.
| | - Petr Man
- BioCeV - Institute of Microbiology, Czech Academy of Sciences, Vestec, Czech Republic.,Faculty of Science, Charles University in Prague, Prague, Czech Republic
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Abstract
The structural analysis of viruses is often a complex task. In many cases, the details of the viral architecture, especially for enveloped viruses, are limited to low-resolution techniques such as electron microscopy. These structural proteins and assemblies of viruses often populate multiple conformational states and undergo dramatic structural changes, making them difficult to study by most structural methods. They also frequently include highly dynamic regions that are of key functional importance. Many viruses present large surface glycoproteins, which have also proved to be challenging for structural biology due to the intrinsic flexibility and heterogeneity of the glycan decorations. Over the past two decades, hydrogen deuterium exchange coupled to mass spectrometry (HDX-MS) has provided a wealth of information on many diverse viral proteins, glycoproteins, and complexes, in many cases, in multiple conformational states. Here, we describe the methodology for using HDX-MS to investigate the rich structural dynamics of viral systems, and we briefly review the type of systems that have been examined through this type of approach. Though the technique is relatively simple, several potential pitfalls exist at both the sample preparation and the data analysis stage that investigators should be aware of for obtaining reliable data.
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Affiliation(s)
- Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington, USA.
| | - Kelly K Lee
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington, USA.
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31
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Pirrone GF, Vernon BC, Kent MS, Engen JR. Hydrogen Exchange Mass Spectrometry of Proteins at Langmuir Monolayers. Anal Chem 2015; 87:7022-9. [PMID: 26134943 DOI: 10.1021/acs.analchem.5b01724] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Hydrogen exchange (HX) mass spectrometry (MS) is valuable for providing conformational information for proteins/peptides that are very difficult to analyze with other methods such as peripheral membrane proteins and peptides that interact with membranes. We developed a new type of HX MS measurement that integrates Langmuir monolayers. A lipid monolayer was generated, a peptide or protein associated with it, and then the monolayer-associated peptide or protein was exposed to deuterium. The deuterated species was recovered from the monolayer, digested, and deuterium incorporation monitored by MS. Test peptides showed that deuterium recovery in an optimized protocol was equivalent to deuterium recovery in conventional solution HX MS. The reproducibility of the measurements was high, despite the requirement of generating a new monolayer for each deuterium labeling time. We validated that known conformational changes in the presence of a monolayer/membrane could be observed with the peptide melittin and the myristoylated protein Arf-1. Results in an accompanying paper show that the method can reveal details of conformational changes in a protein (HIV-1 Nef), which adopts a different conformation, depending on whether or not it is able to insert into the lipid layer. Overall, the HX MS Langmuir monolayer method provided new and meaningful conformational information for proteins that associate with lipid layers. The combination of HX MS results with neutron or X-ray reflection of the same proteins in Langmuir monolayers can be more informative than the isolated use of either method.
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Affiliation(s)
- Gregory F Pirrone
- †Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, Massachusetts 02115-5000, United States
| | - Briana C Vernon
- ‡Bioenergy and Defense Technologies, Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
| | - Michael S Kent
- ‡Bioenergy and Defense Technologies, Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
| | - John R Engen
- †Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, Massachusetts 02115-5000, United States
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Krásný L, Pompach P, Strnadová M, Hynek R, Vališ K, Havlíček V, Novák P, Volný M. High-throughput workflow for identification of phosphorylated peptides by LC-MALDI-TOF/TOF-MS coupled to in situ enrichment on MALDI plates functionalized by ion landing. JOURNAL OF MASS SPECTROMETRY : JMS 2015; 50:802-811. [PMID: 26169134 DOI: 10.1002/jms.3586] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Revised: 02/23/2015] [Accepted: 02/24/2015] [Indexed: 06/04/2023]
Abstract
We report an MS-based workflow for identification of phosphorylated peptides from trypsinized protein mixtures and cell lysates that is suitable for high-throughput sample analysis. The workflow is based on an in situ enrichment on matrix-assisted laser desorption/ionization (MALDI) plates that were functionalized by TiO2 using automated ion landing apparatus that can operate unsupervised. The MALDI plate can be functionalized by TiO2 into any array of predefined geometry (here, 96 positions for samples and 24 for mass calibration standards) made compatible with a standard MALDI spotter and coupled with high-performance liquid chromatography. The in situ MALDI plate enrichment was compared with a standard precolumn-based separation and achieved comparable or better results than the standard method. The performance of this new workflow was demonstrated on a model mixture of proteins as well as on Jurkat cells lysates. The method showed improved signal-to-noise ratio in a single MS spectrum, which resulted in better identification by MS/MS and a subsequent database search. Using the workflow, we also found specific phosphorylations in Jurkat cells that were nonspecifically activated by phorbol 12-myristate 13-acetate. These phosphorylations concerned the mitogen-activated protein kinase/extracellular signal-regulated kinase signaling pathway and its targets and were in agreement with the current knowledge of this signaling cascade. Control sample of non-activated cells was devoid of these phosphorylations. Overall, the presented analytical workflow is able to detect dynamic phosphorylation events in minimally processed mammalian cells while using only a short high-performance liquid chromatography gradient.
