51
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Hu B, Yao ZP. Mobility of Proteins in Porous Substrates under Electrospray Ionization Conditions. Anal Chem 2016; 88:5585-9. [DOI: 10.1021/acs.analchem.6b00894] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Bin Hu
- State
Key Laboratory for Chirosciences, Food Safety and Technology Research
Centre and Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong
Kong SAR, China
- State
Key Laboratory of Chinese Medicine and Molecular Pharmacology (Incubation)
and Shenzhen Key Laboratory
of Food Biological Safety Control, Shenzhen Research Institute of The Hong Kong Polytechnic University, Shenzhen, 518057, China
| | - Zhong-Ping Yao
- State
Key Laboratory for Chirosciences, Food Safety and Technology Research
Centre and Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong
Kong SAR, China
- Key Laboratory of Natural Resources of Changbai Mountain and Functional Molecules (Yanbian University), Ministry of Education, Yanji, 133002, China
- State
Key Laboratory of Chinese Medicine and Molecular Pharmacology (Incubation)
and Shenzhen Key Laboratory
of Food Biological Safety Control, Shenzhen Research Institute of The Hong Kong Polytechnic University, Shenzhen, 518057, China
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52
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Ewing MA, Glover MS, Clemmer DE. Hybrid ion mobility and mass spectrometry as a separation tool. J Chromatogr A 2016; 1439:3-25. [DOI: 10.1016/j.chroma.2015.10.080] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 10/05/2015] [Accepted: 10/21/2015] [Indexed: 11/29/2022]
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53
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Zhang L, Li W, Fang T, Li S. Ab initio molecular dynamics with intramolecular noncovalent interactions for unsolvated polypeptides. Theor Chem Acc 2016. [DOI: 10.1007/s00214-015-1799-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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54
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Allen SJ, Giles K, Gilbert T, Bush MF. Ion mobility mass spectrometry of peptide, protein, and protein complex ions using a radio-frequency confining drift cell. Analyst 2016; 141:884-91. [DOI: 10.1039/c5an02107c] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A new drift cell was used to measure collision cross sections and characterize the origins of ion mobility peak broadening for biological molecules and assemblies.
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55
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Liu FC, Kirk SR, Bleiholder C. On the structural denaturation of biological analytes in trapped ion mobility spectrometry – mass spectrometry. Analyst 2016; 141:3722-30. [DOI: 10.1039/c5an02399h] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Trapped ion mobility spectra recorded for ubiquitin are consistent with structures reported for the native state by NMR.
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Affiliation(s)
- Fanny C. Liu
- Department of Chemistry and Biochemistry
- Florida State University
- Tallahassee
- USA
| | - Samuel R. Kirk
- Department of Chemistry and Biochemistry
- Florida State University
- Tallahassee
- USA
| | - Christian Bleiholder
- Department of Chemistry and Biochemistry
- Florida State University
- Tallahassee
- USA
- Institute of Molecular Biophysics
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56
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Zhang W, Quernheim M, Räder HJ, Müllen K. Collision-Induced Dissociation Ion Mobility Mass Spectrometry for the Elucidation of Unknown Structures in Strained Polycyclic Aromatic Hydrocarbon Macrocycles. Anal Chem 2015; 88:952-9. [DOI: 10.1021/acs.analchem.5b03704] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Wen Zhang
- Max Planck Institute for Polymer Research, Ackermannweg
10, D55128 Mainz, Germany
| | - Martin Quernheim
- Max Planck Institute for Polymer Research, Ackermannweg
10, D55128 Mainz, Germany
| | - Hans Joachim Räder
- Max Planck Institute for Polymer Research, Ackermannweg
10, D55128 Mainz, Germany
| | - Klaus Müllen
- Max Planck Institute for Polymer Research, Ackermannweg
10, D55128 Mainz, Germany
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57
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Rajabi K, Ashcroft AE, Radford SE. Mass spectrometric methods to analyze the structural organization of macromolecular complexes. Methods 2015; 89:13-21. [DOI: 10.1016/j.ymeth.2015.03.004] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Revised: 02/25/2015] [Accepted: 03/06/2015] [Indexed: 01/14/2023] Open
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58
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Konijnenberg A, van Dyck JF, Kailing LL, Sobott F. Extending native mass spectrometry approaches to integral membrane proteins. Biol Chem 2015; 396:991-1002. [DOI: 10.1515/hsz-2015-0136] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Accepted: 07/06/2015] [Indexed: 12/23/2022]
Abstract
Abstract
Recent developments in native mass spectrometry and ion mobility have made it possible to analyze the composition and structure of membrane protein complexes in the gas-phase. In this short review we discuss the experimental strategies that allow to elucidate aspects of the dynamic structure of these important drug targets, such as the structural effects of lipid binding or detection of co-populated conformational and assembly states during gating on an ion channel. As native mass spectrometry relies on nano-electrospray of natively reconstituted proteins, a number of commonly used lipid- and detergent-based reconstitution systems have been evaluated for their compatibility with this approach, and parameters for the release of intact, native-like folded membrane proteins studied in the gas-phase. The strategy thus developed can be employed for the investigation of the subunit composition and stoichiometry, oligomeric state, conformational changes, and lipid and drug binding of integral membrane proteins.
