551
|
Abstract
Membrane proteins interact with a myriad of lipid species in the biological membrane, leading to a bewildering number of possible protein-lipid assemblies. Despite this inherent complexity, the identification of specific protein-lipid interactions and the crucial role of lipids in the folding, structure, and function of membrane proteins is emerging from an increasing number of reports. Fundamental questions remain, however, regarding the ability of specific lipid binding events to membrane proteins to alter remote binding sites for lipids of a different type, a property referred to as allostery [Monod J, Wyman J, Changeux JP (1965) J Mol Biol 12:88-118]. Here, we use native mass spectrometry to determine the allosteric nature of heterogeneous lipid binding events to membrane proteins. We monitored individual lipid binding events to the ammonia channel (AmtB) from Escherichia coli, enabling determination of their equilibrium binding constants. We found that different lipid pairs display a range of allosteric modulation. In particular, the binding of phosphatidylethanolamine and cardiolipin-like molecules to AmtB exhibited the largest degree of allosteric modulation, inspiring us to determine the cocrystal structure of AmtB in this lipid environment. The 2.45-Å resolution structure reveals a cardiolipin-like molecule bound to each subunit of the trimeric complex. Mutation of a single residue in AmtB abolishes the positive allosteric modulation observed for binding phosphatidylethanolamine and cardiolipin-like molecules. Our results demonstrate that specific lipid-protein interactions can act as allosteric modulators for the binding of different lipid types to integral membrane proteins.
Collapse
|
552
|
Bern M, Caval T, Kil YJ, Tang W, Becker C, Carlson E, Kletter D, Sen KI, Galy N, Hagemans D, Franc V, Heck AJR. Parsimonious Charge Deconvolution for Native Mass Spectrometry. J Proteome Res 2018; 17:1216-1226. [PMID: 29376659 PMCID: PMC5838638 DOI: 10.1021/acs.jproteome.7b00839] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Indexed: 12/20/2022]
Abstract
Charge deconvolution infers the mass from mass over charge (m/z) measurements in electrospray ionization mass spectra. When applied over a wide input m/z or broad target mass range, charge-deconvolution algorithms can produce artifacts, such as false masses at one-half or one-third of the correct mass. Indeed, a maximum entropy term in the objective function of MaxEnt, the most commonly used charge deconvolution algorithm, favors a deconvolved spectrum with many peaks over one with fewer peaks. Here we describe a new "parsimonious" charge deconvolution algorithm that produces fewer artifacts. The algorithm is especially well-suited to high-resolution native mass spectrometry of intact glycoproteins and protein complexes. Deconvolution of native mass spectra poses special challenges due to salt and small molecule adducts, multimers, wide mass ranges, and fewer and lower charge states. We demonstrate the performance of the new deconvolution algorithm on a range of samples. On the heavily glycosylated plasma properdin glycoprotein, the new algorithm could deconvolve monomer and dimer simultaneously and, when focused on the m/z range of the monomer, gave accurate and interpretable masses for glycoforms that had previously been analyzed manually using m/z peaks rather than deconvolved masses. On therapeutic antibodies, the new algorithm facilitated the analysis of extensions, truncations, and Fab glycosylation. The algorithm facilitates the use of native mass spectrometry for the qualitative and quantitative analysis of protein and protein assemblies.
Collapse
Affiliation(s)
- Marshall Bern
- Protein
Metrics, Inc., San Carlos, California 94070, United States
| | - Tomislav Caval
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, Science4Life, Utrecht University and Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Yong J. Kil
- Protein
Metrics, Inc., San Carlos, California 94070, United States
| | - Wilfred Tang
- Protein
Metrics, Inc., San Carlos, California 94070, United States
| | | | - Eric Carlson
- Protein
Metrics, Inc., San Carlos, California 94070, United States
| | - Doron Kletter
- Protein
Metrics, Inc., San Carlos, California 94070, United States
| | - K. Ilker Sen
- Protein
Metrics, Inc., San Carlos, California 94070, United States
| | - Nicolas Galy
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, Science4Life, Utrecht University and Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Dominique Hagemans
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, Science4Life, Utrecht University and Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Vojtech Franc
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, Science4Life, Utrecht University and Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Albert J. R. Heck
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, Science4Life, Utrecht University and Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands
| |
Collapse
|
553
|
Politis A, Schmidt C. Structural characterisation of medically relevant protein assemblies by integrating mass spectrometry with computational modelling. J Proteomics 2018; 175:34-41. [DOI: 10.1016/j.jprot.2017.04.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 04/13/2017] [Accepted: 04/18/2017] [Indexed: 01/14/2023]
|
554
|
Hochberg GKA, Shepherd DA, Marklund EG, Santhanagoplan I, Degiacomi MT, Laganowsky A, Allison TM, Basha E, Marty MT, Galpin MR, Struwe WB, Baldwin AJ, Vierling E, Benesch JLP. Structural principles that enable oligomeric small heat-shock protein paralogs to evolve distinct functions. Science 2018; 359:930-935. [PMID: 29472485 PMCID: PMC6587588 DOI: 10.1126/science.aam7229] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Revised: 09/25/2017] [Accepted: 01/08/2018] [Indexed: 12/26/2022]
Abstract
Oligomeric proteins assemble with exceptional selectivity, even in the presence of closely related proteins, to perform their cellular roles. We show that most proteins related by gene duplication of an oligomeric ancestor have evolved to avoid hetero-oligomerization and that this correlates with their acquisition of distinct functions. We report how coassembly is avoided by two oligomeric small heat-shock protein paralogs. A hierarchy of assembly, involving intermediates that are populated only fleetingly at equilibrium, ensures selective oligomerization. Conformational flexibility at noninterfacial regions in the monomers prevents coassembly, allowing interfaces to remain largely conserved. Homomeric oligomers must overcome the entropic benefit of coassembly and, accordingly, homomeric paralogs comprise fewer subunits than homomers that have no paralogs.
Collapse
Affiliation(s)
- Georg K A Hochberg
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Dale A Shepherd
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Erik G Marklund
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Indu Santhanagoplan
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, USA
| | - Matteo T Degiacomi
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Arthur Laganowsky
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Timothy M Allison
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Eman Basha
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, USA
| | - Michael T Marty
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Martin R Galpin
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Weston B Struwe
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Andrew J Baldwin
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Elizabeth Vierling
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, USA
| | - Justin L P Benesch
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK.
| |
Collapse
|
555
|
Eyers CE, Vonderach M, Ferries S, Jeacock K, Eyers PA. Understanding protein–drug interactions using ion mobility–mass spectrometry. Curr Opin Chem Biol 2018; 42:167-176. [DOI: 10.1016/j.cbpa.2017.12.013] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 12/08/2017] [Accepted: 12/22/2017] [Indexed: 01/23/2023]
|
556
|
Smith FD, Esseltine JL, Nygren PJ, Veesler D, Byrne DP, Vonderach M, Strashnov I, Eyers CE, Eyers PA, Langeberg LK, Scott JD. Local protein kinase A action proceeds through intact holoenzymes. Science 2018. [PMID: 28642438 DOI: 10.1126/science.aaj1669] [Citation(s) in RCA: 150] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Hormones can transmit signals through adenosine 3',5'-monophosphate (cAMP) to precise intracellular locations. The fidelity of these responses relies on the activation of localized protein kinase A (PKA) holoenzymes. Association of PKA regulatory type II (RII) subunits with A-kinase-anchoring proteins (AKAPs) confers location, and catalytic (C) subunits phosphorylate substrates. Single-particle electron microscopy demonstrated that AKAP79 constrains RII-C subassemblies within 150 to 250 angstroms of its targets. Native mass spectrometry established that these macromolecular assemblies incorporated stoichiometric amounts of cAMP. Chemical-biology- and live cell-imaging techniques revealed that catalytically active PKA holoenzymes remained intact within the cytoplasm. These findings indicate that the parameters of anchored PKA holoenzyme action are much more restricted than originally anticipated.
Collapse
Affiliation(s)
- F Donelson Smith
- Howard Hughes Medical Institute, Department of Pharmacology, University of Washington, Seattle, WA 98195, USA
| | - Jessica L Esseltine
- Howard Hughes Medical Institute, Department of Pharmacology, University of Washington, Seattle, WA 98195, USA
| | - Patrick J Nygren
- Howard Hughes Medical Institute, Department of Pharmacology, University of Washington, Seattle, WA 98195, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Dominic P Byrne
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Matthias Vonderach
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Ilya Strashnov
- School of Chemistry, The University of Manchester, Manchester M13 9PL, UK
| | - Claire E Eyers
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Patrick A Eyers
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Lorene K Langeberg
- Howard Hughes Medical Institute, Department of Pharmacology, University of Washington, Seattle, WA 98195, USA
| | - John D Scott
- Howard Hughes Medical Institute, Department of Pharmacology, University of Washington, Seattle, WA 98195, USA.
