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Henrich E, Peetz O, Hein C, Laguerre A, Hoffmann B, Hoffmann J, Dötsch V, Bernhard F, Morgner N. Analyzing native membrane protein assembly in nanodiscs by combined non-covalent mass spectrometry and synthetic biology. eLife 2017; 6. [PMID: 28067619 PMCID: PMC5291076 DOI: 10.7554/elife.20954] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 01/04/2017] [Indexed: 01/01/2023] Open
Abstract
Membrane proteins frequently assemble into higher order homo- or hetero-oligomers within their natural lipid environment. This complex formation can modulate their folding, activity as well as substrate selectivity. Non-disruptive methods avoiding critical steps, such as membrane disintegration, transfer into artificial environments or chemical modifications are therefore essential to analyze molecular mechanisms of native membrane protein assemblies. The combination of cell-free synthetic biology, nanodisc-technology and non-covalent mass spectrometry provides excellent synergies for the analysis of membrane protein oligomerization within defined membranes. We exemplify our strategy by oligomeric state characterization of various membrane proteins including ion channels, transporters and membrane-integrated enzymes assembling up to hexameric complexes. We further indicate a lipid-dependent dimer formation of MraY translocase correlating with the enzymatic activity. The detergent-free synthesis of membrane protein/nanodisc samples and the analysis by LILBID mass spectrometry provide a versatile platform for the analysis of membrane proteins in a native environment.
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Affiliation(s)
- Erik Henrich
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J W Goethe-University, Frankfurt am Main, Germany
| | - Oliver Peetz
- Institute of Physical and Theoretical Chemistry, J W Goethe-University, Frankfurt am Main, Germany
| | - Christopher Hein
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J W Goethe-University, Frankfurt am Main, Germany
| | - Aisha Laguerre
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J W Goethe-University, Frankfurt am Main, Germany
| | - Beate Hoffmann
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J W Goethe-University, Frankfurt am Main, Germany
| | - Jan Hoffmann
- Institute of Physical and Theoretical Chemistry, J W Goethe-University, Frankfurt am Main, Germany
| | - Volker Dötsch
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J W Goethe-University, Frankfurt am Main, Germany
| | - Frank Bernhard
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J W Goethe-University, Frankfurt am Main, Germany
| | - Nina Morgner
- Institute of Physical and Theoretical Chemistry, J W Goethe-University, Frankfurt am Main, Germany
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52
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Watkinson TG, Calabrese AN, Ault JR, Radford SE, Ashcroft AE. FPOP-LC-MS/MS Suggests Differences in Interaction Sites of Amphipols and Detergents with Outer Membrane Proteins. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:50-55. [PMID: 27343183 PMCID: PMC5174144 DOI: 10.1007/s13361-016-1421-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 05/10/2016] [Accepted: 05/11/2016] [Indexed: 05/24/2023]
Abstract
Amphipols are a class of novel surfactants that are capable of stabilizing the native state of membrane proteins. They have been shown to be highly effective, in some cases more so than detergent micelles, at maintaining the structural integrity of membrane proteins in solution, and have shown promise as vehicles for delivering native membrane proteins into the gas phase for structural interrogation. Here, we use fast photochemical oxidation of proteins (FPOP), which irreversibly labels the side chains of solvent-accessible residues with hydroxyl radicals generated by laser photolysis of hydrogen peroxide, to compare the solvent accessibility of the outer membrane protein OmpT when solubilized with the amphipol A8-35 or with n-dodecyl-β-maltoside (DDM) detergent micelles. Using quantitative mass spectrometry analyses, we show that fast photochemical oxidation reveals differences in the extent of solvent accessibility of residues between the A8-35 and DDM solubilized states, providing a rationale for the increased stability of membrane proteins solubilized with amphipol compared with detergent micelles, as a result of additional intermolecular contacts. Graphical Abstract ᅟ.
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Affiliation(s)
- Thomas G Watkinson
- Astbury Center for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Antonio N Calabrese
- Astbury Center for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - James R Ault
- Astbury Center for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Sheena E Radford
- Astbury Center for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK.
| | - Alison E Ashcroft
- Astbury Center for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK.
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53
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Mikhailov VA, Liko I, Mize TH, Bush MF, Benesch JLP, Robinson CV. Infrared Laser Activation of Soluble and Membrane Protein Assemblies in the Gas Phase. Anal Chem 2016; 88:7060-7. [PMID: 27328020 DOI: 10.1021/acs.analchem.6b00645] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Collision-induced dissociation (CID) is the dominant method for probing intact macromolecular complexes in the gas phase by means of mass spectrometry (MS). The energy obtained from collisional activation is dependent on the charge state of the ion and the pressures and potentials within the instrument: these factors limit CID capability. Activation by infrared (IR) laser radiation offers an attractive alternative as the radiation energy absorbed by the ions is charge-state-independent and the intensity and time scale of activation is controlled by a laser source external to the mass spectrometer. Here we implement and apply IR activation, in different irradiation regimes, to study both soluble and membrane protein assemblies. We show that IR activation using high-intensity pulsed lasers is faster than collisional and radiative cooling and requires much lower energy than continuous IR irradiation. We demonstrate that IR activation is an effective means for studying membrane protein assemblies, and liberate an intact V-type ATPase complex from detergent micelles, a result that cannot be achieved by means of CID using standard collision energies. Notably, we find that IR activation can be sufficiently soft to retain specific lipids bound to the complex. We further demonstrate that, by applying a combination of collisional activation, mass selection, and IR activation of the liberated complex, we can elucidate subunit stoichiometry and the masses of specifically bound lipids in a single MS experiment.
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Affiliation(s)
- Victor A Mikhailov
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford , Oxford, OX1 3QZ, United Kingdom
| | - Idlir Liko
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford , Oxford, OX1 3QZ, United Kingdom
| | - Todd H Mize
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford , Oxford, OX1 3QZ, United Kingdom
| | - Matthew F Bush
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford , Oxford, OX1 3QZ, United Kingdom
| | - Justin L P Benesch
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford , Oxford, OX1 3QZ, United Kingdom
| | - Carol V Robinson
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford , Oxford, OX1 3QZ, United Kingdom
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54
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Horne JE, Radford SE. A growing toolbox of techniques for studying β-barrel outer membrane protein folding and biogenesis. Biochem Soc Trans 2016; 44:802-9. [PMID: 27284045 PMCID: PMC4900752 DOI: 10.1042/bst20160020] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Indexed: 01/21/2023]
Abstract
Great strides into understanding protein folding have been made since the seminal work of Anfinsen over 40 years ago, but progress in the study of membrane protein folding has lagged behind that of their water soluble counterparts. Researchers in these fields continue to turn to more advanced techniques such as NMR, mass spectrometry, molecular dynamics (MD) and single molecule methods to interrogate how proteins fold. Our understanding of β-barrel outer membrane protein (OMP) folding has benefited from these advances in the last decade. This class of proteins must traverse the periplasm and then insert into an asymmetric lipid membrane in the absence of a chemical energy source. In this review we discuss old, new and emerging techniques used to examine the process of OMP folding and biogenesis in vitro and describe some of the insights and new questions these techniques have revealed.
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Affiliation(s)
- Jim E Horne
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, The University of Leeds, Leeds LS2 9JT, U.K
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, The University of Leeds, Leeds LS2 9JT, U.K.
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55
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Chait BT, Cadene M, Olinares PD, Rout MP, Shi Y. Revealing Higher Order Protein Structure Using Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:952-65. [PMID: 27080007 PMCID: PMC5125627 DOI: 10.1007/s13361-016-1385-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Revised: 03/14/2016] [Accepted: 03/15/2016] [Indexed: 05/24/2023]
Abstract
The development of rapid, sensitive, and accurate mass spectrometric methods for measuring peptides, proteins, and even intact protein assemblies has made mass spectrometry (MS) an extraordinarily enabling tool for structural biology. Here, we provide a personal perspective of the increasingly useful role that mass spectrometric techniques are exerting during the elucidation of higher order protein structures. Areas covered in this brief perspective include MS as an enabling tool for the high resolution structural biologist, for compositional analysis of endogenous protein complexes, for stoichiometry determination, as well as for integrated approaches for the structural elucidation of protein complexes. We conclude with a vision for the future role of MS-based techniques in the development of a multi-scale molecular microscope. Graphical Abstract ᅟ.