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59
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Borysik AJ. Structure and dynamics of a protein-surfactant assembly studied by ion-mobility mass spectrometry and molecular dynamics simulations. Anal Chem 2015; 87:8970-6. [PMID: 26266526 DOI: 10.1021/acs.analchem.5b02172] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The structure and dynamics of a protein-surfactant assembly studied by ion-mobility mass spectrometry (IMS) and vacuum molecular dynamics (MD) simulations is reported. Direct evidence is provided for the ability of the surfactant dodecyl-β-D-maltoside (DDM) to prevent charge-induced unfolding of the membrane protein (PagP) in the gas-phase. Restraints obtained by IMS are used to map the surfactant positions onto the protein surface. Surfactants occupying more exposed positions at the apexes of the β-barrel structure are most in-line with the experimental observations. MD simulations provide additional evidence for this assembly organization through surfactant inversion and migration on the protein structure in the absence of solvent. Surfactant migration entails a net shift from apolar membrane spanning regions to more polar regions of the protein structure with the DDM molecule remaining attached to the protein via headgroup interactions. These data provide evidence for the role of protein-DDM headgroup interactions in stabilizing membrane protein structure from gas-phase unfolding.
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Affiliation(s)
- Antoni J Borysik
- Department of Chemistry, King's College London , Britannia House, London SE1 1DB, United Kingdom
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60
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Electron cryomicroscopy observation of rotational states in a eukaryotic V-ATPase. Nature 2015; 521:241-5. [PMID: 25971514 DOI: 10.1038/nature14365] [Citation(s) in RCA: 217] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 03/05/2015] [Indexed: 01/19/2023]
Abstract
Eukaryotic vacuolar H(+)-ATPases (V-ATPases) are rotary enzymes that use energy from hydrolysis of ATP to ADP to pump protons across membranes and control the pH of many intracellular compartments. ATP hydrolysis in the soluble catalytic region of the enzyme is coupled to proton translocation through the membrane-bound region by rotation of a central rotor subcomplex, with peripheral stalks preventing the entire membrane-bound region from turning with the rotor. The eukaryotic V-ATPase is the most complex rotary ATPase: it has three peripheral stalks, a hetero-oligomeric proton-conducting proteolipid ring, several subunits not found in other rotary ATPases, and is regulated by reversible dissociation of its catalytic and proton-conducting regions. Studies of ATP synthases, V-ATPases, and bacterial/archaeal V/A-ATPases have suggested that flexibility is necessary for the catalytic mechanism of rotary ATPases, but the structures of different rotational states have never been observed experimentally. Here we use electron cryomicroscopy to obtain structures for three rotational states of the V-ATPase from the yeast Saccharomyces cerevisiae. The resulting series of structures shows ten proteolipid subunits in the c-ring, setting the ATP:H(+) ratio for proton pumping by the V-ATPase at 3:10, and reveals long and highly tilted transmembrane α-helices in the a-subunit that interact with the c-ring. The three different maps reveal the conformational changes that occur to couple rotation in the symmetry-mismatched soluble catalytic region to the membrane-bound proton-translocating region. Almost all of the subunits of the enzyme undergo conformational changes during the transitions between these three rotational states. The structures of these states provide direct evidence that deformation during rotation enables the smooth transmission of power through rotary ATPases.