| |
Collapse
|
557
|
Lipids Shape the Electron Acceptor-Binding Site of the Peripheral Membrane Protein Dihydroorotate Dehydrogenase. Cell Chem Biol 2018; 25:309-317.e4. [PMID: 29358052 PMCID: PMC5856493 DOI: 10.1016/j.chembiol.2017.12.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 11/21/2017] [Accepted: 12/20/2017] [Indexed: 11/23/2022]
Abstract
The interactions between proteins and biological membranes are important for drug development, but remain notoriously refractory to structural investigation. We combine non-denaturing mass spectrometry (MS) with molecular dynamics (MD) simulations to unravel the connections among co-factor, lipid, and inhibitor binding in the peripheral membrane protein dihydroorotate dehydrogenase (DHODH), a key anticancer target. Interrogation of intact DHODH complexes by MS reveals that phospholipids bind via their charged head groups at a limited number of sites, while binding of the inhibitor brequinar involves simultaneous association with detergent molecules. MD simulations show that lipids support flexible segments in the membrane-binding domain and position the inhibitor and electron acceptor-binding site away from the membrane surface, similar to the electron acceptor-binding site in respiratory chain complex I. By complementing MS with MD simulations, we demonstrate how a peripheral membrane protein uses lipids to modulate its structure in a similar manner as integral membrane proteins. Mass spectrometry captures intact complexes of the peripheral membrane protein DHODH Detergent removal in the gas phase reveals lipid and co-factor binding DHODH attaches to the membrane by binding charged phospholipids Lipids stabilize the flexible substrate- and drug-binding site
Collapse
|
558
|
Protonation state of glutamate 73 regulates the formation of a specific dimeric association of mVDAC1. Proc Natl Acad Sci U S A 2018; 115:E172-E179. [PMID: 29279396 PMCID: PMC5777057 DOI: 10.1073/pnas.1715464115] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The voltage-dependent anion channel (VDAC) is the most abundant protein in the outer mitochondrial membrane and constitutes the primary pathway for the exchange of ions and metabolites between the cytosol and the mitochondria. There is accumulating evidence supporting VDAC's role in mitochondrial metabolic regulation and apoptosis, where VDAC oligomerization has been implicated with these processes. Herein, we report a specific pH-dependent dimerization of murine VDAC1 (mVDAC1) identified by double electron-electron resonance and native mass spectrometry. Intermolecular distances on four singly spin-labeled mVDAC1 mutants were used to generate a model of the low-pH dimer, establishing the presence of residue E73 at the interface. This dimer arrangement is different from any oligomeric state previously described, and it forms as a steep function of pH with an apparent pKa of 7.4. Moreover, the monomer-dimer equilibrium affinity constant was determined using native MS, revealing a nearly eightfold enhancement in dimerization affinity at low pH. Mutation of E73 to either alanine or glutamine severely reduces oligomerization, demonstrating the role of protonated E73 in enhancing dimer formation. Based on these results, and the known importance of E73 in VDAC physiology, VDAC dimerization likely plays a significant role in mitochondrial metabolic regulation and apoptosis in response to cytosolic acidification during cellular stress.
Collapse
|
559
|
Affiliation(s)
- Bifan Chen
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Kyle A. Brown
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Ziqing Lin
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Human Proteomics Program, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Human Proteomics Program, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| |
Collapse
|
560
|
Allosteric modulation of protein-protein interactions by individual lipid binding events. Nat Commun 2017; 8:2203. [PMID: 29259178 PMCID: PMC5736629 DOI: 10.1038/s41467-017-02397-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 11/22/2017] [Indexed: 11/29/2022] Open
Abstract
The diverse lipid environment of the biological membrane can modulate the structure and function of membrane proteins. However, little is known about the role that lipids play in modulating protein–protein interactions. Here we employed native mass spectrometry (MS) to determine how individual lipid-binding events to the ammonia channel (AmtB) modulate its interaction with the regulatory protein, GlnK. The thermodynamic signature of AmtB–GlnK in the absence of lipids indicates conformational dynamics. A small number of lipids bound to AmtB is sufficient to modulate the interaction with GlnK, and lipids with different headgroups display a range of allosteric modulation. We also find that lipid chain length and stereochemistry can affect the degree of allosteric modulation, indicating an unforeseen selectivity of membrane proteins toward the chemistry of lipid tails. These results demonstrate that individual lipid-binding events can allosterically modulate the interactions of integral membrane and soluble proteins. Native mass spectrometry (MS) is a technique that preserves non-covalent interactions in the mass spectrometer. Here the authors use native MS to study integral membrane proteins, and find that lipids with different headgroups and tails can allosterically modulate protein-protein interactions in different fashions.
Collapse
|
561
|
Chang HY, Chen CT, Ko CL, Chen YJ, Chen YJ, Hsu WL, Juo CG, Sung TY. iTop-Q: an Intelligent Tool for Top-down Proteomics Quantitation Using DYAMOND Algorithm. Anal Chem 2017; 89:13128-13136. [DOI: 10.1021/acs.analchem.7b02343] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Hui-Yin Chang
- Institute
of Information Science, Academia Sinica, Taipei 115, Taiwan
| | - Ching-Tai Chen
- Institute
of Information Science, Academia Sinica, Taipei 115, Taiwan
| | - Chu-Ling Ko
- Department
of Computer Science, National Chiao Tung University, Hsinchu 300, Taiwan
| | - Yi-Ju Chen
- Institute
of Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Yu-Ju Chen
- Institute
of Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Wen-Lian Hsu
- Institute
of Information Science, Academia Sinica, Taipei 115, Taiwan
| | - Chiun-Gung Juo
- Molecular
Medicine Research Center, Chang Gung University, Taoyuan 333, Taiwan
- PharmaEssentia Corp., Taipei 115, Taiwan
| | - Ting-Yi Sung
- Institute
of Information Science, Academia Sinica, Taipei 115, Taiwan
| |
Collapse
|
562
|
Haupt C, Hofmann T, Wittig S, Kostmann S, Politis A, Schmidt C. Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies. J Vis Exp 2017. [PMID: 29286378 PMCID: PMC5755487 DOI: 10.3791/56747] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Proteins interact with their ligands to form active and dynamic assemblies which carry out various cellular functions. Elucidating these interactions is therefore fundamental for the understanding of cellular processes. However, many protein complexes are dynamic assemblies and are not accessible by conventional structural techniques. Mass spectrometry contributes to the structural investigation of these assemblies, and particularly the combination of various mass spectrometric techniques delivers valuable insights into their structural arrangement. In this article, we describe the application and combination of two complementary mass spectrometric techniques, namely chemical cross-linking coupled with mass spectrometry and native mass spectrometry. Chemical cross-linking involves the covalent linkage of amino acids in close proximity by using chemical reagents. After digestion with proteases, cross-linked di-peptides are identified by mass spectrometry and protein interactions sites are uncovered. Native mass spectrometry on the other hand is the analysis of intact protein assemblies in the gas phase of a mass spectrometer. It reveals protein stoichiometries as well as protein and ligand interactions. Both techniques therefore deliver complementary information on the structure of protein-ligand assemblies and their combination proved powerful in previous studies.
Collapse
Affiliation(s)
- Caroline Haupt
- Interdisciplinary research center HALOmem, Martin Luther University Halle-Wittenberg
| | - Tommy Hofmann
- Interdisciplinary research center HALOmem, Martin Luther University Halle-Wittenberg
| | - Sabine Wittig
- Interdisciplinary research center HALOmem, Martin Luther University Halle-Wittenberg
| | - Susann Kostmann
- Interdisciplinary research center HALOmem, Martin Luther University Halle-Wittenberg
| | | | - Carla Schmidt
- Interdisciplinary research center HALOmem, Martin Luther University Halle-Wittenberg;
| |
Collapse
|
563
|
Ahdash Z, Lau AM, Byrne RT, Lammens K, Stüetzer A, Urlaub H, Booth PJ, Reading E, Hopfner KP, Politis A. Mechanistic insight into the assembly of the HerA-NurA helicase-nuclease DNA end resection complex. Nucleic Acids Res 2017; 45:12025-12038. [PMID: 29149348 PMCID: PMC5715905 DOI: 10.1093/nar/gkx890] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 09/20/2017] [Accepted: 09/22/2017] [Indexed: 01/08/2023] Open
Abstract
The HerA-NurA helicase-nuclease complex cooperates with Mre11 and Rad50 to coordinate the repair of double-stranded DNA breaks. Little is known, however, about the assembly mechanism and activation of the HerA-NurA. By combining hybrid mass spectrometry with cryo-EM, computational and biochemical data, we investigate the oligomeric formation of HerA and detail the mechanism of nucleotide binding to the HerA-NurA complex from thermophilic archaea. We reveal that ATP-free HerA and HerA-DNA complexes predominantly exist in solution as a heptamer and act as a DNA loading intermediate. The binding of either NurA or ATP stabilizes the hexameric HerA, indicating that HerA-NurA is activated by substrates and complex assembly. To examine the role of ATP in DNA translocation and processing, we investigated how nucleotides interact with the HerA-NurA. We show that while the hexameric HerA binds six nucleotides in an 'all-or-none' fashion, HerA-NurA harbors a highly coordinated pairwise binding mechanism and enables the translocation and processing of double-stranded DNA. Using molecular dynamics simulations, we reveal novel inter-residue interactions between the external ATP and the internal DNA binding sites. Overall, here we propose a stepwise assembly mechanism detailing the synergistic activation of HerA-NurA by ATP, which allows efficient processing of double-stranded DNA.
Collapse
Affiliation(s)
- Zainab Ahdash
- Department of Chemistry, King's College London, 7 Trinity Street, London SE1 1DB, UK
| | - Andy M. Lau
- Department of Chemistry, King's College London, 7 Trinity Street, London SE1 1DB, UK
| | - Robert Thomas Byrne
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 München, Germany
| | - Katja Lammens
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 München, Germany
| | - Alexandra Stüetzer
- Bioanalytical Mass Spectrometry Group, MPI for Biophysical Chemistry, D-37077 Göttingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, MPI for Biophysical Chemistry, D-37077 Göttingen, Germany
- Bioanalytics Group, Institute for Clinical Chemistry, University Medical Center Göttingen, D-37075 Göttingen, Germany
| | - Paula J. Booth
- Department of Chemistry, King's College London, 7 Trinity Street, London SE1 1DB, UK
| | - Eamonn Reading
- Department of Chemistry, King's College London, 7 Trinity Street, London SE1 1DB, UK
| | - Karl-Peter Hopfner
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 München, Germany
| | - Argyris Politis
- Department of Chemistry, King's College London, 7 Trinity Street, London SE1 1DB, UK
| |
Collapse
|
564
|
Wallin C, Sholts SB, Österlund N, Luo J, Jarvet J, Roos PM, Ilag L, Gräslund A, Wärmländer SKTS. Alzheimer's disease and cigarette smoke components: effects of nicotine, PAHs, and Cd(II), Cr(III), Pb(II), Pb(IV) ions on amyloid-β peptide aggregation. Sci Rep 2017; 7:14423. [PMID: 29089568 PMCID: PMC5663743 DOI: 10.1038/s41598-017-13759-5] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 09/05/2017] [Indexed: 12/14/2022] Open
Abstract
Cigarette smoking is a significant risk factor for Alzheimer's disease (AD), which is associated with extracellular brain deposits of amyloid plaques containing aggregated amyloid-β (Aβ) peptides. Aβ aggregation occurs via multiple pathways that can be influenced by various compounds. Here, we used AFM imaging and NMR, fluorescence, and mass spectrometry to monitor in vitro how Aβ aggregation is affected by the cigarette-related compounds nicotine, polycyclic aromatic hydrocarbons (PAHs) with one to five aromatic rings, and the metal ions Cd(II), Cr(III), Pb(II), and Pb(IV). All PAHs and metal ions modulated the Aβ aggregation process. Cd(II), Cr(III), and Pb(II) ions displayed general electrostatic interactions with Aβ, whereas Pb(IV) ions showed specific transient binding coordination to the N-terminal Aβ segment. Thus, Pb(IV) ions are especially prone to interact with Aβ and affect its aggregation. While Pb(IV) ions affected mainly Aβ dimer and trimer formation, hydrophobic toluene mainly affected formation of larger aggregates such as tetramers. The uncharged and hydrophilic nicotine molecule showed no direct interactions with Aβ, nor did it affect Aβ aggregation. Our Aβ interaction results suggest a molecular rationale for the higher AD prevalence among smokers, and indicate that certain forms of lead in particular may constitute an environmental risk factor for AD.