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Affiliation(s)
- Lukáš Krásný
- Institute of Microbiology ASCR, v.v.i., Vídeňská 1083, Prague, 142 20, Czech Republic
- Institute of Chemical Technology, Technická 5, Prague, 16628, Czech Republic
| | - Petr Pompach
- Institute of Microbiology ASCR, v.v.i., Vídeňská 1083, Prague, 142 20, Czech Republic
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 8, Prague, 128 40, Czech Republic
| | - Marcela Strnadová
- Institute of Microbiology ASCR, v.v.i., Vídeňská 1083, Prague, 142 20, Czech Republic
| | - Radovan Hynek
- Institute of Chemical Technology, Technická 5, Prague, 16628, Czech Republic
| | - Karel Vališ
- Institute of Microbiology ASCR, v.v.i., Vídeňská 1083, Prague, 142 20, Czech Republic
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 8, Prague, 128 40, Czech Republic
| | - Vladimír Havlíček
- Institute of Microbiology ASCR, v.v.i., Vídeňská 1083, Prague, 142 20, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacky University, 17.listopadu 12, Olomouc, 771 46, Czech Republic
| | - Petr Novák
- Institute of Microbiology ASCR, v.v.i., Vídeňská 1083, Prague, 142 20, Czech Republic
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 8, Prague, 128 40, Czech Republic
| | - Michael Volný
- Applied Physics Laboratory, University of Washington, 1013 NE 40th St, Seattle, WA, 98105, USA
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Majumdar R, Middaugh C, Weis DD, Volkin DB. Hydrogen-Deuterium Exchange Mass Spectrometry as an Emerging Analytical Tool for Stabilization and Formulation Development of Therapeutic Monoclonal Antibodies. J Pharm Sci 2015; 104:327-45. [DOI: 10.1002/jps.24224] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Revised: 09/24/2014] [Accepted: 09/26/2014] [Indexed: 12/11/2022]
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Engen JR, Wales TE. Analytical Aspects of Hydrogen Exchange Mass Spectrometry. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2015; 8:127-48. [PMID: 26048552 PMCID: PMC4989240 DOI: 10.1146/annurev-anchem-062011-143113] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
This article reviews the analytical aspects of measuring hydrogen exchange by mass spectrometry (HX MS). We describe the nature of analytical selectivity in hydrogen exchange, then review the analytical tools required to accomplish fragmentation, separation, and the mass spectrometry measurements under restrictive exchange quench conditions. In contrast to analytical quantitation that relies on measurements of peak intensity or area, quantitation in HX MS depends on measuring a mass change with respect to an undeuterated or deuterated control, resulting in a value between zero and the maximum amount of deuterium that can be incorporated. Reliable quantitation is a function of experimental fidelity and to achieve high measurement reproducibility, a large number of experimental variables must be controlled during sample preparation and analysis. The method also reports on important qualitative aspects of the sample, including conformational heterogeneity and population dynamics.
