101
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Hanozin E, Morsa D, De Pauw E. Energetics and structural characterization of isomers using ion mobility and gas-phase H/D exchange: Learning from lasso peptides. Proteomics 2015; 15:2823-34. [DOI: 10.1002/pmic.201400534] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Revised: 03/03/2015] [Accepted: 03/17/2015] [Indexed: 12/29/2022]
Affiliation(s)
- Emeline Hanozin
- Mass Spectrometry Laboratory, Department of Chemistry; University of Liege; Liege Belgium
| | - Denis Morsa
- Mass Spectrometry Laboratory, Department of Chemistry; University of Liege; Liege Belgium
| | - Edwin De Pauw
- Mass Spectrometry Laboratory, Department of Chemistry; University of Liege; Liege Belgium
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102
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Pacholarz KJ, Barran PE. Distinguishing Loss of Structure from Subunit Dissociation for Protein Complexes with Variable Temperature Ion Mobility Mass Spectrometry. Anal Chem 2015; 87:6271-9. [DOI: 10.1021/acs.analchem.5b01063] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Kamila J. Pacholarz
- University of Edinburgh, School of Chemistry, West Mains Road, Edinburgh EH9 3JJ, United Kingdom
- University of Manchester, School of Chemistry, Manchester
Institute of Biotechnology, Michael Barber Centre for Collaborative
Mass Spectrometry, 131
Princess Street, Manchester M1 7DN, United Kingdom
| | - Perdita E. Barran
- University of Manchester, School of Chemistry, Manchester
Institute of Biotechnology, Michael Barber Centre for Collaborative
Mass Spectrometry, 131
Princess Street, Manchester M1 7DN, United Kingdom
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103
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Marty MT, Baldwin AJ, Marklund EG, Hochberg GKA, Benesch JLP, Robinson CV. Bayesian deconvolution of mass and ion mobility spectra: from binary interactions to polydisperse ensembles. Anal Chem 2015; 87:4370-6. [PMID: 25799115 PMCID: PMC4594776 DOI: 10.1021/acs.analchem.5b00140] [Citation(s) in RCA: 570] [Impact Index Per Article: 63.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Interpretation of mass spectra is challenging because they report a ratio of two physical quantities, mass and charge, which may each have multiple components that overlap in m/z. Previous approaches to disentangling the two have focused on peak assignment or fitting. However, the former struggle with complex spectra, and the latter are generally computationally intensive and may require substantial manual intervention. We propose a new data analysis approach that employs a Bayesian framework to separate the mass and charge dimensions. On the basis of this approach, we developed UniDec (Universal Deconvolution), software that provides a rapid, robust, and flexible deconvolution of mass spectra and ion mobility-mass spectra with minimal user intervention. Incorporation of the charge-state distribution in the Bayesian prior probabilities provides separation of the m/z spectrum into its physical mass and charge components. We have evaluated our approach using systems of increasing complexity, enabling us to deduce lipid binding to membrane proteins, to probe the dynamics of subunit exchange reactions, and to characterize polydispersity in both protein assemblies and lipoprotein Nanodiscs. The general utility of our approach will greatly facilitate analysis of ion mobility and mass spectra.
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Affiliation(s)
- Michael T. Marty
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, U.K
| | - Andrew J. Baldwin
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, U.K
| | - Erik G. Marklund
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, U.K
| | - Georg K. A. Hochberg
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, U.K
| | - Justin L. P. Benesch
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, U.K
| | - Carol V. Robinson
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, U.K
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104
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Chen F, Gerber S, Korkhov VM, Mireku S, Bucher M, Locher KP, Zenobi R. On the efficiency of NHS ester cross-linkers for stabilizing integral membrane protein complexes. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:493-498. [PMID: 25404159 DOI: 10.1007/s13361-014-1035-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 10/20/2014] [Accepted: 10/21/2014] [Indexed: 06/04/2023]
Abstract
We have previously presented a straightforward approach based on high-mass matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) to study membrane proteins. In addition, the stoichiometry of integral membrane protein complexes could be determined by MALDI-MS, following chemical cross-linking via glutaraldehyde. However, glutaraldehyde polymerizes in solution and reacts nonspecifically with various functional groups of proteins, limiting its usefulness for structural studies of protein complexes. Here, we investigated the capability of N-hydroxysuccinimide (NHS) esters, which react much more specifically, to cross-link membrane protein complexes such as PglK and BtuC(2)D(2). We present clear evidence that NHS esters are capable of stabilizing membrane protein complexes in situ, in the presence of detergents such as DDM, C12E8, and LDAO. The stabilization efficiency strongly depends on the membrane protein structure (i.e, the number of primary amine groups and the distances between primary amines). A minimum number of primary amine groups is required, and the distances between primary amines govern whether a cross-linker with a specific spacer arm length is able to bridge two amine groups.