Collapse
Affiliation(s)
- Cecilia Wallin
- Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, 106 91, Stockholm, Sweden
| | - Sabrina B Sholts
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Nicklas Österlund
- Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, 106 91, Stockholm, Sweden
- Department of Environmental Science and Analytical Chemistry, Arrhenius Laboratories, Stockholm University, 106 91, Stockholm, Sweden
| | - Jinghui Luo
- Chemical Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford Ox, 1 3TA, UK
| | - Jüri Jarvet
- Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, 106 91, Stockholm, Sweden
- The National Institute of Chemical Physics and Biophysics, Tallinn, Estonia
| | - Per M Roos
- Institute of Environmental Medicine, Karolinska Institutet, Nobels väg 13, 171 77, Stockholm, Sweden
- Department of Clinical Physiology, Capio St.Göran Hospital, St.Göransplan 1, 112 19, Stockholm, Sweden
| | - Leopold Ilag
- Department of Environmental Science and Analytical Chemistry, Arrhenius Laboratories, Stockholm University, 106 91, Stockholm, Sweden
| | - Astrid Gräslund
- Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, 106 91, Stockholm, Sweden
| | - Sebastian K T S Wärmländer
- Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, 106 91, Stockholm, Sweden.
| |
Collapse
|
565
|
Reid DJ, Keener JE, Wheeler AP, Zambrano DE, Diesing JM, Reinhardt-Szyba M, Makarov A, Marty MT. Engineering Nanodisc Scaffold Proteins for Native Mass Spectrometry. Anal Chem 2017; 89:11189-11192. [PMID: 29048874 DOI: 10.1021/acs.analchem.7b03569] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Lipoprotein nanodiscs are ideally suited for native mass spectrometry because they provide a relatively monodisperse nanoscale lipid bilayer environment for delivering membrane proteins into the gas phase. However, native mass spectrometry of nanodiscs produces complex spectra that can be challenging to assign unambiguously. To simplify interpretation of nanodisc spectra, we engineered a series of mutant membrane scaffold proteins (MSP) that do not affect nanodisc formation but shift the masses of nanodiscs in a controllable way, eliminating isobaric interference from the lipids. Moreover, by mixing two different belts before assembly, the stoichiometry of MSP is encoded in the peak shape, which allows the stoichiometry to be assigned unambiguously from a single spectrum. Finally, we demonstrate the use of mixed belt nanodiscs with embedded membrane proteins to confirm the dissociation of MSP prior to desolvation.
Collapse
Affiliation(s)
- Deseree J Reid
- Department of Chemistry and Biochemistry, University of Arizona , Tucson, Arizona 85721, United States
| | - James E Keener
- Department of Chemistry and Biochemistry, University of Arizona , Tucson, Arizona 85721, United States
| | - Andrew P Wheeler
- Department of Chemistry and Biochemistry, University of Arizona , Tucson, Arizona 85721, United States
| | - Dane Evan Zambrano
- Department of Chemistry and Biochemistry, University of Arizona , Tucson, Arizona 85721, United States
| | - Jessica M Diesing
- Department of Chemistry and Biochemistry, University of Arizona , Tucson, Arizona 85721, United States
| | | | | | - Michael T Marty
- Department of Chemistry and Biochemistry, University of Arizona , Tucson, Arizona 85721, United States
| |
Collapse
|
566
|
Foldability of a Natural De Novo Evolved Protein. Structure 2017; 25:1687-1696.e4. [PMID: 29033289 DOI: 10.1016/j.str.2017.09.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Revised: 07/22/2017] [Accepted: 09/15/2017] [Indexed: 12/13/2022]
Abstract
The de novo evolution of protein-coding genes from noncoding DNA is emerging as a source of molecular innovation in biology. Studies of random sequence libraries, however, suggest that young de novo proteins will not fold into compact, specific structures typical of native globular proteins. Here we show that Bsc4, a functional, natural de novo protein encoded by a gene that evolved recently from noncoding DNA in the yeast S. cerevisiae, folds to a partially specific three-dimensional structure. Bsc4 forms soluble, compact oligomers with high β sheet content and a hydrophobic core, and undergoes cooperative, reversible denaturation. Bsc4 lacks a specific quaternary state, however, existing instead as a continuous distribution of oligomer sizes, and binds dyes indicative of amyloid oligomers or molten globules. The combination of native-like and non-native-like properties suggests a rudimentary fold that could potentially act as a functional intermediate in the emergence of new folded proteins de novo.
Collapse
|
567
|
Schiffrin B, Calabrese AN, Higgins AJ, Humes JR, Ashcroft AE, Kalli AC, Brockwell DJ, Radford SE. Effects of Periplasmic Chaperones and Membrane Thickness on BamA-Catalyzed Outer-Membrane Protein Folding. J Mol Biol 2017; 429:3776-3792. [PMID: 28919234 PMCID: PMC5692476 DOI: 10.1016/j.jmb.2017.09.008] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 09/08/2017] [Accepted: 09/09/2017] [Indexed: 11/18/2022]
Abstract
The biogenesis of outer-membrane proteins (OMPs) in gram-negative bacteria involves delivery by periplasmic chaperones to the β-barrel assembly machinery (BAM), which catalyzes OMP insertion into the outer membrane. Here, we examine the effects of membrane thickness, the Escherichia coli periplasmic chaperones Skp and SurA, and BamA, the central subunit of the BAM complex, on the folding kinetics of a model OMP (tOmpA) using fluorescence spectroscopy, native mass spectrometry, and molecular dynamics simulations. We show that prefolded BamA promotes the release of tOmpA from Skp despite the nM affinity of the Skp:tOmpA complex. This activity is located in the BamA β-barrel domain, but is greater when full-length BamA is present, indicating that both the β-barrel and polypeptide transport-associated (POTRA) domains are required for maximal activity. By contrast, SurA is unable to release tOmpA from Skp, providing direct evidence against a sequential chaperone model. By varying lipid acyl chain length in synthetic liposomes we show that BamA has a greater catalytic effect on tOmpA folding in thicker bilayers, suggesting that BAM catalysis involves lowering of the kinetic barrier imposed by the hydrophobic thickness of the membrane. Consistent with this, molecular dynamics simulations reveal that increases in membrane thinning/disorder by the transmembrane domain of BamA is greatest in thicker bilayers. Finally, we demonstrate that cross-linking of the BamA barrel does not affect tOmpA folding kinetics in 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) liposomes, suggesting that lateral gating of the BamA barrel and/or hybrid barrel formation is not required, at least for the assembly of a small 8-stranded OMP in vitro. Mechanisms of OMP periplasmic transport and folding by BAM are poorly understood. BamA catalyzes folding by reducing the kinetic barrier imposed by membrane thickness. BamA proteoliposomes promote folding of Skp-bound tOmpA. Lateral gating is not required for BamA-catalyzed folding of tOmpA in DMPC bilayers.
Collapse
Affiliation(s)
- Bob Schiffrin
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Antonio N Calabrese
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Anna J Higgins
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Julia R Humes
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Alison E Ashcroft
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Antreas C Kalli
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK; Leeds Institute of Cancer and Pathology, University of Leeds, St. James's University Hospital, Wellcome Trust Brenner Building, Leeds LS9 7TF, UK
| | - David J Brockwell
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.
| |
Collapse
|
568
|
Calabrese AN, Jackson SM, Jones LN, Beckstein O, Heinkel F, Gsponer J, Sharples D, Sans M, Kokkinidou M, Pearson AR, Radford SE, Ashcroft AE, Henderson PJF. Topological Dissection of the Membrane Transport Protein Mhp1 Derived from Cysteine Accessibility and Mass Spectrometry. Anal Chem 2017; 89:8844-8852. [PMID: 28726379 PMCID: PMC5588088 DOI: 10.1021/acs.analchem.7b01310] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Accepted: 07/20/2017] [Indexed: 01/01/2023]
Abstract
Cys accessibility and quantitative intact mass spectrometry (MS) analyses have been devised to study the topological transitions of Mhp1, the membrane protein for sodium-linked transport of hydantoins from Microbacterium liquefaciens. Mhp1 has been crystallized in three forms (outward-facing open, outward-facing occluded with substrate bound, and inward-facing open). We show that one natural cysteine residue, Cys327, out of three, has an enhanced solvent accessibility in the inward-facing (relative to the outward-facing) form. Reaction of the purified protein, in detergent, with the thiol-reactive N-ethylmalemide (NEM), results in modification of Cys327, suggesting that Mhp1 adopts predominantly inward-facing conformations. Addition of either sodium ions or the substrate 5-benzyl-l-hydantoin (L-BH) does not shift this conformational equilibrium, but systematic co-addition of the two results in an attenuation of labeling, indicating a shift toward outward-facing conformations that can be interpreted using conventional enzyme kinetic analyses. Such measurements can afford the Km for each ligand as well as the stoichiometry of ion-substrate-coupled conformational changes. Mutations that perturb the substrate binding site either result in the protein being unable to adopt outward-facing conformations or in a global destabilization of structure. The methodology combines covalent labeling, mass spectrometry, and kinetic analyses in a straightforward workflow applicable to a range of systems, enabling the interrogation of changes in a protein's conformation required for function at varied concentrations of substrates, and the consequences of mutations on these conformational transitions.