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Affiliation(s)
- John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115;
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Wang H, So PK, Ng TT, Yao ZP. Rapid analysis of raw solution samples by C18 pipette-tip electrospray ionization mass spectrometry. Anal Chim Acta 2014; 844:1-7. [DOI: 10.1016/j.aca.2014.07.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2014] [Revised: 07/10/2014] [Accepted: 07/12/2014] [Indexed: 12/22/2022]
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36
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Meyer JG. In Silico Proteome Cleavage Reveals Iterative Digestion Strategy for High Sequence Coverage. ISRN COMPUTATIONAL BIOLOGY 2014; 2014:960902. [PMID: 30687733 PMCID: PMC6347401 DOI: 10.1155/2014/960902] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
In the postgenome era, biologists have sought to measure the complete complement of proteins, termed proteomics. Currently, the most effective method to measure the proteome is with shotgun, or bottom-up, proteomics, in which the proteome is digested into peptides that are identified followed by protein inference. Despite continuous improvements to all steps of the shotgun proteomics workflow, observed proteome coverage is often low; some proteins are identified by a single peptide sequence. Complete proteome sequence coverage would allow comprehensive characterization of RNA splicing variants and all posttranslational modifications, which would drastically improve the accuracy of biological models. There are many reasons for the sequence coverage deficit, but ultimately peptide length determines sequence observability. Peptides that are too short are lost because they match many protein sequences and their true origin is ambiguous. The maximum observable peptide length is determined by several analytical challenges. This paper explores computationally how peptide lengths produced from several common proteome digestion methods limit observable proteome coverage. Iterative proteome cleavage strategies are also explored. These simulations reveal that maximized proteome coverage can be achieved by use of an iterative digestion protocol involving multiple proteases and chemical cleavages that theoretically allow 92.9% proteome coverage.
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Affiliation(s)
- Jesse G Meyer
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0378, USA
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37
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Bagag A, Jault JM, Sidahmed-Adrar N, Réfrégiers M, Giuliani A, Le Naour F. Characterization of hydrophobic peptides in the presence of detergent by photoionization mass spectrometry. PLoS One 2013; 8:e79033. [PMID: 24236085 PMCID: PMC3827311 DOI: 10.1371/journal.pone.0079033] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Accepted: 09/18/2013] [Indexed: 12/18/2022] Open
Abstract
The characterization of membrane proteins is still challenging. The major issue is the high hydrophobicity of membrane proteins that necessitates the use of detergents for their extraction and solubilization. The very poor compatibility of mass spectrometry with detergents remains a tremendous obstacle in studies of membrane proteins. Here, we investigated the potential of atmospheric pressure photoionization (APPI) for mass spectrometry study of membrane proteins. This work was focused on the tetraspanin CD9 and the multidrug transporter BmrA. A set of peptides from CD9, exhibiting a broad range of hydropathicity, was investigated using APPI as compared to electrospray ionization (ESI). Mass spectrometry experiments revealed that the most hydrophobic peptides were hardly ionized by ESI whereas all peptides, including the highly hydrophobic one that corresponds to the full sequence of the first transmembrane domain of CD9, were easily ionized by APPI. The native protein BmrA purified in the presence of the non-ionic detergent beta-D-dodecyl maltoside (DDM) was digested in-solution using trypsin. The resulting peptides were investigated by flow injection analysis of the mixture followed by mass spectrometry. Upon ESI, only detergent ions were detected and the ionic signals from the peptides were totally suppressed. In contrast, APPI allowed many peptides distributed along the sequence of the protein to be detected. Furthermore, the parent ion corresponding to the first transmembrane domain of the protein BmrA was detected under APPI conditions. Careful examination of the APPI mass spectrum revealed a-, b-, c- and y- fragment ions generated by in-source fragmentation. Those fragment ions allowed unambiguous structural characterization of the transmembrane domain. In conclusion, APPI-MS appears as a versatile method allowing the ionization and fragmentation of hydrophobic peptides in the presence of detergent.