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Affiliation(s)
- Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, 10065, USA.
| | - Martine Cadene
- CBM, CNRS UPR4301, Rue Charles Sadron, CS 80054, 45071, Orleans Cedex 2, France
| | - Paul Dominic Olinares
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, 10065, USA
| | - Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY, 10065, USA
| | - Yi Shi
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, 10065, USA
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56
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Hoi KK, Robinson CV, Marty MT. Unraveling the Composition and Behavior of Heterogeneous Lipid Nanodiscs by Mass Spectrometry. Anal Chem 2016; 88:6199-204. [PMID: 27206251 DOI: 10.1021/acs.analchem.6b00851] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Mass spectrometry (MS) has emerged as a powerful tool to study membrane protein complexes and protein-lipid interactions. Because they provide a precisely defined lipid bilayer environment, lipoprotein Nanodiscs offer a promising cassette for membrane protein MS analysis. However, heterogeneous lipids create several potential challenges for native MS: additional spectral complexity, ambiguous assignments, and differing gas-phase behaviors. Here, we present strategies to address these challenges and streamline analysis of heterogeneous-lipid Nanodiscs. We show that using two lipids of similar mass limits the complexity of the spectra in heterogeneous Nanodiscs and that the lipid composition can be determined by using a dual Fourier transform approach to obtain the average lipid mass. Further, the relationship between gas-phase behavior, lipid composition, and instrumental polarity was investigated to determine the effects of lipid headgroup chemistry on Nanodisc dissociation mechanisms. These results provide unique mechanistic and methodological insights into characterization of complex and heterogeneous systems by mass spectrometry.
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Affiliation(s)
- Kin Kuan Hoi
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford , South Parks Road, Oxford OX1 3QZ, U.K
| | - Carol V Robinson
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford , South Parks Road, Oxford OX1 3QZ, U.K
| | - Michael T Marty
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford , South Parks Road, Oxford OX1 3QZ, U.K
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57
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Ben-Nissan G, Chotiner A, Tarnavsky M, Sharon M. Structural Characterization of Missense Mutations Using High Resolution Mass Spectrometry: A Case Study of the Parkinson's-Related Protein, DJ-1. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:1062-1070. [PMID: 27048419 PMCID: PMC5152731 DOI: 10.1007/s13361-016-1379-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 03/06/2016] [Accepted: 03/07/2016] [Indexed: 06/02/2023]
Abstract
Missense mutations that lead to the expression of mutant proteins carrying single amino acid substitutions are the cause of numerous diseases. Unlike gene lesions, insertions, deletions, nonsense mutations, or modified RNA splicing, which affect the length of a polypeptide, or determine whether a polypeptide is translated at all, missense mutations exert more subtle effects on protein structure, which are often difficult to evaluate. Here, we took advantage of the spectral resolution afforded by the EMR Orbitrap platform, to generate a mass spectrometry-based approach relying on simultaneous measurements of the wild-type protein and the missense variants. This approach not only considerably shortens the analysis time due to the concurrent acquisition but, more importantly, enables direct comparisons between the wild-type protein and the variants, allowing identification of even subtle structural changes. We demonstrate our approach using the Parkinson's-associated protein, DJ-1. Together with the wild-type protein, we examined two missense mutants, DJ-1A104T and DJ-1D149A, which lead to early-onset familial Parkinson's disease. Gas-phase, thermal, and chemical stability assays indicate clear alterations in the conformational stability of the two mutants: the structural stability of DJ-1D149A is reduced, whereas that of DJ-1A104T is enhanced. Overall, we anticipate that the methodology presented here will be applicable to numerous other missense mutants, promoting the structural investigations of multiple variants of the same protein. Graphical Abstract ᅟ.
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Affiliation(s)
- Gili Ben-Nissan
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Almog Chotiner
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Mark Tarnavsky
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Michal Sharon
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, 7610001, Israel.
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58
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van Coevorden-Hameete MH, Titulaer MJ, Schreurs MWJ, de Graaff E, Sillevis Smitt PAE, Hoogenraad CC. Detection and Characterization of Autoantibodies to Neuronal Cell-Surface Antigens in the Central Nervous System. Front Mol Neurosci 2016; 9:37. [PMID: 27303263 PMCID: PMC4885853 DOI: 10.3389/fnmol.2016.00037] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 05/09/2016] [Indexed: 01/07/2023] Open
Abstract
Autoimmune encephalitis (AIE) is a group of disorders in which autoantibodies directed at antigens located on the plasma membrane of neurons induce severe neurological symptoms. In contrast to classical paraneoplastic disorders, AIE patients respond well to immunotherapy. The detection of neuronal surface autoantibodies in patients' serum or CSF therefore has serious consequences for the patients' treatment and follow-up and requires the availability of sensitive and specific diagnostic tests. This mini-review provides a guideline for both diagnostic and research laboratories that work on the detection of known surface autoantibodies and/or the identification of novel surface antigens. We discuss the strengths and pitfalls of different techniques for anti-neuronal antibody detection: (1) Immunohistochemistry (IHC) and immunofluorescence on rat/primate brain sections; (2) Immunocytochemistry (ICC) of living cultured hippocampal neurons; and (3) Cell Based Assay (CBA). In addition, we discuss the use of immunoprecipitation and mass spectrometry analysis for the detection of novel neuronal surface antigens, which is a crucial step in further disease classification and the development of novel CBAs.
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Affiliation(s)
- Marleen H. van Coevorden-Hameete
- Department of Biology, Division of Cell Biology, Faculty of Science, Utrecht UniversityUtrecht, Netherlands
- Department of Neurology, Erasmus Medical CenterRotterdam, Netherlands
| | | | | | - Esther de Graaff
- Department of Biology, Division of Cell Biology, Faculty of Science, Utrecht UniversityUtrecht, Netherlands
| | | | - Casper C. Hoogenraad
- Department of Biology, Division of Cell Biology, Faculty of Science, Utrecht UniversityUtrecht, Netherlands
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59
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Liu F, Koval M, Ranganathan S, Fanayan S, Hancock WS, Lundberg EK, Beavis RC, Lane L, Duek P, McQuade L, Kelleher NL, Baker MS. Systems Proteomics View of the Endogenous Human Claudin Protein Family. J Proteome Res 2016; 15:339-59. [PMID: 26680015 DOI: 10.1021/acs.jproteome.5b00769] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Claudins are the major transmembrane protein components of tight junctions in human endothelia and epithelia. Tissue-specific expression of claudin members suggests that this protein family is not only essential for sustaining the role of tight junctions in cell permeability control but also vital in organizing cell contact signaling by protein-protein interactions. How this protein family is collectively processed and regulated is key to understanding the role of junctional proteins in preserving cell identity and tissue integrity. The focus of this review is to first provide a brief overview of the functional context, on the basis of the extensive body of claudin biology research that has been thoroughly reviewed, for endogenous human claudin members and then ascertain existing and future proteomics techniques that may be applicable to systematically characterizing the chemical forms and interacting protein partners of this protein family in human. The ability to elucidate claudin-based signaling networks may provide new insight into cell development and differentiation programs that are crucial to tissue stability and manipulation.