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61
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Bleiholder C, Johnson NR, Contreras S, Wyttenbach T, Bowers MT. Molecular Structures and Ion Mobility Cross Sections: Analysis of the Effects of He and N2 Buffer Gas. Anal Chem 2015; 87:7196-203. [DOI: 10.1021/acs.analchem.5b01429] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Christian Bleiholder
- Department of Chemistry and
Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Nicholas R. Johnson
- Department of Chemistry and
Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Stephanie Contreras
- Department of Chemistry and
Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Thomas Wyttenbach
- Department of Chemistry and
Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Michael T. Bowers
- Department of Chemistry and
Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
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62
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Politis A, Borysik AJ. Assembling the pieces of macromolecular complexes: Hybrid structural biology approaches. Proteomics 2015; 15:2792-803. [DOI: 10.1002/pmic.201400507] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 01/26/2015] [Accepted: 02/24/2015] [Indexed: 01/14/2023]
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63
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Mehmood S, Allison TM, Robinson CV. Mass Spectrometry of Protein Complexes: From Origins to Applications. Annu Rev Phys Chem 2015; 66:453-74. [DOI: 10.1146/annurev-physchem-040214-121732] [Citation(s) in RCA: 140] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Shahid Mehmood
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom;
| | - Timothy M. Allison
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom;
| | - Carol V. Robinson
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom;
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64
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Collision Cross Sections for Structural Proteomics. Structure 2015; 23:791-9. [DOI: 10.1016/j.str.2015.02.010] [Citation(s) in RCA: 191] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 02/13/2015] [Accepted: 02/18/2015] [Indexed: 01/19/2023]
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65
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Boeri Erba E, Petosa C. The emerging role of native mass spectrometry in characterizing the structure and dynamics of macromolecular complexes. Protein Sci 2015; 24:1176-92. [PMID: 25676284 DOI: 10.1002/pro.2661] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Revised: 02/06/2015] [Accepted: 02/06/2015] [Indexed: 12/31/2022]
Abstract
Mass spectrometry (MS) is a powerful tool for determining the mass of biomolecules with high accuracy and sensitivity. MS performed under so-called "native conditions" (native MS) can be used to determine the mass of biomolecules that associate noncovalently. Here we review the application of native MS to the study of protein-ligand interactions and its emerging role in elucidating the structure of macromolecular assemblies, including soluble and membrane protein complexes. Moreover, we discuss strategies aimed at determining the stoichiometry and topology of subunits by inducing partial dissociation of the holo-complex. We also survey recent developments in "native top-down MS", an approach based on Fourier Transform MS, whereby covalent bonds are broken without disrupting non-covalent interactions. Given recent progress, native MS is anticipated to play an increasingly important role for researchers interested in the structure of macromolecular complexes.
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Affiliation(s)
- Elisabetta Boeri Erba
- Université Grenoble Alpes, Institut de Biologie Structurale (IBS), 71 Avenue des Martyrs, F-38044, Grenoble, France.,Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), DSV, IBS, F-38044, Grenoble, France.,Centre National de la Recherche Scientifique (CNRS), IBS, F-38044, Grenoble, France
| | - Carlo Petosa
- Université Grenoble Alpes, Institut de Biologie Structurale (IBS), 71 Avenue des Martyrs, F-38044, Grenoble, France.,Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), DSV, IBS, F-38044, Grenoble, France.,Centre National de la Recherche Scientifique (CNRS), IBS, F-38044, Grenoble, France
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66
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Gülbakan B, Barylyuk K, Zenobi R. Determination of thermodynamic and kinetic properties of biomolecules by mass spectrometry. Curr Opin Biotechnol 2015; 31:65-72. [DOI: 10.1016/j.copbio.2014.08.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 08/08/2014] [Accepted: 08/12/2014] [Indexed: 01/13/2023]
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67
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Bleiholder C. A local collision probability approximation for predicting momentum transfer cross sections. Analyst 2015; 140:6804-13. [DOI: 10.1039/c5an00712g] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The local collision probability approximation (LCPA) method is introduced to compute molecular momentum transfer cross sections for comparison to ion mobility experiments.