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Affiliation(s)
- Aïcha Bagag
- Inserm, U785, Villejuif, France
- Université Paris-Sud 11, Institut André Lwoff, Villejuif, France
| | - Jean-Michel Jault
- Université Joseph Fourier-Grenoble 1, Institut de Biologie Structurale, Grenoble, France
- CNRS, UMR 5075, Grenoble, France
- CEA, Institut de Biologie Structurale, Grenoble, France
| | - Nazha Sidahmed-Adrar
- Inserm, U785, Villejuif, France
- Université Paris-Sud 11, Institut André Lwoff, Villejuif, France
| | | | - Alexandre Giuliani
- Synchrotron SOLEIL, Gif-sur-Yvette, France
- INRA, UAR 1008 CEPIA, Nantes, France
| | - François Le Naour
- Inserm, U785, Villejuif, France
- Université Paris-Sud 11, Institut André Lwoff, Villejuif, France
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Rey M, Forest E, Pelosi L. Exploring the conformational dynamics of the bovine ADP/ATP carrier in mitochondria. Biochemistry 2012; 51:9727-35. [PMID: 23136955 DOI: 10.1021/bi300759x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The mitochondrial ADP/ATP carrier catalyzes the transport of ADP and ATP across the mitochondrial inner membrane by switching between two different conformations. They can be blocked by two inhibitors: carboxyatractyloside (CATR) and bongkrekic acid (BA). Our understanding of the ADP/ATP transport process is largely based on analysis of structural differences between the individual inhibited states. The X-ray crystallographic three-dimensional structure of bovine ADP/ATP carrier isoform 1 (bAnc1p) complexed with CATR was determined, but the structure of the BA-carrier complex remains unknown. We recently investigated the conformational dynamics of bAnc1p in detergent solution using hydrogen/deuterium exchange and mass spectrometry (HDX-MS). This study shed light on some features of ADP/ATP translocation, but the mechanism itself and the organization of bAnc1p in the membrane required further investigation. This paper describes the first study of bAnc1p in the mitochondria on the whole-protein scale using HDX-MS. Membrane-embedded bAnc1p was deuterated and purified under HDX-MS-compatible conditions. Our results for the carrier in the mitochondrial inner membrane differed from those published for the carrier in a detergent solution. These differences were mainly in the upper half of the cavity that globally showed a limited H/D exchange whatever the complex analyzed and at the level of the matrix loops that were less accessible to the solvent in the BA-carrier complex than in the CATR-carrier complex. They are discussed with respect to published data for bAnc1p and have provided new insights into the conformation of the matrix loops of the bovine carrier in complex with BA in mitochondria.
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Affiliation(s)
- Martial Rey
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Direction des Sciences du Vivant (DSV), Institut de Recherches en Technologies et Sciences pour le Vivant (iRTSV), Laboratoire de Biologie à Grande Echelle (BGE), Grenoble F-38054, France
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Boschetti E, Righetti PG. Breakfast at Tiffany's? Only with a low-abundance proteomic signature! Electrophoresis 2012; 33:2228-39. [DOI: 10.1002/elps.201200003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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40
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Ye X, Li L. Microwave-Assisted Protein Solubilization for Mass Spectrometry-Based Shotgun Proteome Analysis. Anal Chem 2012; 84:6181-91. [DOI: 10.1021/ac301169q] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Xiaoxia Ye
- Department of Chemistry, University of Alberta, Edmonton,
Alberta T6G 2G2, Canada
| | - Liang Li
- Department of Chemistry, University of Alberta, Edmonton,
Alberta T6G 2G2, Canada
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41
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Brock A. Fragmentation hydrogen exchange mass spectrometry: A review of methodology and applications. Protein Expr Purif 2012; 84:19-37. [DOI: 10.1016/j.pep.2012.04.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Accepted: 04/13/2012] [Indexed: 01/19/2023]
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42
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Steric and allosteric factors prevent simultaneous binding of transferrin-binding proteins A and B to transferrin. Biochem J 2012; 444:189-97. [DOI: 10.1042/bj20112133] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The ability to acquire iron directly from host Tf (transferrin) is an adaptation common to important bacterial pathogens belonging to the Pasteurellaceae, Moraxellaceae and Neisseriaceae families. A surface receptor comprising an integral outer membrane protein, TbpA (Tf-binding protein A), and a surface-exposed lipoprotein, TbpB (Tf-binding protein B), mediates the iron acquisition process. TbpB is thought to extend from the cell surface for capture of Tf to initiate the process and deliver Tf to TbpA. TbpA functions as a gated channel for the passage of iron into the periplasm. In the present study we have mapped the effect of TbpA from Actinobacillus pleuropneumoniae on pTf (porcine Tf) using H/DX-MS (hydrogen/deuterium exchange coupled to MS) and compare it with a previously determined binding site for TbpB. The proposed TbpA footprint is adjacent to and potentially overlapping the TbpB-binding site, and induces a structural instability in the TbpB site. This suggests that simultaneous binding to pTf by both receptors would be hindered. We demonstrate that a recombinant TbpB lacking a portion of its anchor peptide is unable to form a stable ternary TbpA–pTf–TbpB complex. This truncated TbpB does not bind to a preformed Tf–TbpA complex, and TbpA removes pTf from a preformed Tf–TbpB complex. Thus the results of the present study support a model whereby TbpB ‘hands-off’ pTf to TbpA, which completes the iron removal and transport process.
