101
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Wohlgemuth I, Lenz C, Urlaub H. Studying macromolecular complex stoichiometries by peptide-based mass spectrometry. Proteomics 2015; 15:862-79. [PMID: 25546807 PMCID: PMC5024058 DOI: 10.1002/pmic.201400466] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 11/24/2014] [Accepted: 12/22/2014] [Indexed: 11/11/2022]
Abstract
A majority of cellular functions are carried out by macromolecular complexes. A host of biochemical and spectroscopic methods exists to characterize especially protein/protein complexes, however there has been a lack of a universal method to determine protein stoichiometries. Peptide‐based MS, especially as a complementary method to the MS analysis of intact protein complexes, has now been developed to a point where it can be employed to assay protein stoichiometries in a routine manner. While the experimental demands are still significant, peptide‐based MS has been successfully applied to analyze stoichiometries for a variety of protein complexes from very different biological backgrounds. In this review, we discuss the requirements especially for targeted MS acquisition strategies to be used in this context, with a special focus on the interconnected experimental aspects of sample preparation, protein digestion, and peptide stability. In addition, different strategies for the introduction of quantitative peptide standards and their suitability for different scenarios are compared.
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Affiliation(s)
- Ingo Wohlgemuth
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Goettingen, Germany
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102
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A subset of annular lipids is linked to the flippase activity of an ABC transporter. Nat Chem 2015; 7:255-62. [DOI: 10.1038/nchem.2172] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 12/19/2014] [Indexed: 12/18/2022]
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103
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Hopper JTS, Robinson CV. Mass spectrometry quantifies protein interactions--from molecular chaperones to membrane porins. Angew Chem Int Ed Engl 2014; 53:14002-15. [PMID: 25354304 DOI: 10.1002/anie.201403741] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Indexed: 12/16/2022]
Abstract
Proteins possess an intimate relationship between their structure and function, with folded protein structures generating recognition motifs for the binding of ligands and other proteins. Mass spectrometry (MS) can provide information on a number of levels of protein structure, from the primary amino acid sequence to its three-dimensional fold and quaternary interactions. Given that MS is a gas-phase technique, with its foundations in analytical chemistry, it is perhaps counter-intuitive to use it to study the structure and non-covalent interactions of proteins that form in solution. Herein we show, however, that MS can go beyond simply preserving protein interactions in the gas phase by providing new insight into dynamic interaction networks, dissociation mechanisms, and the cooperativity of ligand binding. We consider potential pitfalls in data interpretation and place particular emphasis on recent studies that revealed quantitative information about dynamic protein interactions, in both soluble and membrane-embedded assemblies.
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Affiliation(s)
- Jonathan T S Hopper
- Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ (UK)
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104
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Hopper JTS, Robinson CV. Massenspektrometrie zur Quantifizierung von Wechselwirkungen zwischen Proteinen - von molekularen Chaperonen zu Membranporinen. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201403741] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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105
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Boeri Erba E. Investigating macromolecular complexes using top-down mass spectrometry. Proteomics 2014; 14:1259-70. [PMID: 24723549 DOI: 10.1002/pmic.201300333] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 04/03/2014] [Accepted: 04/08/2014] [Indexed: 12/25/2022]
Abstract
MS has emerged as an important tool to investigate noncovalent interactions between proteins and various ligands (e.g. other proteins, small molecules, or drugs). In particular, ESI under so-called "native conditions" (a.k.a. "native MS") has considerably expanded the scope of such investigations. For instance, ESI quadrupole time of flight (Q-TOF) instruments have been used to probe the precise stoichiometry of protein assemblies, the interactions between subunits and the position of subunits within the complex (i.e. defining core and peripheral subunits). This review highlights several illustrative native Q-TOF-based investigations and recent seminal contributions of top-down MS (i.e. Fourier transform (FT) MS) to the characterization of noncovalent complexes. Combined top-down and native MS, recently demonstrated in "high-mass modified" orbitrap mass spectrometers, and further improvements needed for the enhanced investigation of biologically significant noncovalent interactions by MS will be discussed.