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Affiliation(s)
| | - Michael Koval
- Department of Medicine, Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, and Department of Cell Biology, Emory University School of Medicine , 205 Whitehead Biomedical Research Building, 615 Michael Street, Atlanta, Georgia 30322, United States
| | | | | | - William S Hancock
- Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University , Boston, Massachusetts 02115, United States
| | - Emma K Lundberg
- SciLifeLab, School of Biotechnology, Royal Institute of Technology (KTH) , SE-171 21 Solna, Stockholm, Sweden
| | - Ronald C Beavis
- Department of Biochemistry and Medical Genetics, University of Manitoba , 744 Bannatyne Avenue, Winnipeg, Manitoba R3E 0W3, Canada
| | - Lydie Lane
- SIB-Swiss Institute of Bioinformatics , CMU - Rue Michel-Servet 1, 1211 Geneva, Switzerland
| | - Paula Duek
- SIB-Swiss Institute of Bioinformatics , CMU - Rue Michel-Servet 1, 1211 Geneva, Switzerland
| | | | - Neil L Kelleher
- Department of Chemistry, Department of Molecular Biosciences, and Proteomics Center of Excellence, Northwestern University , 2145 North Sheridan Road, Evanston, Illinois 60208, United States
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60
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Morrison LJ, Brodbelt JS. Charge site assignment in native proteins by ultraviolet photodissociation (UVPD) mass spectrometry. Analyst 2016; 141:166-76. [PMID: 26596460 PMCID: PMC4679510 DOI: 10.1039/c5an01819f] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Characterization of all gas-phase charge sites of natively sprayed proteins and peptides is demonstrated using 193 nm UVPD. The high sequence coverage offered by UVPD is exploited for the accurate determination of charge sites in protein systems up to 18 kDa, allowing charge site to be studied as a function of protein conformation and the presence of disulfide bonds. Charging protons are found on both basic sidechains and on the amide backbone of less basic amino acids such as serine, glutamine, and proline. UVPD analysis was performed on the 3+ charge state of melittin, the 5+ to 8+ charge states of ubiquitin, and the 8+ charge state of reduced and oxidized β-lactoglobulin. The location of charges in gas-phase proteins is known to impact structure; molecular modeling of different charge site motifs of 3+ melittin demonstrates how placement of protons in simulations can dramatically impact the predicted structure of the molecule. The location of positive charge sites in ubiquitin and β-lactoglobulin are additionally found to depend on the presence or absence of salt-bridges, columbic repulsion across the length of the peptide, and protein conformation. Charge site isomers are demonstrated for ubiquitin and β-lactoglobulin but found to be much less numerous than previously predicted.
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61
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Chen F, Gülbakan B, Weidmann S, Fagerer SR, Ibáñez AJ, Zenobi R. Applying mass spectrometry to study non-covalent biomolecule complexes. MASS SPECTROMETRY REVIEWS 2016; 35:48-70. [PMID: 25945814 DOI: 10.1002/mas.21462] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 12/09/2014] [Indexed: 05/10/2023]
Abstract
Non-covalent interactions are essential for the structural organization of biomacromolecules and play an important role in molecular recognition processes, such as the interactions between proteins, glycans, lipids, DNA, and RNA. Mass spectrometry (MS) is a powerful tool for studying of non-covalent interactions, due to the low sample consumption, high sensitivity, and label-free nature. Nowadays, native-ESI MS is heavily used in studies of non-covalent interactions and to understand the architecture of biomolecular complexes. However, MALDI-MS is also becoming increasingly useful. It is challenging to detect the intact complex without fragmentation when analyzing non-covalent interactions with MALDI-MS. There are two methodological approaches to do so. In the first approach, different experimental and instrumental parameters are fine-tuned in order to find conditions under which the complex is stable, such as applying non-acidic matrices and collecting first-shot spectra. In the second approach, the interacting species are "artificially" stabilized by chemical crosslinking. Both approaches are capable of studying non-covalently bound biomolecules even in quite challenging systems, such as membrane protein complexes. Herein, we review and compare native-ESI and MALDI MS for the study of non-covalent interactions.
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Affiliation(s)
- Fan Chen
- Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093, Zürich, Switzerland
| | - Basri Gülbakan
- Institute of Child Health, Division of Pediatric Basic Sciences, Hacettepe University, 06100 Ankara, Turkey
| | - Simon Weidmann
- Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093, Zürich, Switzerland
| | - Stephan R Fagerer
- Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093, Zürich, Switzerland
| | - Alfredo J Ibáñez
- Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093, Zürich, Switzerland
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093, Zürich, Switzerland
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62
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Yasueda Y, Tamura T, Kuwara K, Takaoka Y, Hamachi I. Biomembrane-embedded Catalysts for Membrane-associated Protein Labeling on Red Blood Cells. CHEM LETT 2015. [DOI: 10.1246/cl.150797] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Yuki Yasueda
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University
| | - Tomonori Tamura
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University
| | - Keiko Kuwara
- Institute of Transformative Bio-Molecules (ITbM), Nagoya University
| | | | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency
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63
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Kocer A. Mechanisms of mechanosensing - mechanosensitive channels, function and re-engineering. Curr Opin Chem Biol 2015; 29:120-7. [PMID: 26610201 DOI: 10.1016/j.cbpa.2015.10.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 09/30/2015] [Accepted: 10/06/2015] [Indexed: 10/22/2022]
Abstract
Sensing and responding to mechanical stimuli is an ancient behavior and ubiquitous to all forms of life. One of its players 'mechanosensitive ion channels' are involved in processes from osmosensing in bacteria to pain in humans. However, the mechanism of mechanosensing is yet to be elucidated. This review describes recent developments in the understanding of a bacterial mechanosensitive channel. Force from the lipid principle of mechanosensation, new methods to understand protein-lipid interactions, the role of water in the gating, the use of engineered mechanosensitive channels in the understanding of the gating mechanism and application of the accumulated knowledge in the field of drug delivery, drug design and sensor technologies are discussed.
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Affiliation(s)
- Armagan Kocer
- University of Groningen, University Medical Center Groningen, Ant. Deusinglaan 1, 9713 AV Groningen, The Netherlands.
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64
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Bricker TM, Mummadisetti MP, Frankel LK. Recent advances in the use of mass spectrometry to examine structure/function relationships in photosystem II. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2015; 152:227-46. [PMID: 26390944 DOI: 10.1016/j.jphotobiol.2015.08.031] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 08/27/2015] [Accepted: 08/31/2015] [Indexed: 01/24/2023]
Abstract
Tandem mass spectrometry often coupled with chemical modification techniques, is developing into increasingly important tool in structural biology. These methods can provide important supplementary information concerning the structural organization and subunit make-up of membrane protein complexes, identification of conformational changes occurring during enzymatic reactions, identification of the location of posttranslational modifications, and elucidation of the structure of assembly and repair complexes. In this review, we will present a brief introduction to Photosystem II, tandem mass spectrometry and protein modification techniques that have been used to examine the photosystem. We will then discuss a number of recent case studies that have used these techniques to address open questions concerning PS II. These include the nature of subunit-subunit interactions within the phycobilisome, the interaction of phycobilisomes with Photosystem I and the Orange Carotenoid Protein, the location of CyanoQ, PsbQ and PsbP within Photosystem II, and the identification of phosphorylation and oxidative modification sites within the photosystem. Finally, we will discuss some of the future prospects for the use of these methods in examining other open questions in PS II structural biochemistry.
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Affiliation(s)
- Terry M Bricker
- Department of Biological Sciences, Division of Biochemistry and Molecular Biology, Louisiana State University, Baton Rouge, LA 70803, United States.
| | - Manjula P Mummadisetti
- Department of Biological Sciences, Division of Biochemistry and Molecular Biology, Louisiana State University, Baton Rouge, LA 70803, United States
| | - Laurie K Frankel
- Department of Biological Sciences, Division of Biochemistry and Molecular Biology, Louisiana State University, Baton Rouge, LA 70803, United States
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65
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Chang YH, Gregorich ZR, Chen AJ, Hwang L, Guner H, Yu D, Zhang J, Ge Y. New mass-spectrometry-compatible degradable surfactant for tissue proteomics. J Proteome Res 2015; 14:1587-99. [PMID: 25589168 DOI: 10.1021/pr5012679] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Tissue proteomics is increasingly recognized for its role in biomarker discovery and disease mechanism investigation. However, protein solubility remains a significant challenge in mass spectrometry (MS)-based tissue proteomics. Conventional surfactants such as sodium dodecyl sulfate (SDS), the preferred surfactant for protein solubilization, are not compatible with MS. Herein, we have screened a library of surfactant-like compounds and discovered an MS-compatible degradable surfactant (MaSDeS) for tissue proteomics that solubilizes all categories of proteins with performance comparable to SDS. The use of MaSDeS in the tissue extraction significantly improves the total number of protein identifications from commonly used tissues, including tissue from the heart, liver, and lung. Notably, MaSDeS significantly enriches membrane proteins, which are often under-represented in proteomics studies. The acid degradable nature of MaSDeS makes it amenable for high-throughput MS-based proteomics. In addition, the thermostability of MaSDeS allows for its use in experiments requiring high temperature to facilitate protein extraction and solubilization. Furthermore, we have shown that MaSDeS outperforms the other MS-compatible surfactants in terms of overall protein solubility and the total number of identified proteins in tissue proteomics. Thus, the use of MaSDeS will greatly advance tissue proteomics and realize its potential in basic biomedical and clinical research. MaSDeS could be utilized in a variety of proteomics studies as well as general biochemical and biological experiments that employ surfactants for protein solubilization.