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43
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Suzuki Y, Kabayama K. Convenient and rapid removal of detergent from glycolipids in detergent-resistant membrane microdomains. J Lipid Res 2012; 53:599-608. [PMID: 22217704 DOI: 10.1194/jlr.d020545] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Although detergents are often essential in protocols, they are usually incompatible with further biochemical analysis. There are several methods for detergent removal, but the procedures are complicated or suffer from sample loss. Here, we describe a convenient and rapid method for detergent removal from sialic acid-containing glycosphingolipids (gangliosides) and neutral glycolipids in detergent-resistant membrane (DRM) microdomain. It is based on selective detergent extraction, in which the sample is dried on a glass tube, followed by washing with organic solvent. We investigated 18 organic solvents and used high performance thin-layer chromatography (HPTLC) and matrix-assisted laser desorption/ionization quadrupole ion trap time-of-flight mass spectrometry (MALDI-QIT-TOF MS) to confirm that dichloroethane (DCE) was the most suitable solvent and completely removed the nonionic detergent Triton X-100. Furthermore, DCE extraction effectively removed interference caused by other nonionic, zwitterionic, or ionic detergents in MALDI-QIT-TOF MS analysis.
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Affiliation(s)
- Yusuke Suzuki
- Institute of Glycoscience, Tokai University, Kanagawa, Japan
| | - Kazuya Kabayama
- Institute of Glycoscience, Tokai University, Kanagawa, Japan.
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44
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Pan Y, Piyadasa H, O'Neil JD, Konermann L. Conformational dynamics of a membrane transport protein probed by H/D exchange and covalent labeling: the glycerol facilitator. J Mol Biol 2011; 416:400-13. [PMID: 22227391 DOI: 10.1016/j.jmb.2011.12.052] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2011] [Revised: 12/21/2011] [Accepted: 12/21/2011] [Indexed: 01/22/2023]
Abstract
Glycerol facilitator (GF) is a tetrameric membrane protein responsible for the selective permeation of glycerol and water. Each of the four GF subunits forms a transmembrane channel. Every subunit consists of six helices that completely span the lipid bilayer, as well as two half-helices (TM7 and TM3). X-ray crystallography has revealed that the selectivity of GF is due to its unique amphipathic channel interior. To explore the structural dynamics of GF, we employ hydrogen/deuterium exchange (HDX) and oxidative labeling with mass spectrometry (MS). HDX-MS reveals that transmembrane helices are generally more protected than extramembrane segments, consistent with data previously obtained for other membrane proteins. Interestingly, TM7 does not follow this trend. Instead, this half-helix undergoes rapid deuteration, indicative of a highly dynamic local structure. The oxidative labeling behavior of most GF residues is consistent with the static crystal structure. However, the side chains of C134 and M237 undergo labeling although they should be inaccessible according to the X-ray structure. In agreement with our HDX-MS data, this observation attests to the fact that TM7 is only marginally stable. We propose that the highly mobile nature of TM7 aids in the efficient diffusion of guest molecules through the channel ("molecular lubrication"). In the absence of such dynamics, host-guest molecular recognition would favor semipermanent binding of molecules inside the channel, thereby impeding transport. The current work highlights the complementary nature of HDX, covalent labeling, and X-ray crystallography for the characterization of membrane proteins.
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Affiliation(s)
- Yan Pan
- Department of Chemistry, The University of Western Ontario, London, ON, Canada N6A 5B7
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45
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Shimada T, Toyama A, Aoki C, Aoki Y, Tanaka K, Sato TA. Direct antigen detection from immunoprecipitated beads using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry; a new method for immunobeads-mass spectrometry (iMS). RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2011; 25:3521-3526. [PMID: 22095500 DOI: 10.1002/rcm.5259] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
One-step detection of biological molecules is one of the principal techniques for clinical diagnosis, and the potential of mass spectrometry for biomarker detection has been a promising new approach in the field of medical sciences. We demonstrate here a new and high-sensitivity method that we termed immunobeads-mass spectrometry (iMS), which combines conventional immunoprecipitation and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The key feature of iMS is the MS-compatible condition of immunoprecipitation using detergents with a monosaccaride-C8 alkyl chain or a disaccharide-C10 alkyl chain, and the minimized number of steps required for high-sensitivity detection of target peptides in serum or biological fluid. This was achieved by optimizing the wash buffer and subjecting the immunobeads directly to MALDI-TOF MS analysis. Using this method, we showed that 1 fmol of amyloid beta peptide spiked in serum was readily detectable, demonstrating the powerful tool of iMS as a biomarker detection method.