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Affiliation(s)
- Elisabetta Boeri Erba
- Institute of Structural Biology (Institut de Biologie Structurale), Centre National de la Recherche Scientifique (CNRS), University of Grenoble Alpes (Université de Grenoble Alpes), Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), DSV, Grenoble, France
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106
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Twenty years of gas phase structural biology. Structure 2014; 21:1541-50. [PMID: 24010713 DOI: 10.1016/j.str.2013.08.002] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Revised: 08/06/2013] [Accepted: 08/06/2013] [Indexed: 01/01/2023]
Abstract
Over the past two decades, mass spectrometry (MS) of protein complexes from their native state has made inroads into structural biology. To coincide with the 20(th) anniversary of Structure, and given that it is now approximately 20 years since the first mass spectra of noncovalent protein complexes were reported, it is timely to consider progress of MS as a structural biology tool. Early reports focused on soluble complexes, contributing to ligand binding studies, subunit interaction maps, and topological models. Recent discoveries have enabled delivery of membrane complexes, encapsulated in detergent micelles, prompting new opportunities. By maintaining interactions between membrane and cytoplasmic subunits in the gas phase, it is now possible to investigate the effects of lipids, nucleotides, and drugs on intact membrane assemblies. These investigations reveal allosteric and synergistic effects of small molecule binding and expose the consequences of posttranslational modifications. In this review, we consider recent progress in the study of protein complexes, focusing particularly on complexes extracted from membranes, and outline future prospects for gas phase structural biology.
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107
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Marty MT, Zhang H, Cui W, Gross ML, Sligar SG. Interpretation and deconvolution of nanodisc native mass spectra. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:269-77. [PMID: 24353133 PMCID: PMC3918181 DOI: 10.1007/s13361-013-0782-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 10/27/2013] [Accepted: 11/08/2013] [Indexed: 05/11/2023]
Abstract
Nanodiscs are a promising system for studying gas-phase and solution complexes of membrane proteins and lipids. We previously demonstrated that native electrospray ionization allows mass spectral analysis of intact Nanodisc complexes at single lipid resolution. This report details an improved theoretical framework for interpreting and deconvoluting native mass spectra of Nanodisc lipoprotein complexes. In addition to the intrinsic lipid count and charge distributions, Nanodisc mass spectra are significantly shaped by constructive overlap of adjacent charge states at integer multiples of the lipid mass. We describe the mathematical basis for this effect and develop a probability-based algorithm to deconvolute the underlying mass and charge distributions. The probability-based deconvolution algorithm is applied to a series of dimyristoylphosphatidylcholine Nanodisc native mass spectra and used to provide a quantitative picture of the lipid loss in gas-phase fragmentation.
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Affiliation(s)
- Michael T. Marty
- University of Illinois Urbana-Champaign, Department of Chemistry, Urbana, IL 61801
| | - Hao Zhang
- Washington University in St. Louis, Department of Chemistry, St. Louis, MO 63130
- Washington University in St. Louis, Photosynthetic Antenna Research Center (PARC), St. Louis, MO 63130
| | - Weidong Cui
- Washington University in St. Louis, Department of Chemistry, St. Louis, MO 63130
| | - Michael L. Gross
- Washington University in St. Louis, Department of Chemistry, St. Louis, MO 63130
| | - Stephen G. Sligar
- University of Illinois Urbana-Champaign, Department of Chemistry, Urbana, IL 61801
- University of Illinois Urbana-Champaign, Department of Biochemistry, Urbana, IL 61801
- Address reprint requests to: Stephen G. Sligar, 116 Morrill Hall, 505 S. Goodwin MC-119, Urbana, IL 61801, , Phone: 217-244-7395, Fax: 217-265-4073
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108
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Schmidt C, Robinson CV. Dynamic protein ligand interactions--insights from MS. FEBS J 2014; 281:1950-64. [PMID: 24393119 PMCID: PMC4154455 DOI: 10.1111/febs.12707] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 12/19/2013] [Accepted: 12/30/2013] [Indexed: 12/31/2022]
Abstract
Proteins undergo dynamic interactions with carbohydrates, lipids and nucleotides to form catalytic cores, fine‐tuned for different cellular actions. The study of dynamic interactions between proteins and their cognate ligands is therefore fundamental to the understanding of biological systems. During the last two decades MS, and its associated techniques, has become accepted as a method for the study of protein–ligand interactions, not only for covalent complexes, where the use of MS is well established, but also, and significantly for protein–ligand interactions, for noncovalent assemblies. In this review, we employ a broad definition of a ligand to encompass protein subunits, drug molecules, oligonucleotides, carbohydrates, and lipids. Under the appropriate conditions, MS can reveal the composition, heterogeneity and dynamics of these protein–ligand interactions, and in some cases their structural arrangements and binding affinities. Herein, we highlight MS approaches for studying protein–ligand complexes, including those containing integral membrane subunits, and showcase examples from recent literature. Specifically, we tabulate the myriad of methodologies, including hydrogen exchange, proteomics, hydroxyl radical footprinting, intact complexes, and crosslinking, which, when combined with MS, provide insights into conformational changes and subtle modifications in response to ligand‐binding interactions.