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Affiliation(s)
- Ying-Hua Chang
- Department of Cell and Regenerative Biology, ‡Molecular and Cellular Pharmacology Program, §Department of Chemistry, ∥Human Proteomics Program, and ⊥Molecular and Environmental Toxicology Program, University of Wisconsin-Madison , 1300 University Avenue, Madison 53706, Wisconsin, United States
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66
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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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67
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Calabrese AN, Watkinson TG, Henderson PJF, Radford SE, Ashcroft AE. Amphipols outperform dodecylmaltoside micelles in stabilizing membrane protein structure in the gas phase. Anal Chem 2014; 87:1118-26. [PMID: 25495802 PMCID: PMC4636139 DOI: 10.1021/ac5037022] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Noncovalent mass spectrometry (MS) is emerging as an invaluable technique to probe the structure, interactions, and dynamics of membrane proteins (MPs). However, maintaining native-like MP conformations in the gas phase using detergent solubilized proteins is often challenging and may limit structural analysis. Amphipols, such as the well characterized A8-35, are alternative reagents able to maintain the solubility of MPs in detergent-free solution. In this work, the ability of A8-35 to retain the structural integrity of MPs for interrogation by electrospray ionization-ion mobility spectrometry-mass spectrometry (ESI-IMS-MS) is compared systematically with the commonly used detergent dodecylmaltoside. MPs from the two major structural classes were selected for analysis, including two β-barrel outer MPs, PagP and OmpT (20.2 and 33.5 kDa, respectively), and two α-helical proteins, Mhp1 and GalP (54.6 and 51.7 kDa, respectively). Evaluation of the rotationally averaged collision cross sections of the observed ions revealed that the native structures of detergent solubilized MPs were not always retained in the gas phase, with both collapsed and unfolded species being detected. In contrast, ESI-IMS-MS analysis of the amphipol solubilized MPs studied resulted in charge state distributions consistent with less gas phase induced unfolding, and the presence of lowly charged ions which exhibit collision cross sections comparable with those calculated from high resolution structural data. The data demonstrate that A8-35 can be more effective than dodecylmaltoside at maintaining native MP structure and interactions in the gas phase, permitting noncovalent ESI-IMS-MS analysis of MPs from the two major structural classes, while gas phase dissociation from dodecylmaltoside micelles leads to significant gas phase unfolding, especially for the α-helical MPs studied.
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Affiliation(s)
- Antonio N Calabrese
- School of Molecular and Cellular Biology and ‡School of Biomedical Sciences, Astbury Centre for Structural Molecular Biology, University of Leeds , Leeds, LS2 9JT, United Kingdom
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68
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Patrick JW, Gamez RC, Russell DH. Elucidation of Conformer Preferences for a Hydrophobic Antimicrobial Peptide by Vesicle Capture-Freeze-Drying: A Preparatory Method Coupled to Ion Mobility-Mass Spectrometry. Anal Chem 2014; 87:578-83. [DOI: 10.1021/ac503163g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- John W. Patrick
- The Laboratory for Biological Mass Spectrometry, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Roberto C. Gamez
- The Laboratory for Biological Mass Spectrometry, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - David H. Russell
- The Laboratory for Biological Mass Spectrometry, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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69
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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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70
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Koshy SS, Li X, Eyles SJ, Weis RM, Thompson LK. Hydrogen exchange differences between chemoreceptor signaling complexes localize to functionally important subdomains. Biochemistry 2014; 53:7755-64. [PMID: 25420045 PMCID: PMC4270382 DOI: 10.1021/bi500657v] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The goal of understanding mechanisms of transmembrane signaling, one of many key life processes mediated by membrane proteins, has motivated numerous studies of bacterial chemotaxis receptors. Ligand binding to the receptor causes a piston motion of an α helix in the periplasmic and transmembrane domains, but it is unclear how the signal is then propagated through the cytoplasmic domain to control the activity of the associated kinase CheA. Recent proposals suggest that signaling in the cytoplasmic domain involves opposing changes in dynamics in different subdomains. However, it has been difficult to measure dynamics within the functional system, consisting of extended arrays of receptor complexes with two other proteins, CheA and CheW. We have combined hydrogen exchange mass spectrometry with vesicle template assembly of functional complexes of the receptor cytoplasmic domain to reveal that there are significant signaling-associated changes in exchange, and these changes localize to key regions of the receptor involved in the excitation and adaptation responses. The methylation subdomain exhibits complex changes that include slower hydrogen exchange in complexes in a kinase-activating state, which may be partially consistent with proposals that this subdomain is stabilized in this state. The signaling subdomain exhibits significant protection from hydrogen exchange in complexes in a kinase-activating state, suggesting a tighter and/or larger interaction interface with CheA and CheW in this state. These first measurements of the stability of protein subdomains within functional signaling complexes demonstrate the promise of this approach for measuring functionally important protein dynamics within the various physiologically relevant states of multiprotein complexes.
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Affiliation(s)
- Seena S Koshy
- Department of Chemistry, ‡Department of Biochemistry and Molecular Biology, and §Program in Molecular and Cellular Biology, University of Massachusetts , Amherst, Massachusetts 01003, United States
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71
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Li H, Wongkongkathep P, Van Orden SL, Loo RRO, Loo JA. Revealing ligand binding sites and quantifying subunit variants of noncovalent protein complexes in a single native top-down FTICR MS experiment. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:2060-8. [PMID: 24912433 PMCID: PMC4444062 DOI: 10.1007/s13361-014-0928-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 05/09/2014] [Accepted: 05/12/2014] [Indexed: 05/11/2023]
Abstract
"Native" mass spectrometry (MS) has been proven to be increasingly useful for structural biology studies of macromolecular assemblies. Using horse liver alcohol dehydrogenase (hADH) and yeast alcohol dehydrogenase (yADH) as examples, we demonstrate that rich information can be obtained in a single native top-down MS experiment using Fourier transform ion cyclotron mass spectrometry (FTICR MS). Beyond measuring the molecular weights of the protein complexes, isotopic mass resolution was achieved for yeast ADH tetramer (147 kDa) with an average resolving power of 412,700 at m/z 5466 in absorption mode, and the mass reflects that each subunit binds to two zinc atoms. The N-terminal 89 amino acid residues were sequenced in a top-down electron capture dissociation (ECD) experiment, along with the identifications of the zinc binding site at Cys46 and a point mutation (V58T). With the combination of various activation/dissociation techniques, including ECD, in-source dissociation (ISD), collisionally activated dissociation (CAD), and infrared multiphoton dissociation (IRMPD), 40% of the yADH sequence was derived directly from the native tetramer complex. For hADH, native top-down ECD-MS shows that both E and S subunits are present in the hADH sample, with a relative ratio of 4:1. Native top-down ISD of the hADH dimer shows that each subunit (E and S chains) binds not only to two zinc atoms, but also the NAD/NADH ligand, with a higher NAD/NADH binding preference for the S chain relative to the E chain. In total, 32% sequence coverage was achieved for both E and S chains.
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Affiliation(s)
- Huilin Li
- Department of Biological Chemistry, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA, 90095, USA
| | - Piriya Wongkongkathep
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
| | | | - Rachel R. Ogorzalek Loo
- Department of Biological Chemistry, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA, 90095, USA
| | - Joseph A. Loo
- Department of Biological Chemistry, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
- Correspondence to: Joseph A. Loo;
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72
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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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73
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Global structural changes of an ion channel during its gating are followed by ion mobility mass spectrometry. Proc Natl Acad Sci U S A 2014; 111:17170-5. [PMID: 25404294 DOI: 10.1073/pnas.1413118111] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Mechanosensitive ion channels are sensors probing membrane tension in all species; despite their importance and vital role in many cell functions, their gating mechanism remains to be elucidated. Here, we determined the conditions for releasing intact mechanosensitive channel of large conductance (MscL) proteins from their detergents in the gas phase using native ion mobility-mass spectrometry (IM-MS). By using IM-MS, we could detect the native mass of MscL from Escherichia coli, determine various global structural changes during its gating by measuring the rotationally averaged collision cross-sections, and show that it can function in the absence of a lipid bilayer. We could detect global conformational changes during MscL gating as small as 3%. Our findings will allow studying native structure of many other membrane proteins.