Collapse
Affiliation(s)
| | | | | | - Oliver Beckstein
- Department of Physics, Arizona State University , Tempe, Arizona 85287-1504, United States
| | - Florian Heinkel
- Centre for High-Throughput Biology, University of British Columbia , Vancouver, British Columbia, Canada V6T 1Z4
| | - Joerg Gsponer
- Centre for High-Throughput Biology, University of British Columbia , Vancouver, British Columbia, Canada V6T 1Z4
| | | | - Marta Sans
- Hamburg Centre for Ultrafast Imaging, Institute for Nanostructure and Solid State Physics, Universität Hamburg , Hamburg 22761, Germany
| | - Maria Kokkinidou
- Hamburg Centre for Ultrafast Imaging, Institute for Nanostructure and Solid State Physics, Universität Hamburg , Hamburg 22761, Germany
| | - Arwen R Pearson
- Hamburg Centre for Ultrafast Imaging, Institute for Nanostructure and Solid State Physics, Universität Hamburg , Hamburg 22761, Germany
| | | | | | | |
Collapse
|
569
|
Root K, Wittwer Y, Barylyuk K, Anders U, Zenobi R. Insight into Signal Response of Protein Ions in Native ESI-MS from the Analysis of Model Mixtures of Covalently Linked Protein Oligomers. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1863-1875. [PMID: 28593376 DOI: 10.1007/s13361-13017-11690-13363] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 04/12/2017] [Accepted: 04/13/2017] [Indexed: 05/25/2023]
Abstract
Native ESI-MS is increasingly used for quantitative analysis of biomolecular interactions. In such analyses, peak intensity ratios measured in mass spectra are treated as abundance ratios of the respective molecules in solution. While signal intensities of similar-size analytes, such as a protein and its complex with a small molecule, can be directly compared, significant distortions of the peak ratio due to unequal signal response of analytes impede the application of this approach for large oligomeric biomolecular complexes. We use a model system based on concatenated maltose binding protein units (MBPn, n = 1, 2, 3) to systematically study the behavior of protein mixtures in ESI-MS. The MBP concatamers differ from each other only by their mass while the chemical composition and other properties remain identical. We used native ESI-MS to analyze model mixtures of MBP oligomers, including equimolar mixtures of two proteins, as well as binary mixtures containing different fractions of the individual components. Pronounced deviation from a linear dependence of the signal intensity with concentration was observed for all binary mixtures investigated. While equimolar mixtures showed linear signal dependence at low concentrations, distinct ion suppression was observed above 20 μM. We systematically studied factors that are most often used in the literature to explain the origin of suppression effects. Implications of this effect for quantifying protein-protein binding affinity by native ESI-MS are discussed in general and demonstrated for an example of an anti-MBP antibody with its ligand, MBP. Graphical Abstract ᅟ.
Collapse
Affiliation(s)
- Katharina Root
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Yves Wittwer
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Konstantin Barylyuk
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Ulrike Anders
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland.
| |
Collapse
|
570
|
Root K, Wittwer Y, Barylyuk K, Anders U, Zenobi R. Insight into Signal Response of Protein Ions in Native ESI-MS from the Analysis of Model Mixtures of Covalently Linked Protein Oligomers. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1863-1875. [PMID: 28593376 DOI: 10.1007/s13361-017-1690-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 04/12/2017] [Accepted: 04/13/2017] [Indexed: 05/28/2023]
Abstract
Native ESI-MS is increasingly used for quantitative analysis of biomolecular interactions. In such analyses, peak intensity ratios measured in mass spectra are treated as abundance ratios of the respective molecules in solution. While signal intensities of similar-size analytes, such as a protein and its complex with a small molecule, can be directly compared, significant distortions of the peak ratio due to unequal signal response of analytes impede the application of this approach for large oligomeric biomolecular complexes. We use a model system based on concatenated maltose binding protein units (MBPn, n = 1, 2, 3) to systematically study the behavior of protein mixtures in ESI-MS. The MBP concatamers differ from each other only by their mass while the chemical composition and other properties remain identical. We used native ESI-MS to analyze model mixtures of MBP oligomers, including equimolar mixtures of two proteins, as well as binary mixtures containing different fractions of the individual components. Pronounced deviation from a linear dependence of the signal intensity with concentration was observed for all binary mixtures investigated. While equimolar mixtures showed linear signal dependence at low concentrations, distinct ion suppression was observed above 20 μM. We systematically studied factors that are most often used in the literature to explain the origin of suppression effects. Implications of this effect for quantifying protein-protein binding affinity by native ESI-MS are discussed in general and demonstrated for an example of an anti-MBP antibody with its ligand, MBP. Graphical Abstract ᅟ.
Collapse
Affiliation(s)
- Katharina Root
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Yves Wittwer
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Konstantin Barylyuk
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Ulrike Anders
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland.
| |
Collapse
|
571
|
Hines KM, Ross DH, Davidson KL, Bush MF, Xu L. Large-Scale Structural Characterization of Drug and Drug-Like Compounds by High-Throughput Ion Mobility-Mass Spectrometry. Anal Chem 2017; 89:9023-9030. [PMID: 28764324 PMCID: PMC5616088 DOI: 10.1021/acs.analchem.7b01709] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
![]()
Ion mobility-mass spectrometry (IM-MS)
can provide orthogonal information,
i.e., m/z and collision cross section
(CCS), for the identification of drugs and drug metabolites. However,
only a small number of CCS values are available for drugs, which limits
the use of CCS as an identification parameter and the assessment of
structure–function relationships of drugs using IM-MS. Here,
we report the development of a rapid workflow for the measurement
of CCS values of a large number of drug or drug-like molecules in
nitrogen on the widely available traveling wave IM-MS (TWIM-MS) platform.
Using a combination of small molecule and polypeptide CCS calibrants,
we successfully determined the nitrogen CCS values of 1425 drug or
drug-like molecules in the MicroSource Discovery Systems’ Spectrum
Collection using flow injection analysis of 384-well plates. Software
was developed to streamline data extraction, processing, and calibration.
We found that the overall drug collection covers a wide CCS range
for the same mass, suggesting a large structural diversity of these
drugs. However, individual drug classes appear to occupy a narrow
and unique space in the CCS–mass 2D spectrum, suggesting a
tight structure–function relationship for each class of drugs
with a specific target. We observed bimodal distributions for several
antibiotic species due to multiple protomers, including the known
fluoroquinolone protomers and the new finding of cephalosporin protomers.
Lastly, we demonstrated the utility of the high-throughput method
and drug CCS database by quickly and confidently confirming the active
component in a pharmaceutical product.
Collapse
Affiliation(s)
- Kelly M Hines
- Department of Medicinal Chemistry, ‡Department of Chemistry, University of Washington , Seattle, Washington 98195, United States
| | - Dylan H Ross
- Department of Medicinal Chemistry, ‡Department of Chemistry, University of Washington , Seattle, Washington 98195, United States
| | - Kimberly L Davidson
- Department of Medicinal Chemistry, ‡Department of Chemistry, University of Washington , Seattle, Washington 98195, United States
| | - Matthew F Bush
- Department of Medicinal Chemistry, ‡Department of Chemistry, University of Washington , Seattle, Washington 98195, United States
| | - Libin Xu
- Department of Medicinal Chemistry, ‡Department of Chemistry, University of Washington , Seattle, Washington 98195, United States
| |
Collapse
|
572
|
Rouse SL, Hawthorne WJ, Berry JL, Chorev DS, Ionescu SA, Lambert S, Stylianou F, Ewert W, Mackie U, Morgan RML, Otzen D, Herbst FA, Nielsen PH, Dueholm M, Bayley H, Robinson CV, Hare S, Matthews S. A new class of hybrid secretion system is employed in Pseudomonas amyloid biogenesis. Nat Commun 2017; 8:263. [PMID: 28811582 PMCID: PMC5557850 DOI: 10.1038/s41467-017-00361-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 06/23/2017] [Indexed: 11/25/2022] Open
Abstract
Gram-negative bacteria possess specialised biogenesis machineries that facilitate the export of amyloid subunits for construction of a biofilm matrix. The secretion of bacterial functional amyloid requires a bespoke outer-membrane protein channel through which unfolded amyloid substrates are translocated. Here, we combine X-ray crystallography, native mass spectrometry, single-channel electrical recording, molecular simulations and circular dichroism measurements to provide high-resolution structural insight into the functional amyloid transporter from Pseudomonas, FapF. FapF forms a trimer of gated β-barrel channels in which opening is regulated by a helical plug connected to an extended coil-coiled platform spanning the bacterial periplasm. Although FapF represents a unique type of secretion system, it shares mechanistic features with a diverse range of peptide translocation systems. Our findings highlight alternative strategies for handling and export of amyloid protein sequences. Gram-negative bacteria assemble biofilms from amyloid fibres, which translocate across the outer membrane as unfolded amyloid precursors through a secretion system. Here, the authors characterise the structural details of the amyloid transporter FapF in Pseudomonas.
Collapse
Affiliation(s)
- Sarah L Rouse
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW72AZ, UK
| | - William J Hawthorne
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW72AZ, UK
| | - Jamie-Lee Berry
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW72AZ, UK
| | - Dror S Chorev
- Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, UK
| | - Sandra A Ionescu
- Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, UK
| | - Sebastian Lambert
- Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Fisentzos Stylianou
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW72AZ, UK
| | - Wiebke Ewert
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW72AZ, UK
| | - Uma Mackie
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW72AZ, UK.,Walthamstow School for Girls, London, E17 9RZ, UK
| | - R Marc L Morgan
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW72AZ, UK
| | - Daniel Otzen
- Interdisciplinary Nanoscience Center (iNANO), Centre for Insoluble Protein Structures (inSPIN), Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
| | - Florian-Alexander Herbst
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Per H Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Morten Dueholm
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Hagan Bayley
- Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, UK
| | - Carol V Robinson
- Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, UK
| | - Stephen Hare
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW72AZ, UK
| | - Stephen Matthews
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW72AZ, UK.
| |
Collapse
|
573
|
Borovcová L, Hermannová M, Pauk V, Šimek M, Havlíček V, Lemr K. Simple area determination of strongly overlapping ion mobility peaks. Anal Chim Acta 2017; 981:71-79. [DOI: 10.1016/j.aca.2017.05.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 05/01/2017] [Accepted: 05/05/2017] [Indexed: 10/19/2022]
|
574
|
Larson AG, Elnatan D, Keenen MM, Trnka MJ, Johnston JB, Burlingame AL, Agard DA, Redding S, Narlikar GJ. Liquid droplet formation by HP1α suggests a role for phase separation in heterochromatin. Nature 2017; 547:236-240. [PMID: 28636604 PMCID: PMC5606208 DOI: 10.1038/nature22822] [Citation(s) in RCA: 1122] [Impact Index Per Article: 160.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 05/16/2017] [Indexed: 01/15/2023]
Abstract
Gene silencing by heterochromatin is proposed to occur in part as a result of the ability of heterochromatin protein 1 (HP1) proteins to spread across large regions of the genome, compact the underlying chromatin and recruit diverse ligands. Here we identify a new property of the human HP1α protein: the ability to form phase-separated droplets. While unmodified HP1α is soluble, either phosphorylation of its N-terminal extension or DNA binding promotes the formation of phase-separated droplets. Phosphorylation-driven phase separation can be promoted or reversed by specific HP1α ligands. Known components of heterochromatin such as nucleosomes and DNA preferentially partition into the HP1α droplets, but molecules such as the transcription factor TFIIB show no preference. Using a single-molecule DNA curtain assay, we find that both unmodified and phosphorylated HP1α induce rapid compaction of DNA strands into puncta, although with different characteristics. We show by direct protein delivery into mammalian cells that an HP1α mutant incapable of phase separation in vitro forms smaller and fewer nuclear puncta than phosphorylated HP1α. These findings suggest that heterochromatin-mediated gene silencing may occur in part through sequestration of compacted chromatin in phase-separated HP1 droplets, which are dissolved or formed by specific ligands on the basis of nuclear context.