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Affiliation(s)
- Takashi Shimada
- Life Science Research Center, Shimadzu Corporation, Kanda-Nishikicho 1, Tokyo 101-8448, Japan
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46
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Bagag A, Giuliani A, Canon F, Réfrégiers M, Le Naour F. Separation of peptides from detergents using ion mobility spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2011; 25:3436-3440. [PMID: 22002698 DOI: 10.1002/rcm.5242] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Mass spectrometry (MS) has dramatically evolved in the last two decades and has been the driving force of the spectacular expansion of proteomics during this period. However, the very poor compatibility of MS with detergents is still a technical obstacle in some studies, in particular on membrane proteins. Indeed, the high hydrophobicity of membrane proteins necessitates the use of detergents for their extraction and solubilization. Here, we address the analytical potential of high-field asymmetric waveform ion mobility spectrometry (FAIMS) for separating peptides from detergents. The study was focused on peptides from the human integral membrane protein CD9. A tryptic peptide was mixed with the non-ionic detergents Triton X-100 or beta-D-dodecyl maltoside (DDM) as well as with the ionic detergents sodium dodecyl sulfate (SDS) or sodium deoxycholate (SDC). Although electrospray ionization (ESI) alone led to a total suppression of the peptide ion signal on mass spectra with only detection of the detergents, use of FAIMS allowed separation and clear identification of the peptide with any of the detergents studied. The detection and identification of the target compound in the presence of an excess of detergents are then feasible. FAIMS should prove especially useful in the structural and proteomic analysis of membrane proteins.
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47
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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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48
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Mandal MK, Chen LC, Yu Z, Nonami H, Erra-Balsells R, Hiraoka K. Detection of protein from detergent solutions by probe electrospray ionization mass spectrometry (PESI-MS). JOURNAL OF MASS SPECTROMETRY : JMS 2011; 46:967-975. [PMID: 22012662 DOI: 10.1002/jms.1977] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Detergents are necessarily used for different extraction protocols of proteins from biological cells or tissues. After the extraction, elimination of detergent is necessary for the better performance of electrospray ionization mass spectrometry (ESI-MS). Elimination of detergents is laborious and time-consuming, and also sample loss may be unavoidable. Probe electrospray ionization (PESI) developed in our laboratory has been found to be tolerant to the presence of salts and buffers in sample solutions. In this report, it was examined whether PESI is applicable to the sample solutions that contain high-concentration of detergents. It was found that PESI is highly tolerant to the presence of sodium dodecyl sulphate, cetyl trimethylamminium bromide, Triton X100 and 3-[(3-cholamidopropyl) dimethylammonio]-1-propanesulfonate compared with conventional ESI and nanoESI. Therefore, PESI can be a potential analytical tool for direct analysis of protein extracts and digests containing high-concentration detergents.
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Affiliation(s)
- Mridul Kanti Mandal
- Clean Energy Research Center, University of Yamanashi, Kofu, Yamanashi, Japan
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49
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Clémençon B, Rey M, Trézéguet V, Forest E, Pelosi L. Yeast ADP/ATP carrier isoform 2: conformational dynamics and role of the RRRMMM signature sequence methionines. J Biol Chem 2011; 286:36119-36131. [PMID: 21868387 DOI: 10.1074/jbc.m111.277376] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The mitochondrial ADP/ATP carrier, or Ancp, is a member of the mitochondrial carrier family responsible for exchanging ADP and ATP across the mitochondrial inner membrane. ADP/ATP transport involves Ancp switching between two conformational states. These can be analyzed using specific inhibitors, carboxyatractyloside (CATR) and bongkrekic acid (BA). The high resolution three-dimensional structure of bovine Anc1p (bAnc1p), as a CATR-carrier complex, has been solved. However, because the structure of the BA-carrier complex has not yet been determined, the detailed mechanism of transport remains unknown. Recently, sample processing for hydrogen/deuterium exchange experiments coupled to mass spectrometry was improved, providing novel insights into bAnc1p conformational transitions due to inhibitor binding. In this work we performed both hydrogen/deuterium exchange-mass spectrometry experiments and genetic manipulations. Because these are very difficult to apply with bovine Anc1p, we used Saccharomyces cerevisiae Anc isoform 2 (ScAnc2p). Significant differences in solvent accessibility were observed throughout the amino acid sequence for ScAnc2p complexed to either CATR or BA. Interestingly, in detergent solution, the conformational dynamics of ScAnc2p were dissimilar to those of bAnc1p, in particular for the upper half of the cavity, toward the intermembrane space, and the m2 loop, which is thought to be easily accessible to the solvent from the matrix in bAnc1p. Our study then focused on the methionyl residues of the Ancp signature sequence, RRRMMM. All our results indicate that the methionine cluster is involved in the ADP/ATP transport mechanism and confirm that the Ancp cavity is a highly dynamic structure.