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74
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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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75
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Zhou M, Robinson CV. Flexible membrane proteins: functional dynamics captured by mass spectrometry. Curr Opin Struct Biol 2014; 28:122-30. [DOI: 10.1016/j.sbi.2014.08.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 07/23/2014] [Accepted: 08/13/2014] [Indexed: 10/24/2022]
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76
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Van Simaeys D, Turek D, Champanhac C, Vaizer J, Sefah K, Zhen J, Sutphen R, Tan W. Identification of cell membrane protein stress-induced phosphoprotein 1 as a potential ovarian cancer biomarker using aptamers selected by cell systematic evolution of ligands by exponential enrichment. Anal Chem 2014; 86:4521-7. [PMID: 24654750 PMCID: PMC4018121 DOI: 10.1021/ac500466x] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2014] [Accepted: 03/21/2014] [Indexed: 02/01/2023]
Abstract
In this paper, we describe the elucidation of the target of an aptamer against ovarian cancer previously obtained by cell-SELEX (SELEX = systematic evolution of ligands by exponential enrichment). The target's identity, stress-induced phosphoprotein 1 (STIP1), was determined by mass spectrometry and validated by flow cytometry, using siRNA silencing and protein blotting. Initial oncologic studies show that the aptamer inhibits cell invasion, indicating that STIP1, which is currently under investigation as a potential biomarker for ovarian cancer, plays a critical role in this process. These results serve as an excellent example of how protein target identification of aptamers obtained by cell-SELEX can serve as a means to identify promising biomarker candidates and can promote the development of aptamers as a new drug class to block important oncological processes.
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Affiliation(s)
- Dimitri Van Simaeys
- Center
for Research at Bio/Nano Interface, Departments of Chemistry and of
Physiology and Functional Genomics, Shands Cancer Center, UF Genetics
Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Diane Turek
- Center
for Research at Bio/Nano Interface, Departments of Chemistry and of
Physiology and Functional Genomics, Shands Cancer Center, UF Genetics
Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Carole Champanhac
- Center
for Research at Bio/Nano Interface, Departments of Chemistry and of
Physiology and Functional Genomics, Shands Cancer Center, UF Genetics
Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Julia Vaizer
- Center
for Research at Bio/Nano Interface, Departments of Chemistry and of
Physiology and Functional Genomics, Shands Cancer Center, UF Genetics
Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Kwame Sefah
- Center
for Research at Bio/Nano Interface, Departments of Chemistry and of
Physiology and Functional Genomics, Shands Cancer Center, UF Genetics
Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Jing Zhen
- Center
for Research at Bio/Nano Interface, Departments of Chemistry and of
Physiology and Functional Genomics, Shands Cancer Center, UF Genetics
Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
- Molecular
Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing
and Chemometrics, Colleges of Chemistry and Chemical Engineering and
of Biology, Collaborative Innovation Center for Molecular Engineering
and Theranostics, Hunan University, Changsha 410082, China
| | - Rebecca Sutphen
- Morsani
School of Medicine, University of South
Florida, Tampa, Florida 33612, United
States
| | - Weihong Tan
- Center
for Research at Bio/Nano Interface, Departments of Chemistry and of
Physiology and Functional Genomics, Shands Cancer Center, UF Genetics
Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
- Molecular
Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing
and Chemometrics, Colleges of Chemistry and Chemical Engineering and
of Biology, Collaborative Innovation Center for Molecular Engineering
and Theranostics, Hunan University, Changsha 410082, China
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77
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Paslawski W, Mysling S, Thomsen K, Jørgensen TJD, Otzen DE. Co-existence of Two Different α-Synuclein Oligomers with Different Core Structures Determined by Hydrogen/Deuterium Exchange Mass Spectrometry. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201400491] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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78
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Paslawski W, Mysling S, Thomsen K, Jørgensen TJD, Otzen DE. Co-existence of Two Different α-Synuclein Oligomers with Different Core Structures Determined by Hydrogen/Deuterium Exchange Mass Spectrometry. Angew Chem Int Ed Engl 2014; 53:7560-3. [DOI: 10.1002/anie.201400491] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 03/06/2014] [Indexed: 12/24/2022]
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79
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Wyttenbach T, Pierson NA, Clemmer DE, Bowers MT. Ion Mobility Analysis of Molecular Dynamics. Annu Rev Phys Chem 2014; 65:175-96. [DOI: 10.1146/annurev-physchem-040513-103644] [Citation(s) in RCA: 154] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Thomas Wyttenbach
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106;
| | | | - David E. Clemmer
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405;
| | - Michael T. Bowers
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106;
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80
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Rouse SL, Marcoux J, Robinson CV, Sansom MSP. Dodecyl maltoside protects membrane proteins in vacuo. Biophys J 2014; 105:648-56. [PMID: 23931313 DOI: 10.1016/j.bpj.2013.06.025] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Revised: 05/14/2013] [Accepted: 06/17/2013] [Indexed: 11/26/2022] Open
Abstract
Molecular dynamics simulations have been used to characterize the effects of transfer from aqueous solution to a vacuum to inform our understanding of mass spectrometry of membrane-protein-detergent complexes. We compared two membrane protein architectures (an α-helical bundle versus a β-barrel) and two different detergent types (phosphocholines versus an alkyl sugar) with respect to protein stability and detergent packing. The β-barrel membrane protein remained stable as a protein-detergent complex in vacuum. Zwitterionic detergents formed conformationally destabilizing interactions with an α-helical membrane protein after detergent micelle inversion driven by dehydration in vacuum. In contrast, a nonionic alkyl sugar detergent resisted micelle inversion, maintaining the solution-phase conformation of the protein. This helps to explain the relative stability of membrane proteins in the presence of alkyl sugar detergents such as dodecyl maltoside.
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Affiliation(s)
- Sarah L Rouse
- Department of Biochemistry, University of Oxford, United Kingdom
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81
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Parker CH, Morgan C, Rand KD, Engen JR, Jorgenson J, Stafford DW. A conformational investigation of propeptide binding to the integral membrane protein γ-glutamyl carboxylase using nanodisc hydrogen exchange mass spectrometry. Biochemistry 2014; 53:1511-20. [PMID: 24512177 PMCID: PMC3970815 DOI: 10.1021/bi401536m] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 02/07/2014] [Indexed: 01/16/2023]
Abstract
Gamma (γ)-glutamyl carboxylase (GGCX) is an integral membrane protein responsible for the post-translational catalytic conversion of select glutamic acid (Glu) residues to γ-carboxy glutamic acid (Gla) in vitamin K-dependent (VKD) proteins. Understanding the mechanism of carboxylation and the role of GGCX in the vitamin K cycle is of biological interest in the development of therapeutics for blood coagulation disorders. Historically, biophysical investigations and structural characterizations of GGCX have been limited due to complexities involving the availability of an appropriate model membrane system. In previous work, a hydrogen exchange mass spectrometry (HX MS) platform was developed to study the structural configuration of GGCX in a near-native nanodisc phospholipid environment. Here we have applied the nanodisc-HX MS approach to characterize specific domains of GGCX that exhibit structural rearrangements upon binding the high-affinity consensus propeptide (pCon; AVFLSREQANQVLQRRRR). pCon binding was shown to be specific for monomeric GGCX-nanodiscs and promoted enhanced structural stability to the nanodisc-integrated complex while maintaining catalytic activity in the presence of carboxylation co-substrates. Noteworthy modifications in HX of GGCX were prominently observed in GGCX peptides 491-507 and 395-401 upon pCon association, consistent with regions previously identified as sites for propeptide and glutamate binding. Several additional protein regions exhibited minor gains in solvent protection upon propeptide incorporation, providing evidence for a structural reorientation of the GGCX complex in association with VKD carboxylation. The results herein demonstrate that nanodisc-HX MS can be utilized to study molecular interactions of membrane-bound enzymes in the absence of a complete three-dimensional structure and to map dynamic rearrangements induced upon ligand binding.