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Affiliation(s)
- Fan Chen
- Department of Chemistry and Applied Biosciences, ETH Zürich, 8093, Zürich, Switzerland
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105
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Reading E, Liko I, Allison TM, Benesch JLP, Laganowsky A, Robinson CV. The Role of the Detergent Micelle in Preserving the Structure of Membrane Proteins in the Gas Phase. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201411622] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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106
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Reading E, Liko I, Allison TM, Benesch JLP, Laganowsky A, Robinson CV. The role of the detergent micelle in preserving the structure of membrane proteins in the gas phase. Angew Chem Int Ed Engl 2015; 54:4577-81. [PMID: 25693501 DOI: 10.1002/anie.201411622] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Indexed: 11/12/2022]
Abstract
Despite the growing importance of the mass spectrometry of membrane proteins, it is not known how their transfer from solution into vacuum affects their stability and structure. To address this we have carried out a systematic investigation of ten membrane proteins solubilized in different detergents and used mass spectrometry to gain physicochemical insight into the mechanism of their ionization and desolvation. We show that the chemical properties of the detergents mediate the charge state, both during ionization and detergent removal. Using ion mobility mass spectrometry, we monitor the conformations of membrane proteins and show how the surface charge density dictates the stability of folded states. We conclude that the gas-phase stability of membrane proteins is increased when a greater proportion of their surface is lipophilic and is consequently protected by the physical presence of the micelle.
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Affiliation(s)
- Eamonn Reading
- Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, OX1 3QZ (UK)
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107
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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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108
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The Sum Is More Than The Parts: Crystal And Solution Data Reveal That The PIDDosome Core Complex Is a Dynamic Assembly. J Mol Biol 2015; 427:715-717. [DOI: 10.1016/j.jmb.2014.12.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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109
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Kondrat FDL, Struwe WB, Benesch JLP. Native mass spectrometry: towards high-throughput structural proteomics. Methods Mol Biol 2015; 1261:349-371. [PMID: 25502208 DOI: 10.1007/978-1-4939-2230-7_18] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Native mass spectrometry (MS) has become a sensitive method for structural proteomics, allowing practitioners to gain insight into protein self-assembly, including stoichiometry and three-dimensional architecture, as well as complementary thermodynamic and kinetic aspects. Although MS is typically performed in vacuum, a body of literature has described how native solution-state structure is largely retained on the timescale of the experiment. Native MS offers the benefit that it requires substantially smaller quantities of a sample than traditional structural techniques such as NMR and X-ray crystallography, and is therefore well suited to high-throughput studies. Here we first describe the native MS approach and outline the structural proteomic data that it can deliver. We then provide practical details of experiments to examine the structural and dynamic properties of protein assemblies, highlighting potential pitfalls as well as principles of best practice.