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Affiliation(s)
- Benjamin Clémençon
- Commissariat à l'Energie Atomique (CEA), Direction des Sciences du Vivant (DSV), Institut de Recherches en Technologies et Sciences pour le Vivant, Laboratoire de Biologie à Grande Echelle, Grenoble, F-38054, France; Université Joseph Fourier, Grenoble, F-38000, France; INSERM, U1038, Grenoble, F-38054, France
| | - Martial Rey
- Commissariat à l'Energie Atomique (CEA), Direction des Sciences du Vivant (DSV), Institut de Recherches en Technologies et Sciences pour le Vivant, Laboratoire de Biologie à Grande Echelle, Grenoble, F-38054, France; Université Joseph Fourier, Grenoble, F-38000, France; INSERM, U1038, Grenoble, F-38054, France
| | - Véronique Trézéguet
- Laboratoire de Physiologie Moléculaire et Cellulaire, UMR 5095 CNRS, Institut de Biochimie et Génétique Cellulaires, 1 rue Camille Saint-Saëns, F-33077 Bordeaux, France; Université Victor Segalen, Bordeaux, F-33076, France
| | - Eric Forest
- Université Joseph Fourier, Grenoble, F-38000, France; CEA, DSV, Institut de Biologie Structurale, Grenoble, F-38054, France; Laboratoire de Spectrométrie de Masse des Protéines, UMR 5075 CNRS, Grenoble, F-38027, France.
| | - Ludovic Pelosi
- Commissariat à l'Energie Atomique (CEA), Direction des Sciences du Vivant (DSV), Institut de Recherches en Technologies et Sciences pour le Vivant, Laboratoire de Biologie à Grande Echelle, Grenoble, F-38054, France; Université Joseph Fourier, Grenoble, F-38000, France.
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50
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Chalmers MJ, Busby SA, Pascal BD, West GM, Griffin PR. Differential hydrogen/deuterium exchange mass spectrometry analysis of protein-ligand interactions. Expert Rev Proteomics 2011; 8:43-59. [PMID: 21329427 DOI: 10.1586/epr.10.109] [Citation(s) in RCA: 187] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Functional regulation of ligand-activated receptors is driven by alterations in the conformational dynamics of the protein upon ligand binding. Differential hydrogen/deuterium exchange (HDX) coupled with mass spectrometry has emerged as a rapid and sensitive approach for characterization of perturbations in conformational dynamics of proteins following ligand binding. While this technique is sensitive to detecting ligand interactions and alterations in receptor dynamics, it also can provide important mechanistic insights into ligand regulation. For example, HDX has been used to determine a novel mechanism of ligand activation of the nuclear receptor peroxisome proliferator activated receptor-γ, perform detailed analyses of binding modes of ligands within the ligand-binding pocket of two estrogen receptor isoforms, providing insight into selectivity, and helped classify different types of estrogen receptor-α ligands by correlating their pharmacology with the way they interact with the receptor based solely on hierarchical clustering of receptor HDX signatures. Beyond small-molecule-receptor interactions, this technique has also been applied to study protein-protein complexes, such as mapping antibody-antigen interactions. In this article, we summarize the current state of the differential HDX approaches and the future outlook. We summarize how HDX analysis of protein-ligand interactions has had an impact on biology and drug discovery.
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Affiliation(s)
- Michael J Chalmers
- The Scripps Research Molecular Screening Center, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA
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