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109
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Snijder J, Heck AJR. Analytical approaches for size and mass analysis of large protein assemblies. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2014; 7:43-64. [PMID: 25014341 DOI: 10.1146/annurev-anchem-071213-020015] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Analysis of the size and mass of nanoparticles, whether they are natural biomacromolecular or synthetic supramolecular assemblies, is an important step in the characterization of such molecular species. In recent years, electrospray ionization (ESI) has emerged as a technology through which particles with masses up to 100 MDa can be ionized and transferred into the gas phase, preparing them for accurate mass analysis. Here we review currently used methodologies, with a clear focus on native mass spectrometry (MS). Additional complementary methodologies are also covered, including ion-mobility analysis, nanomechanical mass sensors, and charge-detection MS. The literature discussed clearly demonstrates the great potential of ESI-based methodologies for the size and mass analysis of nanoparticles, including very large naturally occurring protein assemblies. The analytical approaches discussed are powerful tools in not only structural biology, but also nanotechnology.
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Affiliation(s)
- Joost Snijder
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CH Utrecht, the Netherlands; ,
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110
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Peng WP, Chou SW, Patil AA. Measuring masses of large biomolecules and bioparticles using mass spectrometric techniques. Analyst 2014; 139:3507-23. [DOI: 10.1039/c3an02329j] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Mass spectrometric techniques can measure the masses and fragments of large biomolecules and bioparticles.
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Affiliation(s)
- Wen-Ping Peng
- Department of Physics
- National Dong Hwa University
- Hualien, Republic of China
| | - Szu-Wei Chou
- Department of Physics
- National Dong Hwa University
- Hualien, Republic of China
| | - Avinash A. Patil
- Department of Physics
- National Dong Hwa University
- Hualien, Republic of China
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111
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Hopper JT, Yu YTC, Li D, Raymond A, Bostock M, Liko I, Mikhailov V, Laganowsky A, Benesch JL, Caffrey M, Nietlispach D, Robinson CV. Detergent-free mass spectrometry of membrane protein complexes. Nat Methods 2013; 10:1206-8. [PMID: 24122040 PMCID: PMC3868940 DOI: 10.1038/nmeth.2691] [Citation(s) in RCA: 127] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 08/29/2013] [Indexed: 02/02/2023]
Abstract
We developed a method that allows release of intact membrane protein complexes from amphipols, bicelles and nanodiscs in the gas phase for observation by mass spectrometry (MS). Current methods involve release of membrane protein complexes from detergent micelles, which reveals subunit composition and lipid binding. We demonstrated that oligomeric complexes or proteins requiring defined lipid environments are stabilized to a greater extent in the absence of detergent.
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Affiliation(s)
- Jonathan T.S. Hopper
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ
| | - Yvonne Ting-Chun Yu
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA
| | - Dianfan Li
- School of Medicine Trinity College Dublin, Dublin, Ireland
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
| | - Alison Raymond
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ
| | - Mark Bostock
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA
| | - Idlir Liko
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ
| | - Victor Mikhailov
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ
| | - Arthur Laganowsky
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ
| | - Justin L.P. Benesch
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ
| | - Martin Caffrey
- School of Medicine Trinity College Dublin, Dublin, Ireland
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
| | - Daniel Nietlispach
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA
| | - Carol V. Robinson
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ
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112
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Tseng YH, Uetrecht C, Yang SC, Barendregt A, Heck AJR, Peng WP. Game-Theory-Based Search Engine to Automate the Mass Assignment in Complex Native Electrospray Mass Spectra. Anal Chem 2013; 85:11275-83. [DOI: 10.1021/ac401940e] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Yao-Hsin Tseng
- Department
of Physics, National Dong Hwa University, Shoufeng, Hualien, Taiwan 97401, R.O.C
| | - Charlotte Uetrecht
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, and Netherlands Proteomics Centre, Padualaan
8, 3584 CH Utrecht, The Netherlands
- Sample
Environment Group, European XFEL GmbH, Notkestraße 85, 22607 Hamburg, Germany
| | - Shih-Chieh Yang
- Department
of Physics, National Dong Hwa University, Shoufeng, Hualien, Taiwan 97401, R.O.C
| | - Arjan Barendregt
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, and Netherlands Proteomics Centre, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Albert J. R. Heck
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, and Netherlands Proteomics Centre, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Wen-Ping Peng
- Department
of Physics, National Dong Hwa University, Shoufeng, Hualien, Taiwan 97401, R.O.C
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113