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Affiliation(s)
- Christine H. Parker
- Department of Chemistry and Department of
Biology, University of North Carolina at
Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Christopher
R. Morgan
- Department
of Chemistry & Chemical Biology, Northeastern
University, Boston, Massachusetts 02115, United States
| | - Kasper D. Rand
- Department
of Chemistry & Chemical Biology, Northeastern
University, Boston, Massachusetts 02115, United States
| | - John R. Engen
- Department
of Chemistry & Chemical Biology, Northeastern
University, Boston, Massachusetts 02115, United States
| | - James
W. Jorgenson
- Department of Chemistry and Department of
Biology, University of North Carolina at
Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Darrel W. Stafford
- Department of Chemistry and Department of
Biology, University of North Carolina at
Chapel Hill, Chapel Hill, North Carolina 27599, United States
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82
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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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83
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Konermann L, Pan Y. Exploring membrane protein structural features by oxidative labeling and mass spectrometry. Expert Rev Proteomics 2014. [DOI: 10.1586/epr.12.42] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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84
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Naulin PA, Alveal NA, Barrera NP. Toward atomic force microscopy and mass spectrometry to visualize and identify lipid rafts in plasmodesmata. FRONTIERS IN PLANT SCIENCE 2014; 5:234. [PMID: 24910637 PMCID: PMC4038920 DOI: 10.3389/fpls.2014.00234] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2013] [Accepted: 05/11/2014] [Indexed: 05/08/2023]
Abstract
Plant cell-to-cell communication is mediated by nanopores called plasmodesmata (PDs) which are complex structures comprising plasma membrane (PM), highly packed endoplasmic reticulum and numerous membrane proteins. Although recent advances on proteomics have led to insights into mechanisms of transport, there is still an inadequate characterization of the lipidic composition of the PM where membrane proteins are inserted. It has been postulated that PDs could be formed by lipid rafts, however no structural evidence has shown to visualize and analyse their lipid components. In this perspective article, we discuss proposed experiments to characterize lipid rafts and proteins in the PDs. By using atomic force microscopy (AFM) and mass spectrometry (MS) of purified PD vesicles it is possible to determine the presence of lipid rafts, specific bound proteins and the lipidomic profile of the PD under physiological conditions and after changing transport permeability. In addition, MS can determine the stoichiometry of intact membrane proteins inserted in lipid rafts. This will give novel insights into the role of membrane proteins and lipid rafts on the PD structure.
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Affiliation(s)
| | | | - Nelson P. Barrera
- *Correspondence: Nelson P. Barrera, Department of Physiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Alameda 340, Santiago 8331150, Chile e-mail:
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85
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Samways DSK. Applications for mass spectrometry in the study of ion channel structure and function. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 806:237-61. [PMID: 24952185 DOI: 10.1007/978-3-319-06068-2_10] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Ion channels are intrinsic membrane proteins that form gated ion-permeable pores across biological membranes. Depending on the type, ion channels exhibit sensitivities to a diverse range of stimuli including changes in membrane potential, binding by diffusible ligands, changes in temperature and direct mechanical force. The purpose of these proteins is to facilitate the passive diffusion of ions down their respective electrochemical gradients into and out of the cell, and between intracellular compartments. In doing so, ion channels can affect transmembrane potentials and regulate the intracellular homeostasis of the important second messenger, Ca(2+). The ion channels of the plasma membrane are of particular clinical interest due to their regulation of cell excitability and cytosolic Ca(2+) levels, and the fact that they are most amenable to manipulation by exogenously applied drugs and toxins. A critical step in improving the pharmacopeia of chemicals available that influence the activity of ion channels is understanding how their three-dimensional structure imparts function. Here, progress has been slow relative to that for soluble protein structures in large part due to the limitations of applying conventional structure determination methods, such as X-ray crystallography, nuclear magnetic resonance imaging, and mass spectrometry, to membrane proteins. Although still an underutilized technique in the assessment of membrane protein structure, recent advances have pushed mass spectrometry to the fore as an important complementary approach to studying the structure and function of ion channels. In addition to revealing the subtle conformational changes in ion channel structure that accompany gating and permeation, mass spectrometry is already being used effectively for identifying tissue-specific posttranslational modifications and mRNA splice variants. Furthermore, the use of mass spectrometry for high-throughput proteomics analysis, which has proven so successful for soluble proteins, is already providing valuable insight into the functional interactions of ion channels within the context of the macromolecular-signaling complexes that they inhabit in vivo. In this chapter, the potential for mass spectrometry as a complementary approach to the study of ion channel structure and function will be reviewed with examples of its application.
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Affiliation(s)
- Damien S K Samways
- Department of Biology, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, 13699, USA,
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86
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Barylyuk K, Gülbakan B, Xie X, Zenobi R. DNA oligonucleotides: a model system with tunable binding strength to study monomer-dimer equilibria with electrospray ionization-mass spectrometry. Anal Chem 2013; 85:11902-12. [PMID: 24274465 DOI: 10.1021/ac402669e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Electrospray ionization (ESI) is increasingly used to measure binding strengths, but it is not always clear whether the ESI process introduces artifacts. Here we propose a model monomer-dimer equilibrium system based on DNA oligonucleotides to systematically explore biomolecular self-association with the ESI-mass spectrometry (MS) titration method. The oligonucleotides are designed to be self-complementary and have the same chemical composition and mass, allowing for equal ionization probability, ion transmission, and detection efficiency in ESI-MS. The only difference is the binding strength, which is determined by the nucleotide sequence and can be tuned to cover a range of dissociation constant values. This experimental design allows one to focus on the impact of ESI on the chemical equilibrium and to avoid the other typical sources of variation in ESI-MS signal responses, which yields a direct comparison of samples with different binding strengths. For a set of seven model DNA oligonucleotides, the monomer-dimer binding equilibrium was probed with the ESI-MS titration method in both positive and negative ion modes. A mathematical model describing the dependence of the monomer-to-dimer peak intensity ratio on the DNA concentration was proposed and used to extract apparent Kd values and the fraction of DNA duplex that irreversibly dissociates in the gas phase. The Kd values determined via ESI-MS titration were compared to those determined in solution with isothermal titration calorimetry and equilibrium thermal denaturation methods and were found to be significantly lower. The observed discrepancy was attributed to a greater electrospray response of dimers relative to that of monomers.
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Affiliation(s)
- Konstantin Barylyuk
- Department of Chemistry and Applied Biosciences, ETH Zurich , Wolfgang-Pauli-Strasse 10, 8093 Zurich, Switzerland
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87
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Koshy SS, Eyles SJ, Weis RM, Thompson LK. Hydrogen exchange mass spectrometry of functional membrane-bound chemotaxis receptor complexes. Biochemistry 2013; 52:8833-42. [PMID: 24274333 DOI: 10.1021/bi401261b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The transmembrane signaling mechanism of bacterial chemotaxis receptors is thought to involve changes in receptor conformation and dynamics. The receptors function in ternary complexes with two other proteins, CheA and CheW, that form extended membrane-bound arrays. Previous studies have shown that attractant binding induces a small (∼2 Å) piston displacement of one helix of the periplasmic and transmembrane domains toward the cytoplasm, but it is not clear how this signal propagates through the cytoplasmic domain to control the kinase activity of the CheA bound at the membrane-distal tip, nearly 200 Å away. The cytoplasmic domain has been shown to be highly dynamic, which raises the question of how a small piston motion could propagate through a dynamic domain to control CheA kinase activity. To address this, we have developed a method for measuring dynamics of the receptor cytoplasmic fragment (CF) in functional complexes with CheA and CheW. Hydrogen-deuterium exchange mass spectrometry (HDX-MS) measurements of global exchange of the CF demonstrate that the CF exhibits significantly slower exchange in functional complexes than in solution. Because the exchange rates in functional complexes are comparable to those of other proteins with similar structures, the CF appears to be a well-structured protein within these complexes, which is compatible with its role in propagating a signal that appears to be a tiny conformational change in the periplasmic and transmembrane domains of the receptor. We also demonstrate the feasibility of this protocol for local exchange measurements by incorporating a pepsin digest step to produce peptides with 87% sequence coverage and only 20% back exchange. This method extends HDX-MS to membrane-bound functional complexes without detergents that may perturb the stability or structure of the system.