Collapse
Affiliation(s)
- Adam G. Larson
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
- Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Daniel Elnatan
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
- Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Madeline M. Keenen
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
- Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Michael J. Trnka
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jonathan B. Johnston
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Alma L. Burlingame
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - David A. Agard
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Sy Redding
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Geeta J. Narlikar
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| |
Collapse
|
575
|
Eschweiler JD, Kerr R, Rabuck-Gibbons J, Ruotolo BT. Sizing Up Protein-Ligand Complexes: The Rise of Structural Mass Spectrometry Approaches in the Pharmaceutical Sciences. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2017; 10:25-44. [PMID: 28301749 DOI: 10.1146/annurev-anchem-061516-045414] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Capturing the dynamic interplay between proteins and their myriad interaction partners is critically important for advancing our understanding of almost every biochemical process and human disease. The importance of this general area has spawned many measurement methods capable of assaying such protein complexes, and the mass spectrometry-based structural biology methods described in this review form an important part of that analytical arsenal. Here, we survey the basic principles of such measurements, cover recent applications of the technology that have focused on protein-small-molecule complexes, and discuss the bright future awaiting this group of technologies.
Collapse
Affiliation(s)
| | - Richard Kerr
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109;
| | | | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109;
| |
Collapse
|
576
|
Yen HY, Hopper JTS, Liko I, Allison TM, Zhu Y, Wang D, Stegmann M, Mohammed S, Wu B, Robinson CV. Ligand binding to a G protein-coupled receptor captured in a mass spectrometer. SCIENCE ADVANCES 2017; 3:e1701016. [PMID: 28630934 PMCID: PMC5473672 DOI: 10.1126/sciadv.1701016] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 04/27/2017] [Indexed: 05/08/2023]
Abstract
G protein (heterotrimeric guanine nucleotide-binding protein)-coupled receptors belong to the largest family of membrane-embedded cell surface proteins and are involved in a diverse array of physiological processes. Despite progress in the mass spectrometry of membrane protein complexes, G protein-coupled receptors have remained intractable because of their low yield and instability after extraction from cell membranes. We established conditions in the mass spectrometer that preserve noncovalent ligand binding to the human purinergic receptor P2Y1. Results established differing affinities for nucleotides and the drug MRS2500 and link antagonist binding with the absence of receptor phosphorylation. Overall, therefore, our results are consistent with drug binding, preventing the conformational changes that facilitate downstream signaling. More generally, we highlight opportunities for mass spectrometry to probe effects of ligand binding on G protein-coupled receptors.
Collapse
Affiliation(s)
- Hsin-Yung Yen
- Chemistry Research Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Jonathan T. S. Hopper
- OMass Technologies Ltd., Centre for Innovation and Enterprise, Begbroke Science Park, Woodstock Road, Oxford OX5 1PF, UK
| | - Idlir Liko
- Chemistry Research Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
- OMass Technologies Ltd., Centre for Innovation and Enterprise, Begbroke Science Park, Woodstock Road, Oxford OX5 1PF, UK
| | - Timothy M. Allison
- Chemistry Research Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Ya Zhu
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai 201203, China
| | - Dejian Wang
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai 201203, China
- School of Life Science and Technology, ShanghaiTech University, 99 Haike Road, Pudong, Shanghai 201203, China
| | - Monika Stegmann
- Departments of Chemistry and Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Shabaz Mohammed
- Departments of Chemistry and Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Beili Wu
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai 201203, China
- School of Life Science and Technology, ShanghaiTech University, 99 Haike Road, Pudong, Shanghai 201203, China
| | - Carol V. Robinson
- Chemistry Research Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| |
Collapse
|
577
|
Göth M, Pagel K. Ion mobility–mass spectrometry as a tool to investigate protein–ligand interactions. Anal Bioanal Chem 2017; 409:4305-4310. [DOI: 10.1007/s00216-017-0384-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 04/13/2017] [Accepted: 04/26/2017] [Indexed: 02/07/2023]
|
578
|
Hopper JTS, Ambrose S, Grant OC, Krumm SA, Allison TM, Degiacomi MT, Tully MD, Pritchard LK, Ozorowski G, Ward AB, Crispin M, Doores KJ, Woods RJ, Benesch JLP, Robinson CV, Struwe WB. The Tetrameric Plant Lectin BanLec Neutralizes HIV through Bidentate Binding to Specific Viral Glycans. Structure 2017; 25:773-782.e5. [PMID: 28434916 DOI: 10.1016/j.str.2017.03.015] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 03/01/2017] [Accepted: 03/23/2017] [Indexed: 11/30/2022]
Abstract
Select lectins have powerful anti-viral properties that effectively neutralize HIV-1 by targeting the dense glycan shield on the virus. Here, we reveal the mechanism by which one of the most potent lectins, BanLec, achieves its inhibition. We identify that BanLec recognizes a subset of high-mannose glycans via bidentate interactions spanning the two binding sites present on each BanLec monomer that were previously considered separate carbohydrate recognition domains. We show that both sites are required for high-affinity glycan binding and virus neutralization. Unexpectedly we find that BanLec adopts a tetrameric stoichiometry in solution whereby the glycan-binding sites are positioned to optimally target glycosylated viral spikes. The tetrameric architecture, together with bidentate binding to individual glycans, leads to layers of multivalency that drive viral neutralization through enhanced avidity effects. These structural insights will prove useful in engineering successful lectin therapeutics targeting the dense glycan shield of HIV.
Collapse
Affiliation(s)
- Jonathan T S Hopper
- Physical & Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Stephen Ambrose
- Physical & Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Oliver C Grant
- Department of Biochemistry, Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
| | - Stefanie A Krumm
- Department of Infectious Diseases, King's College London, London SE1 9RT, UK
| | - Timothy M Allison
- Physical & Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Matteo T Degiacomi
- Physical & Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Mark D Tully
- Diamond Light Source B21, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Laura K Pritchard
- Department of Biochemistry, Oxford Glycobiology Institute, University of Oxford, Oxford OX1 3QU, UK
| | - Gabriel Ozorowski
- Department of Integrative Structural and Computational Biology, CHAVI-ID, IAVI Neutralizing Antibody Center & Collaboration for AIDS Vaccine Discovery (CAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, CHAVI-ID, IAVI Neutralizing Antibody Center & Collaboration for AIDS Vaccine Discovery (CAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Max Crispin
- Department of Biochemistry, Oxford Glycobiology Institute, University of Oxford, Oxford OX1 3QU, UK
| | - Katie J Doores
- Department of Infectious Diseases, King's College London, London SE1 9RT, UK
| | - Robert J Woods
- Department of Biochemistry, Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
| | - Justin L P Benesch
- Physical & Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Carol V Robinson
- Physical & Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Weston B Struwe
- Physical & Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK; Department of Biochemistry, Oxford Glycobiology Institute, University of Oxford, Oxford OX1 3QU, UK.
| |
Collapse
|
579
|
Liu Y, Cong X, Liu W, Laganowsky A. Characterization of Membrane Protein-Lipid Interactions by Mass Spectrometry Ion Mobility Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:579-586. [PMID: 27924494 DOI: 10.1007/s13361-016-1555-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 10/06/2016] [Accepted: 11/03/2016] [Indexed: 05/21/2023]
Abstract
Lipids in the biological membrane can modulate the structure and function of integral and peripheral membrane proteins. Distinguishing individual lipids that bind selectively to membrane protein complexes from an ensemble of lipid-bound species remains a daunting task. Recently, ion mobility mass spectrometry (IM-MS) has proven to be invaluable for interrogating the interactions between protein and individual lipids, where the complex undergoes collision induced unfolding followed by quantification of the unfolding pathway to assess the effect of these interactions. However, gas-phase unfolding experiments for membrane proteins are typically performed on the entire ensemble (apo and lipid bound species), raising uncertainty to the contribution of individual lipids and the species that are ejected in the unfolding process. Here, we describe the application of mass spectrometry ion mobility mass spectrometry (MS-IM-MS) for isolating ions corresponding to lipid-bound states of a model integral membrane protein, ammonia channel (AmtB) from Escherichia coli. Free of ensemble effects, MS-IM-MS reveals that bound lipids are ejected as neutral species; however, no correlation was found between the lipid-induced stabilization of complex and their equilibrium binding constants. In comparison to data obtained by IM-MS, there are surprisingly limited differences in stability measurements from IM-MS and MS-IM-MS. The approach described here to isolate ions of membrane protein complexes will be useful for other MS methods, such as surface induced dissociation or collision induced dissociation to determine the stoichiometry of hetero-oligomeric membrane protein complexes. Graphical Abstract ᅟ.
Collapse
Affiliation(s)
- Yang Liu
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, 77030, USA
| | - Xiao Cong
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, 77030, USA
| | - Wen Liu
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, 77030, USA
| | - Arthur Laganowsky
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, 77030, USA.
- Department of Chemistry, Texas A&M University, College Station, TX, 77842, USA.