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Behrens C, Binotti B, Schmidt C, Robinson CV, Chua JJE, Kühnel K. Crystal structure of the human short coiled coil protein and insights into SCOC-FEZ1 complex formation. PLoS One 2013; 8:e76355. [PMID: 24098481 PMCID: PMC3788124 DOI: 10.1371/journal.pone.0076355] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 08/23/2013] [Indexed: 01/18/2023] Open
Abstract
The short coiled coil protein (SCOC) forms a complex with fasciculation and elongation protein zeta 1 (FEZ1). This complex is involved in autophagy regulation. We determined the crystal structure of the coiled coil domain of human SCOC at 2.7 Å resolution. SCOC forms a parallel left handed coiled coil dimer. We observed two distinct dimers in the crystal structure, which shows that SCOC is conformationally flexible. This plasticity is due to the high incidence of polar and charged residues at the core a/d-heptad positions. We prepared two double mutants, where these core residues were mutated to either leucines or valines (E93V/K97L and N125L/N132V). These mutations led to a dramatic increase in stability and change of oligomerisation state. The oligomerisation state of the mutants was characterized by multi-angle laser light scattering and native mass spectrometry measurements. The E93V/K97 mutant forms a trimer and the N125L/N132V mutant is a tetramer. We further demonstrate that SCOC forms a stable homogeneous complex with the coiled coil domain of FEZ1. SCOC dimerization and the SCOC surface residue R117 are important for this interaction.
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Affiliation(s)
- Caroline Behrens
- Department of Neurobiology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Beyenech Binotti
- Department of Neurobiology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Carla Schmidt
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, United Kingdom
| | - Carol V. Robinson
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, United Kingdom
| | - John Jia En Chua
- Department of Neurobiology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Karin Kühnel
- Department of Neurobiology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
- * E-mail:
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114
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Sivalingam GN, Yan J, Sahota H, Thalassinos K. Amphitrite: A program for processing travelling wave ion mobility mass spectrometry data. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2013; 345-347:54-62. [PMID: 25844045 PMCID: PMC4375678 DOI: 10.1016/j.ijms.2012.09.005] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2012] [Revised: 09/04/2012] [Accepted: 09/13/2012] [Indexed: 05/11/2023]
Abstract
Since the introduction of travelling wave (T-Wave)-based ion mobility in 2007 a large number of research laboratories have embraced the technique, particularly those working in the field of structural biology. The development of software to process the data generated from this technique, however, has been limited. We present a novel software package that enables the processing of T-Wave ion mobility data. The program can deconvolute components in a mass spectrum and uses this information to extract corresponding arrival time distributions (ATDs) with minimal user intervention. It can also be used to automatically create a collision cross section (CCS) calibration and apply this to subsequent files of interest. A number of applications of the software, and how it enhances the information content extracted from the raw data, are illustrated using model proteins.
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Affiliation(s)
- Ganesh N. Sivalingam
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK
| | - Jun Yan
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK
| | - Harpal Sahota
- Institute of Structural and Molecular Biology, Crystallography, Birkbeck College, London, UK
| | - Konstantinos Thalassinos
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK
- Corresponding author. Tel.: +44 20 7679 2197; fax: +44 20 7679 7193.
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115
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Marcoux J, Wang SC, Politis A, Reading E, Ma J, Biggin PC, Zhou M, Tao H, Zhang Q, Chang G, Morgner N, Robinson CV. Mass spectrometry reveals synergistic effects of nucleotides, lipids, and drugs binding to a multidrug resistance efflux pump. Proc Natl Acad Sci U S A 2013; 110:9704-9. [PMID: 23690617 PMCID: PMC3683783 DOI: 10.1073/pnas.1303888110] [Citation(s) in RCA: 141] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Multidrug resistance is a serious barrier to successful treatment of many human diseases, including cancer, wherein chemotherapeutics are exported from target cells by membrane-embedded pumps. The most prevalent of these pumps, the ATP-Binding Cassette transporter P-glycoprotein (P-gp), consists of two homologous halves each comprising one nucleotide-binding domain and six transmembrane helices. The transmembrane region encapsulates a hydrophobic cavity, accessed by portals in the membrane, that binds cytotoxic compounds as well as lipids and peptides. Here we use mass spectrometry (MS) to probe the intact P-gp small molecule-bound complex in a detergent micelle. Activation in the gas phase leads to formation of ions, largely devoid of detergent, yet retaining drug molecules as well as charged or zwitterionic lipids. Measuring the rates of lipid binding and calculating apparent KD values shows that up to six negatively charged diacylglycerides bind more favorably than zwitterionic lipids. Similar experiments confirm binding of cardiolipins and show that prior binding of the immunosuppressant and antifungal antibiotic cyclosporin A enhances subsequent binding of cardiolipin. Ion mobility MS reveals that P-gp exists in an equilibrium between different states, readily interconverted by ligand binding. Overall these MS results show how concerted small molecule binding leads to synergistic effects on binding affinities and conformations of a multidrug efflux pump.