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Affiliation(s)
- Frances D L Kondrat
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK
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110
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Remmele RL, Bee JS, Phillips JJ, Mo WD, Higazi DR, Zhang J, Lindo V, Kippen AD. Characterization of Monoclonal Antibody Aggregates and Emerging Technologies. ACS SYMPOSIUM SERIES 2015. [DOI: 10.1021/bk-2015-1202.ch005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Richard L. Remmele
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune One MedImmune Way, Gaithersburg, Maryland 20878, United States
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune Granta Park, Cambridge CB21 6GH, United Kingdom
| | - Jared S. Bee
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune One MedImmune Way, Gaithersburg, Maryland 20878, United States
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune Granta Park, Cambridge CB21 6GH, United Kingdom
| | - Jonathan J. Phillips
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune One MedImmune Way, Gaithersburg, Maryland 20878, United States
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune Granta Park, Cambridge CB21 6GH, United Kingdom
| | - Wenjun David Mo
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune One MedImmune Way, Gaithersburg, Maryland 20878, United States
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune Granta Park, Cambridge CB21 6GH, United Kingdom
| | - Daniel R. Higazi
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune One MedImmune Way, Gaithersburg, Maryland 20878, United States
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune Granta Park, Cambridge CB21 6GH, United Kingdom
| | - Jifeng Zhang
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune One MedImmune Way, Gaithersburg, Maryland 20878, United States
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune Granta Park, Cambridge CB21 6GH, United Kingdom
| | - Vivian Lindo
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune One MedImmune Way, Gaithersburg, Maryland 20878, United States
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune Granta Park, Cambridge CB21 6GH, United Kingdom
| | - Alistair D. Kippen
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune One MedImmune Way, Gaithersburg, Maryland 20878, United States
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune Granta Park, Cambridge CB21 6GH, United Kingdom
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111
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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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112
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Landreh M, Robinson CV. A new window into the molecular physiology of membrane proteins. J Physiol 2014; 593:355-62. [PMID: 25630257 PMCID: PMC4303381 DOI: 10.1113/jphysiol.2014.283150] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 10/14/2014] [Indexed: 12/18/2022] Open
Abstract
Integral membrane proteins comprise ∼25% of the human proteome. Yet, our understanding of their molecular physiology is still in its infancy. This can be attributed to two factors: the experimental challenges that arise from the difficult chemical nature of membrane proteins, and the unclear relationship between their activity and their native environment. New approaches are therefore required to address these challenges. Recent developments in mass spectrometry have shown that it is possible to study membrane proteins in a solvent-free environment and provide detailed insights into complex interactions, ligand binding and folding processes. Interestingly, not only detergent micelles but also lipid bilayer nanodiscs or bicelles can serve as a means for the gentle desolvation of membrane proteins in the gas phase. In this manner, as well as by direct addition of lipids, it is possible to study the effects of different membrane components on the structure and function of the protein components allowing us to add functional data to the least accessible part of the proteome.
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Affiliation(s)
- Michael Landreh
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 5QY, UK
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113
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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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114
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O'Brien JP, Li W, Zhang Y, Brodbelt JS. Characterization of native protein complexes using ultraviolet photodissociation mass spectrometry. J Am Chem Soc 2014; 136:12920-8. [PMID: 25148649 DOI: 10.1021/ja505217w] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Ultraviolet photodissociation (UVPD) mass spectrometry (MS) was used to characterize the sequences of proteins in native protein-ligand and protein-protein complexes and to provide auxiliary information about the binding sites of the ligands and protein-protein interfaces. UVPD outperformed collisional induced dissociation (CID), higher-energy collisional dissociation (HCD), and electron transfer dissociation (ETD) in terms of yielding the most comprehensive diagnostic primary sequence information about the proteins in the complexes. UVPD also generated noncovalent fragment ions containing a portion of the protein still bound to the ligand which revealed some insight into the nature of the binding sites of myoglobin/heme, eIF4E/m(7)GTP, and human peptidyl-prolyl cis-trans isomerase 1 (Pin1) in complex with the peptide derived from the C-terminal domain of RNA polymerase II (CTD). Noncovalently bound protein-protein fragment ions from oligomeric β-lactoglobulin dimers and hexameric insulin complexes were also produced upon UVPD, providing some illumination of tertiary and quaternary protein structural features.