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M University, Bryan, TX, 77807, USA.
| |
Collapse
|
580
|
Uppal SS, Beasley SE, Scian M, Guttman M. Gas-Phase Hydrogen/Deuterium Exchange for Distinguishing Isomeric Carbohydrate Ions. Anal Chem 2017; 89:4737-4742. [PMID: 28304155 DOI: 10.1021/acs.analchem.7b00683] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The structural diversity of carbohydrates presents a major challenge for glycobiology and the analysis of glycoconjugates. Mass spectrometry has become a primary tool for glycan analysis thanks to its speed and sensitivity, but the information content regarding the glycan structure of protonated glycoconjugates is hindered by the inability to differentiate linkage and stereoisomers. Here, we examine a variety of protonated carbohydrate structures by gas-phase hydrogen/deuterium exchange (HDX) to discover that the exchange rates are distinct for isomeric carbohydrates with even subtle structural differences. By incorporating an internal exchange standard, HDX could effectively distinguish all linkage and stereoisomers that were examined and presents a mass spectrometry-based approach for glycan structural analysis with immense potential.
Collapse
Affiliation(s)
- Sanjit S Uppal
- Department of Medicinal Chemistry, University of Washington , Seattle, Washington 98195, United States
| | - Sarah E Beasley
- Department of Medicinal Chemistry, University of Washington , Seattle, Washington 98195, United States
| | - Michele Scian
- Department of Medicinal Chemistry, University of Washington , Seattle, Washington 98195, United States
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington , Seattle, Washington 98195, United States
| |
Collapse
|
581
|
Abstract
Membrane proteins play a most important part in metabolism, signaling, cell motility, transport, development, and many other biochemical and biophysical processes which constitute fundamentals of life on the molecular level. Detailed understanding of these processes is necessary for the progress of life sciences and biomedical applications. Nanodiscs provide a new and powerful tool for a broad spectrum of biochemical and biophysical studies of membrane proteins and are commonly acknowledged as an optimal membrane mimetic system that provides control over size, composition, and specific functional modifications on the nanometer scale. In this review we attempted to combine a comprehensive list of various applications of nanodisc technology with systematic analysis of the most attractive features of this system and advantages provided by nanodiscs for structural and mechanistic studies of membrane proteins.
Collapse
Affiliation(s)
- Ilia G Denisov
- Department of Biochemistry and Department of Chemistry, University of Illinois , Urbana, Illinois 61801, United States
| | - Stephen G Sligar
- Department of Biochemistry and Department of Chemistry, University of Illinois , Urbana, Illinois 61801, United States
| |
Collapse
|
582
|
The role of interfacial lipids in stabilizing membrane protein oligomers. Nature 2017; 541:421-424. [PMID: 28077870 DOI: 10.1038/nature20820] [Citation(s) in RCA: 288] [Impact Index Per Article: 41.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Accepted: 11/23/2016] [Indexed: 12/20/2022]
Abstract
Oligomerization of membrane proteins in response to lipid binding has a critical role in many cell-signalling pathways but is often difficult to define or predict. Here we report the development of a mass spectrometry platform to determine simultaneously the presence of interfacial lipids and oligomeric stability and to uncover how lipids act as key regulators of membrane-protein association. Evaluation of oligomeric strength for a dataset of 125 α-helical oligomeric membrane proteins reveals an absence of interfacial lipids in the mass spectra of 12 membrane proteins with high oligomeric stability. For the bacterial homologue of the eukaryotic biogenic transporters (LeuT, one of the proteins with the lowest oligomeric stability), we found a precise cohort of lipids within the dimer interface. Delipidation, mutation of lipid-binding sites or expression in cardiolipin-deficient Escherichia coli abrogated dimer formation. Molecular dynamics simulation revealed that cardiolipin acts as a bidentate ligand, bridging across subunits. Subsequently, we show that for the Vibrio splendidus sugar transporter SemiSWEET, another protein with low oligomeric stability, cardiolipin shifts the equilibrium from monomer to functional dimer. We hypothesized that lipids are essential for dimerization of the Na+/H+ antiporter NhaA from E. coli, which has the lowest oligomeric strength, but not for the substantially more stable homologous Thermus thermophilus protein NapA. We found that lipid binding is obligatory for dimerization of NhaA, whereas NapA has adapted to form an interface that is stable without lipids. Overall, by correlating interfacial strength with the presence of interfacial lipids, we provide a rationale for understanding the role of lipids in both transient and stable interactions within a range of α-helical membrane proteins, including G-protein-coupled receptors.
Collapse
|
583
|
Campuzano IDG, Li H, Bagal D, Lippens JL, Svitel J, Kurzeja RJM, Xu H, Schnier PD, Loo JA. Native MS Analysis of Bacteriorhodopsin and an Empty Nanodisc by Orthogonal Acceleration Time-of-Flight, Orbitrap and Ion Cyclotron Resonance. Anal Chem 2016; 88:12427-12436. [PMID: 28193065 PMCID: PMC5505737 DOI: 10.1021/acs.analchem.6b03762] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Over the past two decades, orthogonal acceleration time-of-flight has been the de facto analyzer for solution and membrane-soluble protein native mass spectrometry (MS) studies; this however is gradually changing. Three MS instruments are compared, the Q-ToF, Orbitrap, and the FT-ICR, to analyze, under native instrument and buffer conditions, the seven-transmembrane helical protein bacteriorhodopsin-octylglucoside micelle and the empty nanodisc (MSP1D1-Nd) using both MS and tandem-MS modes of operation. Bacteriorhodopsin can be released from the octylglucoside-micelle efficiently on all three instruments (MS-mode), producing a narrow charge state distribution (z = 8+ to 10+) by either increasing the source lens or collision cell (or HCD) voltages. A lower center-of-mass collision energy (0.20-0.41 eV) is required for optimal bacteriorhodopsin liberation on the FT-ICR, in comparison to the Q-ToF and Orbitrap instruments (0.29-2.47 eV). The empty MSP1D1-Nd can be measured with relative ease on all three instruments, resulting in a highly complex spectrum of overlapping, polydisperse charge states. There is a measurable difference in MSP1D1-Nd charge state distribution (z = 15+ to 26+), average molecular weight (141.7 to 169.6 kDa), and phospholipid incorporation number (143 to 184) under low activation conditions. Utilizing tandem-MS, bacteriorhodopsin can be effectively liberated from the octylglucoside-micelle by collisional (Q-ToF and FT-ICR) or continuous IRMPD activation (FT-ICR). MSP1D1-Nd spectral complexity can also be significantly reduced by tandem-MS (Q-ToF and FT-ICR) followed by mild collisional or continuous IRMPD activation, resulting in a spectrum in which the charge state and phospholipid incorporation levels can easily be determined.
Collapse
Affiliation(s)
| | - Huilin Li
- UCLA Department of Chemistry and Biochemistry, Los Angeles, CA, 90095
| | - Dhanashri Bagal
- Discovery Analytical Sciences, Amgen, South San Francisco, CA, 94080, USA
| | | | - Juraj Svitel
- Department of Process Development, Amgen, Thousand Oaks, CA, 91320, USA
| | | | - Han Xu
- Department of Discovery Technologies, Amgen, Thousand Oaks, CA, 91320, USA
| | - Paul D. Schnier
- Discovery Analytical Sciences, Amgen, South San Francisco, CA, 94080, USA
| | - Joseph A. Loo
- UCLA Department of Chemistry and Biochemistry, Los Angeles, CA, 90095
| |
Collapse
|
584
|
Abstract
Membrane proteins play critical physiological roles and make up the majority of drug targets. Due to their generally low expression levels and amphipathic nature, membrane proteins represent challenging molecular entities for biophysical study. Mass spectrometry offers several sensitive approaches to study the biophysics of membrane proteins. By preserving noncovalent interactions in the gas phase and using collisional activation to remove solubilization agents inside the mass spectrometer, native mass spectrometry (MS) is capable of studying isolated assemblies that would be insoluble in aqueous solution, such as membrane protein oligomers and protein-lipid complexes. Conventional methods use detergent to solubilize the protein prior to electrospray ionization. Gas-phase activation inside the mass spectrometer removes the detergent to yield the isolated proteins with bound ligands. This approach has proven highly successful for ionizing membrane proteins. With the appropriate choice of detergents, membrane proteins with bound lipid species can be observed, which allows characterization of protein-lipid interactions. However, detergents have several limitations. They do not necessarily replicate the native lipid bilayer environment, and only a small number of protein-lipid interactions can be resolved. In this Account, we summarize the development of different membrane mimetics as cassettes for MS analysis of membrane proteins. Examples include amphipols, bicelles, and picodiscs with a special emphasis on lipoprotein nanodiscs. Polydispersity and heterogeneity of the membrane mimetic cassette is a critical issue for study by MS. Ever more complex data sets consisting of overlapping protein charge states and multiple lipid-bound entities have required development of new computational, theoretical, and experimental approaches to interpret both mass and ion mobility spectra. We will present the rationale and limitations of these approaches. Starting with the early work on empty nanodiscs, we chart developments that culminate in recent high-resolution studies of membrane protein-lipid complexes ejected from nanodiscs. For the latter, increasing collision energies allowed progressive removal of nanodisc components, beginning with the scaffold proteins and continuing through successive shells of lipids, allowing direct characterization of the stoichiometry of the annular lipid belt that surrounds the membrane protein. We consider future directions for the study of membrane proteins in membrane mimetics, including the development of mixed lipid systems and native bilayer environments. Unambiguous assignment of these heterogeneous systems will rely heavily upon further enhancements in both data analysis protocols and instrumental resolution. We anticipate that these developments will provide new insights into the factors that control dynamic protein-lipid interactions in a variety of tailored and natural lipid environments.