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Affiliation(s)
| | | | | | | | - Jerome Ma
- Biochemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom
| | - Philip C. Biggin
- Biochemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom
| | | | - Houchao Tao
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037; and
| | - Qinghai Zhang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037; and
| | - Geoffrey Chang
- Skaggs School of Pharmacy and Pharmaceutical Sciences and Department of Pharmacology, School of Medicine, University of California at San Diego, La Jolla, CA 92093
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116
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Schmidt C, Zhou M, Marriott H, Morgner N, Politis A, Robinson CV. Comparative cross-linking and mass spectrometry of an intact F-type ATPase suggest a role for phosphorylation. Nat Commun 2013; 4:1985. [PMID: 23756419 PMCID: PMC3709506 DOI: 10.1038/ncomms2985] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 05/07/2013] [Indexed: 11/13/2022] Open
Abstract
F-type ATPases are highly conserved enzymes used primarily for the synthesis of ATP. Here we apply mass spectrometry to the F1FO-ATPase, isolated from spinach chloroplasts, and uncover multiple modifications in soluble and membrane subunits. Mass spectra of the intact ATPase define a stable lipid 'plug' in the FO complex and reveal the stoichiometry of nucleotide binding in the F1 head. Comparing complexes formed in solution from an untreated ATPase with one incubated with a phosphatase reveals that the dephosphorylated enzyme has reduced nucleotide occupancy and decreased stability. By contrasting chemical cross-linking of untreated and dephosphorylated forms we show that cross-links are retained between the head and base, but are significantly reduced in the head, stators and stalk. Conformational changes at the catalytic interface, evidenced by changes in cross-linking, provide a rationale for reduced nucleotide occupancy and highlight a role for phosphorylation in regulating nucleotide binding and stability of the chloroplast ATPase.
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Affiliation(s)
- Carla Schmidt
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, UK
| | - Min Zhou
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, UK
| | - Hazel Marriott
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, UK
| | - Nina Morgner
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, UK
| | - Argyris Politis
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, UK
| | - Carol V. Robinson
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, UK
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117
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Konijnenberg A, Butterer A, Sobott F. Native ion mobility-mass spectrometry and related methods in structural biology. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1834:1239-56. [PMID: 23246828 DOI: 10.1016/j.bbapap.2012.11.013] [Citation(s) in RCA: 186] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2012] [Revised: 11/19/2012] [Accepted: 11/29/2012] [Indexed: 12/12/2022]
Abstract
Mass spectrometry-based methods have become increasingly important in structural biology - in particular for large and dynamic, even heterogeneous assemblies of biomolecules. Native electrospray ionization coupled to ion mobility-mass spectrometry provides access to stoichiometry, size and architecture of noncovalent assemblies; while non-native approaches such as covalent labeling and H/D exchange can highlight dynamic details of protein structures and capture intermediate states. In this overview article we will describe these methods and highlight some recent applications for proteins and protein complexes, with particular emphasis on native MS analysis. This article is part of a Special Issue entitled: Mass spectrometry in structural biology.
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118
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Morgner N, Montenegro F, Barrera NP, Robinson CV. Mass spectrometry--from peripheral proteins to membrane motors. J Mol Biol 2012; 423:1-13. [PMID: 22750574 PMCID: PMC4058634 DOI: 10.1016/j.jmb.2012.06.033] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Revised: 06/18/2012] [Accepted: 06/20/2012] [Indexed: 10/28/2022]
Abstract
That membrane protein complexes could survive in the gas phase had always seemed impossible. The lack of chargeable residues, high hydrophobicity, and poor solubility and the vast excess of detergent contributed to the view that it would not be possible to obtain mass spectra of intact membrane complexes. With the recent success in recording mass spectra of these complexes, first from recombinant sources and later from the cellular environment, many surprising properties of these gas phase membrane complexes have been revealed. The first of these was that the interactions between membrane and soluble subunits could survive in vacuum, without detergent molecules adhering to the complex. The second unexpected feature was that their hydrophobicity and, consequently, lower charge state did not preclude ionization. The final surprising finding was that these gas phase membrane complexes carry with them lipids, bound specifically in subunit interfaces. This provides us with an opportunity to distinguish annular lipids that surround the membrane complexes, from structural lipids that have a role in maintaining structure and subunit interactions. In this perspective, we track these developments and suggest explanations for the various discoveries made during this research.