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Affiliation(s)
- Christian Bleiholder
- Department of Chemistry and Biochemistry
- Florida State University
- Florida State University
- Tallahassee
- USA
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68
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Zhou A, Rohou A, Schep DG, Bason JV, Montgomery MG, Walker JE, Grigorieff N, Rubinstein JL. Structure and conformational states of the bovine mitochondrial ATP synthase by cryo-EM. eLife 2015; 4:e10180. [PMID: 26439008 PMCID: PMC4718723 DOI: 10.7554/elife.10180] [Citation(s) in RCA: 225] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 10/05/2015] [Indexed: 02/02/2023] Open
Abstract
Adenosine triphosphate (ATP), the chemical energy currency of biology, is synthesized in eukaryotic cells primarily by the mitochondrial ATP synthase. ATP synthases operate by a rotary catalytic mechanism where proton translocation through the membrane-inserted FO region is coupled to ATP synthesis in the catalytic F1 region via rotation of a central rotor subcomplex. We report here single particle electron cryomicroscopy (cryo-EM) analysis of the bovine mitochondrial ATP synthase. Combining cryo-EM data with bioinformatic analysis allowed us to determine the fold of the a subunit, suggesting a proton translocation path through the FO region that involves both the a and b subunits. 3D classification of images revealed seven distinct states of the enzyme that show different modes of bending and twisting in the intact ATP synthase. Rotational fluctuations of the c8-ring within the FO region support a Brownian ratchet mechanism for proton-translocation-driven rotation in ATP synthases.
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Affiliation(s)
- Anna Zhou
- The Hospital for Sick Children Research Institute, Toronto, Canada,Department of Medical Biophysics, The University of Toronto, Ontario, Canada
| | - Alexis Rohou
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Daniel G Schep
- The Hospital for Sick Children Research Institute, Toronto, Canada,Department of Medical Biophysics, The University of Toronto, Ontario, Canada
| | - John V Bason
- MRC Mitochondrial Biology Unit, Cambridge, United Kingdom
| | | | - John E Walker
- MRC Mitochondrial Biology Unit, Cambridge, United Kingdom, (JEW)
| | - Nikolaus Grigorieff
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States, (NG)
| | - John L Rubinstein
- The Hospital for Sick Children Research Institute, Toronto, Canada,Department of Medical Biophysics, The University of Toronto, Ontario, Canada,Department of Biochemistry, The University of Toronto, Ontario, Canada, (JLR)
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69
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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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70
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Topological models of heteromeric protein assemblies from mass spectrometry: application to the yeast eIF3:eIF5 complex. ACTA ACUST UNITED AC 2014; 22:117-28. [PMID: 25544043 PMCID: PMC4306531 DOI: 10.1016/j.chembiol.2014.11.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 10/07/2014] [Accepted: 11/07/2014] [Indexed: 02/05/2023]
Abstract
Describing, understanding, and modulating the function of the cell require elucidation of the structures of macromolecular assemblies. Here, we describe an integrative method for modeling heteromeric complexes using as a starting point disassembly pathways determined by native mass spectrometry (MS). In this method, the pathway data and other available information are encoded as a scoring function on the positions of the subunits of the complex. The method was assessed on its ability to reproduce the native contacts in five benchmark cases with simulated MS data and two cases with real MS data. To illustrate the power of our method, we purified the yeast initiation factor 3 (eIF3) complex and characterized it by native MS and chemical crosslinking MS. We established substoichiometric binding of eIF5 and derived a model for the five-subunit eIF3 complex, at domain level, consistent with its role as a scaffold for other initiation factors. Integrative MS method allows topological characterization of heteromeric complexes Intersubunit crosslinks increase the precision of the predicted topologies A 3D model of eIF3:eIF5 complex was built using restraints from MS-based methods Integrative modeling reveals two submodules within eIF3: eIF3b:i:g and eIF3a:c
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71
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Zhao J, Rubinstein JL. The study of vacuolar-type ATPases by single particle electron microscopy. Biochem Cell Biol 2014; 92:460-6. [DOI: 10.1139/bcb-2014-0086] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Nature’s molecular machines often work through the concerted action of many different protein subunits, which can give rise to large structures with complex activities. Vacuolar-type ATPases (V-ATPases) are membrane-embedded protein assemblies with a unique rotary catalytic mechanism. The dynamic nature and instability of V-ATPases make structural and functional studies of these enzymes challenging. Electron microscopy (EM) techniques, especially single particle electron cryomicroscopy (cryo-EM) and negative-stain EM, have provided extensive insight into the structure and function of these protein complexes. This minireview outlines what has been learned about V-ATPases using electron microscopy, highlights current challenges for their structural study, and discusses what cryo-EM will allow us to learn about these fascinating enzymes in the future.