Collapse
Affiliation(s)
- Michael T. Marty
- Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry Laboratory, South Parks Road, OX1 3QZ (UK)
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85719 (USA)
| | - Kin Kuan Hoi
- Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry Laboratory, South Parks Road, OX1 3QZ (UK)
| | - Carol V. Robinson
- Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry Laboratory, South Parks Road, OX1 3QZ (UK)
| |
Collapse
|
585
|
Iadanza MG, Higgins AJ, Schiffrin B, Calabrese AN, Brockwell DJ, Ashcroft AE, Radford SE, Ranson NA. Lateral opening in the intact β-barrel assembly machinery captured by cryo-EM. Nat Commun 2016; 7:12865. [PMID: 27686148 PMCID: PMC5056442 DOI: 10.1038/ncomms12865] [Citation(s) in RCA: 138] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 08/04/2016] [Indexed: 02/06/2023] Open
Abstract
The β-barrel assembly machinery (BAM) is a ∼203 kDa complex of five proteins (BamA-E), which is essential for viability in E. coli. BAM promotes the folding and insertion of β-barrel proteins into the outer membrane via a poorly understood mechanism. Several current models suggest that BAM functions through a 'lateral gating' motion of the β-barrel of BamA. Here we present a cryo-EM structure of the BamABCDE complex, at 4.9 Å resolution. The structure is in a laterally open conformation showing that gating is independent of BamB binding. We describe conformational changes throughout the complex and interactions between BamA, B, D and E, and the detergent micelle that suggest communication between BAM and the lipid bilayer. Finally, using an enhanced reconstitution protocol and functional assays, we show that for the outer membrane protein OmpT, efficient folding in vitro requires lateral gating in BAM.
Collapse
Affiliation(s)
- Matthew G. Iadanza
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Mount Preston Street, Leeds LS2 9JT, UK
| | - Anna J. Higgins
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Mount Preston Street, Leeds LS2 9JT, UK
| | - Bob Schiffrin
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Mount Preston Street, Leeds LS2 9JT, UK
| | - Antonio N. Calabrese
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Mount Preston Street, Leeds LS2 9JT, UK
| | - David J. Brockwell
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Mount Preston Street, Leeds LS2 9JT, UK
| | - Alison E. Ashcroft
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Mount Preston Street, Leeds LS2 9JT, UK
| | - Sheena E. Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Mount Preston Street, Leeds LS2 9JT, UK
| | - Neil A. Ranson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Mount Preston Street, Leeds LS2 9JT, UK
| |
Collapse
|
586
|
Li J, Richards MR, Bagal D, Campuzano IDG, Kitova EN, Xiong ZJ, Privé GG, Klassen JS. Characterizing the Size and Composition of Saposin A Lipoprotein Picodiscs. Anal Chem 2016; 88:9524-9531. [PMID: 27532319 DOI: 10.1021/acs.analchem.6b02097] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Saposin A (SapA) lipoprotein discs, also known as picodiscs (PDs), represent an attractive method to solubilize glycolipids for protein interaction studies in aqueous solution. Recent electrospray ionization mass spectrometry (ESI-MS) data suggest that the size and composition of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)-containing PDs at neutral pH differs from those of N,N-dimethyldodecylamine N-oxide determined by X-ray crystallography. Using high-resolution ESI-MS, multiangle laser light scattering (MALLS), and molecular dynamics (MD) simulations, the composition, heterogeneity, and structure of POPC-PDs in aqueous ammonium acetate solutions at pH 4.8 and 6.8 were investigated. The ESI-MS and MALLS data revealed that POPC-PDs consist predominantly of (SapA dimer + iPOPC) complexes, with i = 23-29, and have an average molecular weight (MW) of 38.2 ± 3.3 kDa at pH 4.8. In contrast, in freshly prepared solutions at pH 6.8, POPC-PDs are composed predominantly of (SapA tetramer + iPOPC) complexes, with i = 37-60, with an average MW of 68.0 ± 2.7 kDa. However, the (SapA tetramer + iPOPC) complexes are unstable at neutral pH and convert, over a period of hours, to (SapA trimer + iPOPC) complexes, with i = 29-36, with an average MW of 51.1 ± 2.9 kDa. The results of molecular modeling suggest spheroidal structures for the (SapA dimer + iPOPC), (SapA trimer + iPOPC), and (SapA tetramer + iPOPC) complexes in solution. Comparison of measured collision cross sections (Ω) with values calculated for gaseous (SapA dimer + 26POPC)8+, (SapA trimer + 33POPC)12+, and (SapA tetramer + 42POPC)16+ ions produced from modeling suggests that the solution structures are largely preserved in the gas phase, although the lipids do not maintain regular bilayer orientations.
Collapse
Affiliation(s)
- Jun Li
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta , Edmonton, Alberta T6G 2G2, Canada
| | - Michele R Richards
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta , Edmonton, Alberta T6G 2G2, Canada
| | - Dhanashri Bagal
- Amgen, Discovery Analytical Sciences, Thousand Oaks, California 91320, United States
| | - Iain D G Campuzano
- Amgen, Discovery Analytical Sciences, Thousand Oaks, California 91320, United States
| | - Elena N Kitova
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta , Edmonton, Alberta T6G 2G2, Canada
| | - Zi Jian Xiong
- Department of Biochemistry, University of Toronto , Toronto, Ontario M5S 1A8, Canada
| | - Gilbert G Privé
- Department of Biochemistry, University of Toronto , Toronto, Ontario M5S 1A8, Canada.,Princess Margaret Cancer Centre, University Health Network , Toronto, Ontario M5G 1L7, Canada
| | - John S Klassen
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta , Edmonton, Alberta T6G 2G2, Canada
| |
Collapse
|
587
|
Landreh M, Marty MT, Gault J, Robinson CV. A sliding selectivity scale for lipid binding to membrane proteins. Curr Opin Struct Biol 2016; 39:54-60. [PMID: 27155089 PMCID: PMC5287393 DOI: 10.1016/j.sbi.2016.04.005] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 03/11/2016] [Accepted: 04/20/2016] [Indexed: 01/24/2023]
Abstract
Biological membranes form barriers that are essential for cellular integrity and compartmentalisation. Proteins in the membrane have co-evolved with their hydrophobic lipid environment, which serves as a solvent for proteins with very diverse requirements. As a result, their interactions range from non-selective to highly discriminating. Mass spectrometry enables us to monitor how lipids interact with membrane proteins and assess their effects on structure and dynamics. Recent studies illustrate the ability to differentiate specific lipid binding, preferential interactions with lipid subsets, and nonselective annular contacts. Here, we consider the biological implications of different lipid-binding scenarios and propose that binding occurs on a sliding selectivity scale, in line with the view of biological membranes as facilitators of dynamic protein and lipid organization.
Collapse
Affiliation(s)
- Michael Landreh
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, Oxfordshire, OX1 3QZ, United Kingdom
| | - Michael T Marty
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, Oxfordshire, OX1 3QZ, United Kingdom
| | - Joseph Gault
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, Oxfordshire, OX1 3QZ, United Kingdom
| | - Carol V Robinson
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, Oxfordshire, OX1 3QZ, United Kingdom.
| |
Collapse
|
588
|
Cai W, Tucholski TM, Gregorich ZR, Ge Y. Top-down Proteomics: Technology Advancements and Applications to Heart Diseases. Expert Rev Proteomics 2016; 13:717-30. [PMID: 27448560 DOI: 10.1080/14789450.2016.1209414] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
INTRODUCTION Heart diseases are a leading cause of morbidity and mortality for both men and women worldwide, and impose significant economic burdens on the healthcare systems. Despite substantial effort over the last several decades, the molecular mechanisms underlying diseases of the heart remain poorly understood. AREAS COVERED Altered protein post-translational modifications (PTMs) and protein isoform switching are increasingly recognized as important disease mechanisms. Top-down high-resolution mass spectrometry (MS)-based proteomics has emerged as the most powerful method for the comprehensive analysis of PTMs and protein isoforms. Here, we will review recent technology developments in the field of top-down proteomics, as well as highlight recent studies utilizing top-down proteomics to decipher the cardiac proteome for the understanding of the molecular mechanisms underlying diseases of the heart. Expert commentary: Top-down proteomics is a premier method for the global and comprehensive study of protein isoforms and their PTMs, enabling the identification of novel protein isoforms and PTMs, characterization of sequence variations, and quantification of disease-associated alterations. Despite significant challenges, continuous development of top-down proteomics technology will greatly aid the dissection of the molecular mechanisms underlying diseases of the hearts for the identification of novel biomarkers and therapeutic targets.
Collapse
Affiliation(s)
- Wenxuan Cai
- a Department of Cell and Regenerative Biology , University of Wisconsin-Madison , Madison , WI , USA.,b Molecular and Cellular Pharmacology Training Program , University of Wisconsin-Madison , Madison , WI , USA
| | - Trisha M Tucholski
- c Department of Chemistry , University of Wisconsin-Madison , Madison , WI , USA
| | - Zachery R Gregorich
- a Department of Cell and Regenerative Biology , University of Wisconsin-Madison , Madison , WI , USA.,b Molecular and Cellular Pharmacology Training Program , University of Wisconsin-Madison , Madison , WI , USA
| | - Ying Ge
- a Department of Cell and Regenerative Biology , University of Wisconsin-Madison , Madison , WI , USA.,c Department of Chemistry , University of Wisconsin-Madison , Madison , WI , USA.,d Human Proteomics Program , University of Wisconsin-Madison , Madison , WI , USA
| |
Collapse
|
589
|
Cleary SP, Thompson AM, Prell JS. Fourier Analysis Method for Analyzing Highly Congested Mass Spectra of Ion Populations with Repeated Subunits. Anal Chem 2016; 88:6205-13. [DOI: 10.1021/acs.analchem.6b01088] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Sean P. Cleary
- Department
of Chemistry and
Biochemistry, University of Oregon, Eugene, Oregon 97403-1253, United States
| | - Avery M. Thompson
- Department
of Chemistry and
Biochemistry, University of Oregon, Eugene, Oregon 97403-1253, United States
| | - James S. Prell
- Department
of Chemistry and
Biochemistry, University of Oregon, Eugene, Oregon 97403-1253, United States
| |
Collapse
|
590
|
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.