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Affiliation(s)
- Nina Morgner
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 5QY, UK
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119
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Chen H, Lee J, Reilly PTA. High-resolution ultra-high mass spectrometry: increasing the m/z range of protein analysis. Proteomics 2012; 12:3020-9. [PMID: 22930644 DOI: 10.1002/pmic.201270136] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Revised: 07/19/2012] [Accepted: 08/08/2012] [Indexed: 11/06/2022]
Abstract
The proof of principle for high-resolution TOF mass analysis spanning the entire range of intact singly charged proteins has recently been demonstrated. The centers of the isotope distributions of individual proteins in a complex distribution can be defined to within 0.5 Da or better up to 200 kDa with internal calibration. This achievement will have an enormous effect on the process of routine protein analysis over the next few years as the technology mainstreams. The greatest obstacle to high-resolution in the ultra-high mass range (m/z > 20 000) is the expansion-induced kinetic energy (KE) and its spread. The solution to this problem is to trap the ions in a buffer gas so that the motion of the ions can be completely defined by the applied fields. If this can accomplished without mass dependence, then any ion, regardless of size, can be mass analyzed with high resolution. This article discusses the methodology that we used to capture atmosphere sampled singly charged proteins in vacuum at a point just before they enter the mass analyzer to completely eliminate the expansion-induced KE. We then used digitally created quadrupole waveforms to inject the ions into the mass analyzer in a well-collimated plug with a controlled amount of KE. Trapping the ions to remove the expansion-induced KE and then electrodynamically manipulating the ions are the key steps to high-resolution mass analysis at any value of m/z. The impact of this technology will be discussed.
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Affiliation(s)
- Huijuan Chen
- Department of Chemistry, Washington State University, Pullman, WA 99164, USA
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120
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Stengel F, Baldwin AJ, Bush MF, Hilton GR, Lioe H, Basha E, Jaya N, Vierling E, Benesch JL. Dissecting heterogeneous molecular chaperone complexes using a mass spectrum deconvolution approach. CHEMISTRY & BIOLOGY 2012; 19:599-607. [PMID: 22633411 PMCID: PMC3458707 DOI: 10.1016/j.chembiol.2012.04.007] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Revised: 04/02/2012] [Accepted: 04/06/2012] [Indexed: 11/30/2022]
Abstract
Small heat-shock proteins (sHSPs) are molecular chaperones that prevent irreversible aggregation through binding nonnative target proteins. Due to their heterogeneity, these sHSP:target complexes remain poorly understood. We present a nanoelectrospray mass spectrometry analysis algorithm for estimating the distribution of stoichiometries comprising a polydisperse ensemble of oligomers. We thus elucidate the organization of complexes formed between sHSPs and different target proteins. We find that binding is mass dependent, with the resultant complexes reflecting the native quaternary architecture of the target, indicating that protection happens early in the denaturation. Our data therefore explain the apparent paradox of how variable complex morphologies result from the generic mechanism of protection afforded by sHSPs. Our approach is applicable to a range of polydisperse proteins and provides a means for the automated and accurate interpretation of mass spectra derived from heterogeneous protein assemblies.
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Affiliation(s)
- Florian Stengel
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Andrew J. Baldwin
- Departments of Molecular Genetics, Biochemistry, and Chemistry, University of Toronto, Toronto, ON, Canada
| | - Matthew F. Bush
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Gillian R. Hilton
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Hadi Lioe
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Eman Basha
- Botany Department, Faculty of Science, Tanta University, Tanta, Egypt
- Department of Biochemistry & Molecular Biophysics, University of Arizona, Tucson, AZ, USA
| | - Nomalie Jaya
- Department of Biochemistry & Molecular Biophysics, University of Arizona, Tucson, AZ, USA
| | - Elizabeth Vierling
- Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, MA, USA
| | - Justin L.P. Benesch
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
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