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Affiliation(s)
- John P O'Brien
- Department of Chemistry, ‡Department of Molecular Biosciences, and §Institute for Cellular and Molecular Biology, The University of Texas at Austin , 105 East 24th Street Stop A5300, Austin, Texas 78712, United States
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115
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Rathore D, Dodds ED. Collision-induced release, ion mobility separation, and amino acid sequence analysis of subunits from mass-selected noncovalent protein complexes. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:1600-1609. [PMID: 25001382 DOI: 10.1007/s13361-014-0946-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 06/02/2014] [Accepted: 06/04/2014] [Indexed: 06/03/2023]
Abstract
In recent years, mass spectrometry has become a valuable tool for detecting and characterizing protein-protein interactions and for measuring the masses and subunit stoichiometries of noncovalent protein complexes. The gas-phase dissociation of noncovalent protein assemblies via tandem mass spectrometry can be useful in confirming subunit masses and stoichiometries; however, dissociation experiments that are able to yield subunit sequence information must usually be conducted separately. Here, we furnish proof of concept for a method that allows subunit sequence information to be directly obtained from a protein aggregate in a single gas-phase analysis. The experiments were carried out using a quadrupole time-of-flight mass spectrometer equipped with a traveling-wave ion mobility separator. This instrument configuration allows for a noncovalent protein assembly to be quadrupole selected, then subjected to two successive rounds of collision-induced dissociation with an intervening stage of ion mobility separation. This approach was applied to four model proteins as their corresponding homodimers: glucagon, ubiquitin, cytochrome c, and β-lactoglobulin. In each case, b- and y-type fragment ions were obtained upon further collisional activation of the collisionally-released subunits, resulting in up to 50% sequence coverage. Owing to the incorporation of an ion mobility separation, these results also suggest the intriguing possibility of measuring complex mass, complex collisional cross section, subunit masses, subunit collisional cross sections, and sequence information for the subunits in a single gas-phase experiment. Overall, these findings represent a significant contribution towards the realization of protein interactomic analyses, which begin with native complexes and directly yield subunit identities.
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Affiliation(s)
- Deepali Rathore
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588-0304, USA
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116
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Mikhailov VA, Mize TH, Benesch JLP, Robinson CV. Mass-selective soft-landing of protein assemblies with controlled landing energies. Anal Chem 2014; 86:8321-8. [PMID: 25026391 DOI: 10.1021/ac5018327] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Selection and soft-landing of bionanoparticles in vacuum is potentially a preparative approach to separate heterogeneous mixtures for high-resolution structural study or to deposit homogeneous materials for nanotechnological applications. Soft-landing of intact protein assemblies however remains challenging, due to the difficulties of manipulating these heavy species in mass-selective devices and retaining their structure during the experiment. We have developed a tandem mass spectrometer with the capability for controlled ion soft-landing and ex situ visualization of the soft-landed particles by means of transmission electron microscopy. The deposition conditions can be controlled by adjusting the kinetic energies of the ions by applying accelerating or decelerating voltages to a set of ion-steering optics. To validate this approach, we have examined two cage-like protein complexes, GroEL and ferritin, and studied the effect of soft-landing conditions on the method's throughput and the preservation of protein structure. Separation, based on mass-to-charge ratio, of holo- and apo-ferritin complexes after electrospray ionization enabled us to soft-land independently the separated complexes on a grid suitable for downstream transmission electron microscopy analysis. Following negative staining, images of the soft-landed complexes reveal that their structural integrity is largely conserved, with the characteristic central cavity of apoferritin, and iron core of holoferritin, surviving the phase transition from liquid to gas, soft-landing, and dehydration in vacuum.
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Affiliation(s)
- Victor A Mikhailov
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford , Oxford, OX1 3QZ, United Kingdom
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117
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van de Waterbeemd M, Lössl P, Gautier V, Marino F, Yamashita M, Conti E, Scholten A, Heck AJR. Simultane Untersuchung kinetischer, ortsspezifischer und struktureller Aspekte enzymatischer Proteinphosphorylierungen. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201404637] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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118
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van de Waterbeemd M, Lössl P, Gautier V, Marino F, Yamashita M, Conti E, Scholten A, Heck AJR. Simultaneous assessment of kinetic, site-specific, and structural aspects of enzymatic protein phosphorylation. Angew Chem Int Ed Engl 2014; 53:9660-4. [PMID: 25044833 DOI: 10.1002/anie.201404637] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Indexed: 12/27/2022]
Abstract
Protein phosphorylation is a widespread process forming the mechanistic basis of cellular signaling. Up to now, different aspects, for example, site-specificity, kinetics, role of co-factors, and structure-function relationships have been typically investigated by multiple techniques that are incompatible with one another. The approach introduced here maximizes the amount of information gained on protein (complex) phosphorylation while minimizing sample handling. Using high-resolution native mass spectrometry on intact protein (assemblies) up to 150 kDa we track the sequential incorporation of phosphate groups and map their localization by peptide LC-MS/MS. On two model systems, the protein kinase G and the interplay between Aurora kinase A and Bora, we demonstrate the simultaneous monitoring of various aspects of the phosphorylation process, namely the effect of different cofactors on PKG autophosphorylation and the interaction of AurA and Bora as both an enzyme-substrate pair and physical binding partners.