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Affiliation(s)
- Seena S Koshy
- Department of Chemistry, ‡Department of Biochemistry and Molecular Biology, and §Program in Molecular and Cellular Biology, University of Massachusetts , Amherst, Massachusetts 01003, United States
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88
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Zhang J, Roth MJ, Chang AN, Plymire DA, Corbett JR, Greenberg BM, Patrie SM. Top-Down Mass Spectrometry on Tissue Extracts and Biofluids with Isoelectric Focusing and Superficially Porous Silica Liquid Chromatography. Anal Chem 2013; 85:10377-84. [DOI: 10.1021/ac402394w] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Junmei Zhang
- UT Southwestern Medical Center, 5323
Harry Hines Blvd., Dallas, Texas 75390-9072
| | - Michael J. Roth
- UT Southwestern Medical Center, 5323
Harry Hines Blvd., Dallas, Texas 75390-9072
| | - Audrey N. Chang
- UT Southwestern Medical Center, 5323
Harry Hines Blvd., Dallas, Texas 75390-9072
| | - Daniel A. Plymire
- UT Southwestern Medical Center, 5323
Harry Hines Blvd., Dallas, Texas 75390-9072
| | - John R. Corbett
- UT Southwestern Medical Center, 5323
Harry Hines Blvd., Dallas, Texas 75390-9072
| | | | - Steven M. Patrie
- UT Southwestern Medical Center, 5323
Harry Hines Blvd., Dallas, Texas 75390-9072
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89
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Holding AN, Lamers MH, Stephens E, Skehel JM. Hekate: software suite for the mass spectrometric analysis and three-dimensional visualization of cross-linked protein samples. J Proteome Res 2013; 12:5923-33. [PMID: 24010795 PMCID: PMC3859183 DOI: 10.1021/pr4003867] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
Chemical cross-linking
of proteins combined with mass spectrometry
provides an attractive and novel method for the analysis of native
protein structures and protein complexes. Analysis of the data however
is complex. Only a small number of cross-linked peptides are produced
during sample preparation and must be identified against a background
of more abundant native peptides. To facilitate the search and identification
of cross-linked peptides, we have developed a novel software suite,
named Hekate. Hekate is a suite of tools that address the challenges
involved in analyzing protein cross-linking experiments when combined
with mass spectrometry. The software is an integrated pipeline for
the automation of the data analysis workflow and provides a novel
scoring system based on principles of linear peptide analysis. In
addition, it provides a tool for the visualization of identified cross-links
using three-dimensional models, which is particularly useful when
combining chemical cross-linking with other structural techniques.
Hekate was validated by the comparative analysis of cytochrome c (bovine heart) against previously reported data.1 Further validation was carried out on known structural
elements of DNA polymerase III, the catalytic α-subunit of the Escherichia coli DNA replisome along with new insight
into the previously uncharacterized C-terminal domain of the protein.
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Affiliation(s)
- Andrew N Holding
- MRC Laboratory of Molecular Biology , Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
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90
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Zhang Y, Deng L, Kitova EN, Klassen JS. Dissociation of multisubunit protein-ligand complexes in the gas phase. Evidence for ligand migration. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:1573-1583. [PMID: 23943432 DOI: 10.1007/s13361-013-0712-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Revised: 06/19/2013] [Accepted: 06/27/2013] [Indexed: 06/02/2023]
Abstract
The results of collision-induced dissociation (CID) experiments performed on gaseous protonated and deprotonated ions of complexes of cholera toxin B subunit homopentamer (CTB5) with the pentasaccharide (β-D-Galp-(1→3)-β-D-GalpNAc-(1→4)[α-D-Neu5Ac-(2→3)]-β-D-Galp-(1→4)-β-D-Glcp (GM1)) and corresponding glycosphingolipid (β-D-Galp-(1→3)-β-D-GalpNAc-(1→4)[α-D-Neu5Ac-(2→3)]-β-D-Galp-(1→4)-β-D-Glcp-Cer (GM1-Cer)) ligands, and the homotetramer streptavidin (S4) with biotin (B) and 1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine-N-(biotinyl) (Btl), are reported. The protonated (CTB5 + 5GM1)(n+) ions dissociated predominantly by the loss of a single subunit, with the concomitant migration of ligand to another subunit. The simultaneous loss of ligand and subunit was observed as a minor pathway. In contrast, the deprotonated (CTB5 + 5GM1)(n-) ions dissociated preferentially by the loss of deprotonated ligand; the loss of ligand-bound and ligand-free subunit were minor pathways. The presence of ceramide (Cer) promoted ligand migration and the loss of subunit. The main dissociation pathway for the protonated and deprotonated (S4 + 4B)(n+/-) ions, as well as for deprotonated (S4 + 4Btl)(n-) ions, was loss of the ligand. However, subunit loss from the (S4 + 4B)(n+) ions was observed as a minor pathway. The (S4 + 4Btl)(n+) ions dissociated predominantly by the loss of free and ligand-bound subunit. The charge state of the complex and the collision energy were found to have little effect on the relative contribution of the different dissociation channels. Thermally-driven ligand migration between subunits was captured in the results of molecular dynamics simulations performed on protonated (CTB5 + 5GM1)(15+) ions (with a range of charge configurations) at 800 K. Notably, the migration pathway was found to be highly dependent on the charge configuration of the ion. The main conclusion of this study is that the dissociation pathways of multisubunit protein-ligand complexes in the gas phase depend, not only on the native topology of the complex, but also on structural changes that occur upon collisional activation.
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Affiliation(s)
- Yixuan Zhang
- Department of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
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91
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Xia Y, Peng L. Photoactivatable Lipid Probes for Studying Biomembranes by Photoaffinity Labeling. Chem Rev 2013; 113:7880-929. [DOI: 10.1021/cr300419p] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Yi Xia
- Aix-Marseille Université, Centre Interdisciplinaire de Nanoscience de Marseille, CNRS UMR 7325, Campus de Luminy, 13288 Marseille, France
| | - Ling Peng
- Aix-Marseille Université, Centre Interdisciplinaire de Nanoscience de Marseille, CNRS UMR 7325, Campus de Luminy, 13288 Marseille, France
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92
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Pham MD, Yu SSF, Han CC, Chan SI. Improved Mass Spectrometric Analysis of Membrane Proteins Based on Rapid and Versatile Sample Preparation on Nanodiamond Particles. Anal Chem 2013; 85:6748-55. [DOI: 10.1021/ac400713g] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Minh D. Pham
- Taiwan International Graduate Program (TIGP), Academia Sinica, Taipei 11529, Taiwan
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Steve S.-F. Yu
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Chau-Chung Han
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan
| | - Sunney I. Chan
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan
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93
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Anchors aweigh: protein localization and transport mediated by transmembrane domains. Trends Cell Biol 2013; 23:511-7. [PMID: 23806646 PMCID: PMC3783643 DOI: 10.1016/j.tcb.2013.05.005] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Revised: 05/17/2013] [Accepted: 05/20/2013] [Indexed: 11/23/2022]
Abstract
TMDs control the intracellular transport of many membrane proteins. The length and hydrophobicity of TMDs determine their sorting. Some membrane receptors for sorting TMDs have been identified. Lipid partitioning may also participate in the sorting of TMDs.
The transmembrane domains (TMDs) of integral membrane proteins have emerged as major determinants of intracellular localization and transport in the secretory and endocytic pathways. Unlike sorting signals in cytosolic domains, TMD sorting determinants are not conserved amino acid sequences but physical properties such as the length and hydrophilicity of the transmembrane span. The underlying sorting machinery is still poorly characterized, but several mechanisms have been proposed, including TMD recognition by transmembrane sorting receptors and partitioning into membrane lipid domains. Here we review the nature of TMD sorting determinants and how they may dictate transmembrane protein localization and transport.
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94
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Needham SR, Hirsch M, Rolfe DJ, Clarke DT, Zanetti-Domingues LC, Wareham R, Martin-Fernandez ML. Measuring EGFR separations on cells with ~10 nm resolution via fluorophore localization imaging with photobleaching. PLoS One 2013; 8:e62331. [PMID: 23650512 PMCID: PMC3641073 DOI: 10.1371/journal.pone.0062331] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2012] [Accepted: 03/20/2013] [Indexed: 01/17/2023] Open
Abstract
Detecting receptor dimerisation and other forms of clustering on the cell surface depends on methods capable of determining protein-protein separations with high resolution in the ~10-50 nm range. However, this distance range poses a significant challenge because it is too large for fluorescence resonance energy transfer and contains distances too small for all other techniques capable of high-resolution in cells. Here we have adapted the technique of fluorophore localisation imaging with photobleaching to measure inter-receptor separations in the cellular environment. Using the epidermal growth factor receptor, a key cancer target molecule, we demonstrate ~10 nm resolution while continuously covering the range of ~10-80 nm. By labelling the receptor on cells expressing low receptor numbers with a fluorescent antagonist we have found inter-receptor separations all the way up from 8 nm to 59 nm. Our data are consistent with epidermal growth factor receptors being able to form homo-polymers of at least 10 receptors in the absence of activating ligands.