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Affiliation(s)
- Jianhua Zhao
- The Hospital for Sick Children Research Institute, 686 Bay Street, Toronto, ON M5G 0A4, Canada
- Department of Medical Biophysics, The University of Toronto, 1 Kings College Circle, Toronto, ON M5S 1A8, Canada
| | - John L. Rubinstein
- The Hospital for Sick Children Research Institute, 686 Bay Street, Toronto, ON M5G 0A4, Canada
- Department of Medical Biophysics, The University of Toronto, 1 Kings College Circle, Toronto, ON M5S 1A8, Canada
- Department of Biochemistry, The University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada
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72
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Mehmood S, Marcoux J, Hopper JTS, Allison TM, Liko I, Borysik AJ, Robinson CV. Charge reduction stabilizes intact membrane protein complexes for mass spectrometry. J Am Chem Soc 2014; 136:17010-2. [PMID: 25402655 DOI: 10.1021/ja510283g] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The study of intact soluble protein assemblies by means of mass spectrometry is providing invaluable contributions to structural biology and biochemistry. A recent breakthrough has enabled similar study of membrane protein complexes, following their release from detergent micelles in the gas phase. Careful optimization of mass spectrometry conditions, particularly with respect to energy regimes, is essential for maintaining compact folded states as detergent is removed. However, many of the saccharide detergents widely employed in structural biology can cause unfolding of membrane proteins in the gas phase. Here, we investigate the potential of charge reduction by introducing three membrane protein complexes from saccharide detergents and show how reducing their overall charge enables generation of compact states, as evidenced by ion mobility mass spectrometry. We find that charge reduction stabilizes the oligomeric state and enhances the stability of lipid-bound complexes. This finding is significant since maintaining native-like membrane proteins enables ligand binding to be assessed from a range of detergents that retain solubility while protecting the overall fold.
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Affiliation(s)
- Shahid Mehmood
- Department of Chemistry, University of Oxford , Oxford, U.K
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73
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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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74
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Marcoux J, Politis A, Rinehart D, Marshall DP, Wallace MI, Tamm LK, Robinson CV. Mass spectrometry defines the C-terminal dimerization domain and enables modeling of the structure of full-length OmpA. Structure 2014; 22:781-90. [PMID: 24746938 DOI: 10.1016/j.str.2014.03.004] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 02/26/2014] [Accepted: 03/17/2014] [Indexed: 11/17/2022]
Abstract
The transmembrane domain of the outer membrane protein A (OmpA) from Escherichia coli is an excellent model for structural and folding studies of β-barrel membrane proteins. However, full-length OmpA resists crystallographic efforts, and the link between its function and tertiary structure remains controversial. Here we use site-directed mutagenesis and mass spectrometry of different constructs of OmpA, released in the gas phase from detergent micelles, to define the minimal region encompassing the C-terminal dimer interface. Combining knowledge of the location of the dimeric interface with molecular modeling and ion mobility data allows us to propose a low-resolution model for the full-length OmpA dimer. Our model of the dimer is in remarkable agreement with experimental ion mobility data, with none of the unfolding or collapse observed for full-length monomeric OmpA, implying that dimer formation stabilizes the overall structure and prevents collapse of the flexible linker that connects the two domains.
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Affiliation(s)
- Julien Marcoux
- Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, UK
| | - Argyris Politis
- Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, UK
| | - Dennis Rinehart
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
| | - David P Marshall
- Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, UK
| | - Mark I Wallace
- Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, UK
| | - Lukas K Tamm
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
| | - Carol V Robinson
- Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, UK.
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75
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