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Affiliation(s)
- Michiel van de Waterbeemd
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences and Netherlands Proteomics Center, Utrecht University, Padualaan 8, 3584 CH Utrecht (The Netherlands)
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119
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Marcoux J, Politis A, Rinehart D, Marshall DP, Wallace MI, Tamm LK, Robinson CV. Mass spectrometry defines the C-terminal dimerization domain and enables modeling of the structure of full-length OmpA. Structure 2014; 22:781-90. [PMID: 24746938 DOI: 10.1016/j.str.2014.03.004] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 02/26/2014] [Accepted: 03/17/2014] [Indexed: 11/17/2022]
Abstract
The transmembrane domain of the outer membrane protein A (OmpA) from Escherichia coli is an excellent model for structural and folding studies of β-barrel membrane proteins. However, full-length OmpA resists crystallographic efforts, and the link between its function and tertiary structure remains controversial. Here we use site-directed mutagenesis and mass spectrometry of different constructs of OmpA, released in the gas phase from detergent micelles, to define the minimal region encompassing the C-terminal dimer interface. Combining knowledge of the location of the dimeric interface with molecular modeling and ion mobility data allows us to propose a low-resolution model for the full-length OmpA dimer. Our model of the dimer is in remarkable agreement with experimental ion mobility data, with none of the unfolding or collapse observed for full-length monomeric OmpA, implying that dimer formation stabilizes the overall structure and prevents collapse of the flexible linker that connects the two domains.
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Affiliation(s)
- Julien Marcoux
- Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, UK
| | - Argyris Politis
- Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, UK
| | - Dennis Rinehart
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
| | - David P Marshall
- Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, UK
| | - Mark I Wallace
- Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, UK
| | - Lukas K Tamm
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
| | - Carol V Robinson
- Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, UK.
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120
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Pastore A. New challenges in structural biology: catching the complexity of dynamic nanomachines. Front Mol Biosci 2014; 1:3. [PMID: 25988144 PMCID: PMC4428490 DOI: 10.3389/fmolb.2014.00003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Accepted: 03/19/2014] [Indexed: 12/12/2022] Open
Affiliation(s)
- Annalisa Pastore
- Department of Clinical Neuroscience, King's College London London, UK
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121
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Landreh M, Alvelius G, Johansson J, Jörnvall H. Insulin, islet amyloid polypeptide and C-peptide interactions evaluated by mass spectrometric analysis. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2014; 28:178-184. [PMID: 24338965 DOI: 10.1002/rcm.6772] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 10/13/2013] [Accepted: 10/20/2013] [Indexed: 06/03/2023]
Abstract
RATIONALE Insulin, islet amyloid polypeptide (IAPP), and the C-peptide part of proinsulin are co-secreted from the pancreatic beta cell granules. IAPP aggregation can be inhibited by insulin and insulin aggregation by C-peptide, but different binding and disaggregating interactions may apply for the peptide complexes. A more detailed knowledge of these interactions is necessary for the development strategies against diabetic complications that stem from peptide aggregations. METHODS Mass spectrometry (MS) is utilized to investigate pH-dependencies, sequence determinants and association strengths of interactions between pairs of all three peptides. Electrospray ionization (ESI)-MS was used to monitor complex formation and interaction stoichiometries at different pH values. Collision-induced dissociation (CID) was employed to probe relative association strengths and complex dissociation pathways. RESULTS IAPP, like C-peptide, removes insulin oligomers observable by ESI-MS. Both C-peptide and IAPP form stable 1:1 heterodimers with insulin. Complexes of the negatively charged C-peptide with the positively charged IAPP, on the other hand, are easily dissociated. Replacement of the conserved glutamic acid residues in C-peptide with alanine residues increases the stability, indicating that net charge alone does not predict association strength. Binding to insulin has been suggested to stabilize a helical fold in IAPP via charge and hydrophobic interactions, which is in agreement with the now observed high gas-phase stability and sensitivity to low pH. CONCLUSIONS Combined, these results suggest that the C-peptide-insulin and IAPP-insulin interactions are mediated by a defined binding site, while such a feature is not apparent in the IAPP-C-peptide association. Hence, IAPP and C-peptide are interacting in similar manners and with similar monomerizing effects on insulin, suggesting that both peptides can prevent insulin aggregation. Simultaneous interactions of all three peptides cannot be excluded but appear unlikely from the uneven pairwise binding strengths.