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Affiliation(s)
- Sarah R. Needham
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Harwell Oxford, Didcot, Oxfordshire, United Kingdom
| | - Michael Hirsch
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Harwell Oxford, Didcot, Oxfordshire, United Kingdom
| | - Daniel J. Rolfe
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Harwell Oxford, Didcot, Oxfordshire, United Kingdom
| | - David T. Clarke
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Harwell Oxford, Didcot, Oxfordshire, United Kingdom
| | - Laura C. Zanetti-Domingues
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Harwell Oxford, Didcot, Oxfordshire, United Kingdom
| | - Richard Wareham
- Department of Engineering, University of Cambridge, Cambridge, United Kingdom
| | - Marisa L. Martin-Fernandez
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Harwell Oxford, Didcot, Oxfordshire, United Kingdom
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95
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Williams DM, Pukala TL. Novel insights into protein misfolding diseases revealed by ion mobility-mass spectrometry. MASS SPECTROMETRY REVIEWS 2013; 32:169-187. [PMID: 23345084 DOI: 10.1002/mas.21358] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2012] [Revised: 05/23/2012] [Accepted: 05/29/2012] [Indexed: 06/01/2023]
Abstract
Amyloid disorders incorporate a wide range of human diseases arising from the failure of a specific peptide or protein to adopt, or remain in, its native functional conformational state. These pathological conditions, such as Parkinson's disease, Alzheimer's disease and Huntington's disease are highly debilitating, exact enormous costs on both individuals and society, and are predicted to increase in prevalence. Consequently, they form the focus of a topical and rich area of current scientific research. A major goal in attempts to understand and treat protein misfolding diseases is to define the structures and interactions of protein species intermediate between fully folded and aggregated, and extract a description of the aggregation process. This has proven a difficult task due to the inability of traditional structural biology approaches to analyze structurally heterogeneous systems. Continued developments in instrumentation and analytical approaches have seen ion mobility-mass spectrometry (IM-MS) emerge as a complementary approach for protein structure determination, and in some cases, a structural biology tool in its own right. IM-MS is well suited to the study of protein misfolding, and has already yielded significant structural information for selected amyloidogenic systems during the aggregation process. This review describes IM-MS for protein structure investigation, and provides a summary of current research highlighting how this methodology has unequivocally and unprecedentedly provided structural and mechanistic detail pertaining to the oligomerization of a variety of disease related proteins.
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Affiliation(s)
- Danielle M Williams
- School of Chemistry and Physics, The University of Adelaide, North Terrace, Adelaide, South Australia 5005, Australia
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96
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Abstract
Mass spectrometry (MS) of intact soluble protein complexes has emerged as a powerful technique to study the stoichiometry, structure-function and dynamics of protein assemblies. Recent developments have extended this technique to the study of membrane protein complexes, where it has already revealed subunit stoichiometries and specific phospholipid interactions. Here we describe a protocol for MS of membrane protein complexes. The protocol begins with the preparation of the membrane protein complex, enabling not only the direct assessment of stoichiometry, delipidation and quality of the target complex but also the evaluation of the purification strategy. A detailed list of compatible nonionic detergents is included, along with a protocol for screening detergents to find an optimal one for MS, biochemical and structural studies. This protocol also covers the preparation of lipids for protein-lipid binding studies and includes detailed settings for a quadrupole time-of-flight (Q-TOF) mass spectrometer after the introduction of complexes from gold-coated nanoflow capillaries.
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Affiliation(s)
- Arthur Laganowsky
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 5QY, UK
| | - Eamonn Reading
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 5QY, UK
| | - Jonathan T.S. Hopper
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 5QY, UK
| | - Carol V. Robinson
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 5QY, UK
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97
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Schey KL, Grey AC, Nicklay JJ. Mass spectrometry of membrane proteins: a focus on aquaporins. Biochemistry 2013; 52:3807-17. [PMID: 23394619 DOI: 10.1021/bi301604j] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Membrane proteins are abundant, critically important biomolecules that conduct essential functions in all cells and are the targets of a significant number of therapeutic drugs. However, the analysis of their expression, modification, protein-protein interactions, and structure by mass spectrometry has lagged behind similar studies of soluble proteins. Here we review the limitations to analysis of integral membrane and membrane-associated proteins and highlight advances in sample preparation and mass spectrometry methods that have led to the successful analysis of this protein class. Advances in the analysis of membrane protein posttranslational modification, protein-protein interaction, protein structure, and tissue distributions by imaging mass spectrometry are discussed. Furthermore, we focus our discussion on the application of mass spectrometry for the analysis of aquaporins as a prototypical integral membrane protein and how advances in analytical methods have revealed new biological insights into the structure and function of this family of proteins.
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Affiliation(s)
- Kevin L Schey
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States.
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98
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Abstract
Integral membrane proteins reside within the bilayer membranes that surround cells and organelles, playing critical roles in movement of molecules across them and the transduction of energy and signals. While their extreme amphipathicity presents technical challenges, biological mass spectrometry has been applied to all aspects of membrane protein chemistry and biology, including analysis of primary, secondary, tertiary, and quaternary structures as well as the dynamics that accompany functional cycles and catalysis.
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Affiliation(s)
- Julian P Whitelegge
- The Pasarow Mass Spectrometry Laboratory, The NPI-Semel Institute for Neuroscience and Human Behavior, The David Geffen School of Medicine, University of California, Los Angeles, 760 Westwood Plaza, Los Angeles, California 90095, United States.
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99
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Shin JB, Krey JF, Hassan A, Metlagel Z, Tauscher AN, Pagana JM, Sherman NE, Jeffery ED, Spinelli KJ, Zhao H, Wilmarth PA, Choi D, David LL, Auer M, Barr-Gillespie PG. Molecular architecture of the chick vestibular hair bundle. Nat Neurosci 2013; 16:365-74. [PMID: 23334578 PMCID: PMC3581746 DOI: 10.1038/nn.3312] [Citation(s) in RCA: 143] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Accepted: 12/17/2012] [Indexed: 12/31/2022]
Abstract
Hair bundles of the inner ear have a specialized structure and protein composition that underlies their sensitivity to mechanical stimulation. Using mass spectrometry, we identified and quantified >1,100 proteins, present from a few to 400,000 copies per stereocilium, from purified chick bundles; 336 of these were significantly enriched in bundles. Bundle proteins that we detected have been shown to regulate cytoskeleton structure and dynamics, energy metabolism, phospholipid synthesis and cell signaling. Three-dimensional imaging using electron tomography allowed us to count the number of actin-actin cross-linkers and actin-membrane connectors; these values compared well to those obtained from mass spectrometry. Network analysis revealed several hub proteins, including RDX (radixin) and SLC9A3R2 (NHERF2), which interact with many bundle proteins and may perform functions essential for bundle structure and function. The quantitative mass spectrometry of bundle proteins reported here establishes a framework for future characterization of dynamic processes that shape bundle structure and function.
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Affiliation(s)
- Jung-Bum Shin
- Department of Neuroscience, University of Virginia, Charlottesville, Virginia, USA
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100
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Ngounou Wetie AG, Sokolowska I, Woods AG, Roy U, Loo JA, Darie CC. Investigation of stable and transient protein-protein interactions: Past, present, and future. Proteomics 2013. [PMID: 23193082 DOI: 10.1002/pmic.201200328] [Citation(s) in RCA: 107] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
This article presents an overview of the literature and a review of recent advances in the analysis of stable and transient protein-protein interactions (PPIs) with a focus on their function within cells, organs, and organisms. The significance of PTMs within the PPIs is also discussed. We focus on methods to study PPIs and methods of detecting PPIs, with particular emphasis on electrophoresis-based and MS-based investigation of PPIs, including specific examples. The validation of PPIs is emphasized and the limitations of the current methods for studying stable and transient PPIs are discussed. Perspectives regarding PPIs, with focus on bioinformatics and transient PPIs are also provided.
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Affiliation(s)
- Armand G Ngounou Wetie
- Biochemistry & Proteomics Group, Department of Chemistry & Biomolecular Science, Clarkson University, Potsdam, NY 13699, USA
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