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Affiliation(s)
- Michael Landreh
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77, Stockholm, Sweden
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122
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Young LM, Cao P, Raleigh DP, Ashcroft AE, Radford SE. Ion mobility spectrometry-mass spectrometry defines the oligomeric intermediates in amylin amyloid formation and the mode of action of inhibitors. J Am Chem Soc 2014; 136:660-70. [PMID: 24372466 PMCID: PMC3928500 DOI: 10.1021/ja406831n] [Citation(s) in RCA: 149] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Indexed: 12/31/2022]
Abstract
The molecular mechanisms by which different proteins assemble into highly ordered fibrillar deposits and cause disease remain topics of debate. Human amylin (also known as islet amyloid polypeptide/hIAPP) is found in vivo as amyloid deposits in the pancreatic islets of sufferers of type II diabetes mellitus, and its self-aggregation is thought to be a pathogenic factor in disease and to contribute to the failure of islet transplants. Here, electrospray ionization-ion mobility spectrometry-mass spectrometry (ESI-IMS-MS) has been used to monitor oligomer formation from IAPP. The detection, identification and characterization of oligomers from both human and rat amylin (rIAPP) are described. Oligomers up to and including hexamers have been detected for both peptides. From ESI-IMS-MS derived collision cross sections (CCS), these species are shown to be elongated in conformation. Collision-induced dissociation (CID-MS/MS) revealed differences in the gas-phase stability of the oligomers formed from hIAPP and rIAPP, which may contribute to their differences in amyloid propensity. Using ESI-IMS-MS, the mode of inhibition of amyloid formation from hIAPP using small molecules or co-incubation with rIAPP was also investigated. We show that the polyphenolic compounds epigallocatechin gallate (EGCG) and silibinin bind to specific conformers within a dynamic ensemble of hIAPP monomers, altering the progress of oligomerization and fibril assembly. Hetero-oligomer formation also occurs with rIAPP but leads only to inefficient inhibition. The results indicate that although different small molecules can be effective inhibitors of hIAPP self-assembly, their modes of action are distinct and can be distinguished using ESI-IMS-MS.
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Affiliation(s)
- Lydia M Young
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds , Leeds LS2 9JT, U.K
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Petrotchenko EV, Borchers CH. Modern Mass Spectrometry-Based Structural Proteomics. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2014; 95:193-213. [DOI: 10.1016/b978-0-12-800453-1.00006-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
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124
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Konermann L, Vahidi S, Sowole MA. Mass Spectrometry Methods for Studying Structure and Dynamics of Biological Macromolecules. Anal Chem 2013; 86:213-32. [DOI: 10.1021/ac4039306] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario, N6A 5B7 Canada
| | - Siavash Vahidi
- Department of Chemistry, The University of Western Ontario, London, Ontario, N6A 5B7 Canada
| | - Modupeola A. Sowole
- Department of Chemistry, The University of Western Ontario, London, Ontario, N6A 5B7 Canada
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125
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A perspective on proteomics in cell biology. Trends Cell Biol 2013; 24:257-64. [PMID: 24284280 PMCID: PMC3989996 DOI: 10.1016/j.tcb.2013.10.010] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Revised: 10/14/2013] [Accepted: 10/30/2013] [Indexed: 12/21/2022]
Abstract
Proteomic strategies facilitate system-wide analyses of protein complexes. Isotope labelling allows quantitative measurement of protein properties, not only their identification. There is a major need to organise effective community sharing of the proteomic data mountain. The integration of proteomic data with other online data repositories must be improved.
During the past 15 years mass spectrometry (MS)-based analyses have become established as the method of choice for direct protein identification and measurement. Owing to the remarkable improvements in the sensitivity and resolution of MS instruments, this technology has revolutionised the opportunities available for the system-wide characterisation of proteins, with wide applications across virtually the whole of cell biology. In this article we provide a perspective on the current state of the art and discuss how the future of cell biology research may benefit from further developments and applications in the field of MS and proteomics, highlighting the major challenges ahead for the community in organising the effective sharing and integration of the resulting data mountain.
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