Collapse
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
| |
Collapse
|
591
|
Hendus-Altenburger R, Pedraz-Cuesta E, Olesen CW, Papaleo E, Schnell JA, Hopper JTS, Robinson CV, Pedersen SF, Kragelund BB. The human Na(+)/H(+) exchanger 1 is a membrane scaffold protein for extracellular signal-regulated kinase 2. BMC Biol 2016; 14:31. [PMID: 27083547 PMCID: PMC4833948 DOI: 10.1186/s12915-016-0252-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 03/29/2016] [Indexed: 11/22/2022] Open
Abstract
Background Extracellular signal-regulated kinase 2 (ERK2) is an S/T kinase with more than 200 known substrates, and with critical roles in regulation of cell growth and differentiation and currently no membrane proteins have been linked to ERK2 scaffolding. Methods and results Here, we identify the human Na+/H+ exchanger 1 (hNHE1) as a membrane scaffold protein for ERK2 and show direct hNHE1-ERK1/2 interaction in cellular contexts. Using nuclear magnetic resonance (NMR) spectroscopy and immunofluorescence analysis we demonstrate that ERK2 scaffolding by hNHE1 occurs by one of three D-domains and by two non-canonical F-sites located in the disordered intracellular tail of hNHE1, mutation of which reduced cellular hNHE1-ERK1/2 co-localization, as well as reduced cellular ERK1/2 activation. Time-resolved NMR spectroscopy revealed that ERK2 phosphorylated the disordered tail of hNHE1 at six sites in vitro, in a distinct temporal order, with the phosphorylation rates at the individual sites being modulated by the docking sites in a distant dependent manner. Conclusions This work characterizes a new type of scaffolding complex, which we term a “shuffle complex”, between the disordered hNHE1-tail and ERK2, and provides a molecular mechanism for the important ERK2 scaffolding function of the membrane protein hNHE1, which regulates the phosphorylation of both hNHE1 and ERK2. Electronic supplementary material The online version of this article (doi:10.1186/s12915-016-0252-7) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Ruth Hendus-Altenburger
- Cell and Developmental Biology, Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100, Copenhagen Ø, Denmark.,Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200, Copenhagen N, Denmark
| | - Elena Pedraz-Cuesta
- Cell and Developmental Biology, Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100, Copenhagen Ø, Denmark
| | - Christina W Olesen
- Cell and Developmental Biology, Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100, Copenhagen Ø, Denmark
| | - Elena Papaleo
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200, Copenhagen N, Denmark
| | - Jeff A Schnell
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200, Copenhagen N, Denmark
| | - Jonathan T S Hopper
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK
| | - Carol V Robinson
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK
| | - Stine F Pedersen
- Cell and Developmental Biology, Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100, Copenhagen Ø, Denmark.
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200, Copenhagen N, Denmark.
| |
Collapse
|
592
|
Gault J, Donlan JAC, Liko I, Hopper JTS, Gupta K, Housden NG, Struwe WB, Marty MT, Mize T, Bechara C, Zhu Y, Wu B, Kleanthous C, Belov M, Damoc E, Makarov A, Robinson CV. High-resolution mass spectrometry of small molecules bound to membrane proteins. Nat Methods 2016; 13:333-6. [PMID: 26901650 PMCID: PMC4856209 DOI: 10.1038/nmeth.3771] [Citation(s) in RCA: 178] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 01/13/2016] [Indexed: 12/24/2022]
Abstract
Small molecules are known to stabilize membrane proteins and to modulate their function and oligomeric state, but such interactions are often hard to precisely define. Here we develop and apply a high-resolution, Orbitrap mass spectrometry-based method for analyzing intact membrane protein-ligand complexes. Using this platform, we resolve the complexity of multiple binding events, quantify small molecule binding and reveal selectivity for endogenous lipids that differ only in acyl chain length.
Collapse
Affiliation(s)
- Joseph Gault
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Joseph A C Donlan
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Idlir Liko
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Jonathan T S Hopper
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Kallol Gupta
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK
| | | | - Weston B Struwe
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Michael T Marty
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Todd Mize
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Cherine Bechara
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Ya Zhu
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Pudong, China
| | - Beili Wu
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Pudong, China
| | | | | | | | | | - Carol V Robinson
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK
| |
Collapse
|
593
|
Cong X, Liu Y, Liu W, Liang X, Russell DH, Laganowsky A. Determining Membrane Protein-Lipid Binding Thermodynamics Using Native Mass Spectrometry. J Am Chem Soc 2016; 138:4346-9. [PMID: 27015007 DOI: 10.1021/jacs.6b01771] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Membrane proteins are embedded in the biological membrane where the chemically diverse lipid environment can modulate their structure and function. However, the thermodynamics governing the molecular recognition and interaction of lipids with membrane proteins is poorly understood. Here, we report a method using native mass spectrometry (MS), to determine thermodynamics of individual ligand binding events to proteins. Unlike conventional methods, native MS can resolve individual ligand binding events and, coupled with an apparatus to control the temperature, determine binding thermodynamic parameters, such as for protein-lipid interactions. We validated our approach using three soluble protein-ligand systems (maltose binding protein, lysozyme, and nitrogen regulatory protein) and obtained similar results to those using isothermal titration calorimetry and surface plasmon resonance. We also determined for the first time the thermodynamics of individual lipid binding to the ammonia channel (AmtB), an integral membrane protein from Escherichia coli. Remarkably, we observed distinct thermodynamic signatures for the binding of different lipids and entropy-enthalpy compensation for binding lipids of variable chain length. Additionally, using a mutant form of AmtB that abolishes a specific phosphatidylglycerol (PG) binding site, we observed distinct changes in the thermodynamic signatures for binding PG, implying these signatures can identify key residues involved in specific lipid binding and potentially differentiate between specific lipid binding sites.
Collapse
Affiliation(s)
- Xiao Cong
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center , Houston, Texas 77030, United States
| | - Yang Liu
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center , Houston, Texas 77030, United States
| | - Wen Liu
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center , Houston, Texas 77030, United States
| | - Xiaowen Liang
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center , Houston, Texas 77030, United States
| | - David H Russell
- Department of Chemistry, Texas A&M University , College Station, Texas 77842, United States
| | - Arthur Laganowsky
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center , Houston, Texas 77030, United States.,Department of Chemistry, Texas A&M University , College Station, Texas 77842, United States.,Department of Microbial Pathogenesis & Immunology, College of Medicine, Texas A&M Health Science Center , Bryan, Texas 77807, United States
| |
Collapse
|
594
|
Reading E, Walton TA, Liko I, Marty MT, Laganowsky A, Rees DC, Robinson CV. The Effect of Detergent, Temperature, and Lipid on the Oligomeric State of MscL Constructs: Insights from Mass Spectrometry. ACTA ACUST UNITED AC 2016; 22:593-603. [PMID: 26000747 DOI: 10.1016/j.chembiol.2015.04.016] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 04/23/2015] [Accepted: 04/27/2015] [Indexed: 12/17/2022]
Abstract
The mechanosensitive channel of large conductance (MscL) acts as an emergency release valve for osmotic shock of bacteria preventing cell lysis. The large pore size, essential for function, requires the formation of oligomers with tetramers, pentamers, or hexamers observed depending on the species and experimental approach. We applied non-denaturing (native) mass spectrometry to five different homologs of MscL to determine the oligomeric state under more than 50 different experimental conditions elucidating lipid binding and subunit stoichiometry. We found equilibrium between pentameric and tetrameric species, which can be altered by detergent, disrupted by binding specific lipids, and perturbed by increasing temperature (37°C). We also established the presence of lipopolysaccharide bound to MscL and other membrane proteins expressed in Escherichia coli, revealing a potential source of heterogeneity. More generally, we highlight the use of mass spectrometry in probing membrane proteins under a variety of detergent-lipid environments relevant to structural biology.
Collapse
Affiliation(s)
- Eamonn Reading
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3TA, UK
| | - Troy A Walton
- Division of Chemistry and Chemical Engineering 114-96, Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Idlir Liko
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3TA, UK
| | - Michael T Marty
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3TA, UK
| | - Arthur Laganowsky
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3TA, UK
| | - Douglas C Rees
- Division of Chemistry and Chemical Engineering 114-96, Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Carol V Robinson
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3TA, UK.
| |
Collapse
|
595
|
Bonomi M, Camilloni C, Cavalli A, Vendruscolo M. Metainference: A Bayesian inference method for heterogeneous systems. SCIENCE ADVANCES 2016; 2:e1501177. [PMID: 26844300 PMCID: PMC4737209 DOI: 10.1126/sciadv.1501177] [Citation(s) in RCA: 127] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 11/21/2015] [Indexed: 05/22/2023]
Abstract
Modeling a complex system is almost invariably a challenging task. The incorporation of experimental observations can be used to improve the quality of a model and thus to obtain better predictions about the behavior of the corresponding system. This approach, however, is affected by a variety of different errors, especially when a system simultaneously populates an ensemble of different states and experimental data are measured as averages over such states. To address this problem, we present a Bayesian inference method, called "metainference," that is able to deal with errors in experimental measurements and with experimental measurements averaged over multiple states. To achieve this goal, metainference models a finite sample of the distribution of models using a replica approach, in the spirit of the replica-averaging modeling based on the maximum entropy principle. To illustrate the method, we present its application to a heterogeneous model system and to the determination of an ensemble of structures corresponding to the thermal fluctuations of a protein molecule. Metainference thus provides an approach to modeling complex systems with heterogeneous components and interconverting between different states by taking into account all possible sources of errors.
Collapse
Affiliation(s)
- Massimiliano Bonomi
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
- Corresponding author. E-mail: (M.B.); (M.V.)
| | - Carlo Camilloni
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Andrea Cavalli
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
- Institute for Research in Biomedicine, CH-6500 Bellinzona, Switzerland
| | - Michele Vendruscolo
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
- Corresponding author. E-mail: (M.B.); (M.V.)
| |
Collapse
|
596
|
Lu J, Trnka MJ, Roh SH, Robinson PJJ, Shiau C, Fujimori DG, Chiu W, Burlingame AL, Guan S. Improved Peak Detection and Deconvolution of Native Electrospray Mass Spectra from Large Protein Complexes. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:2141-51. [PMID: 26323614 PMCID: PMC5067139 DOI: 10.1007/s13361-015-1235-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 07/20/2015] [Accepted: 07/22/2015] [Indexed: 05/11/2023]
Abstract
Native electrospray-ionization mass spectrometry (native MS) measures biomolecules under conditions that preserve most aspects of protein tertiary and quaternary structure, enabling direct characterization of large intact protein assemblies. However, native spectra derived from these assemblies are often partially obscured by low signal-to-noise as well as broad peak shapes because of residual solvation and adduction after the electrospray process. The wide peak widths together with the fact that sequential charge state series from highly charged ions are closely spaced means that native spectra containing multiple species often suffer from high degrees of peak overlap or else contain highly interleaved charge envelopes. This situation presents a challenge for peak detection, correct charge state and charge envelope assignment, and ultimately extraction of the relevant underlying mass values of the noncovalent assemblages being investigated. In this report, we describe a comprehensive algorithm developed for addressing peak detection, peak overlap, and charge state assignment in native mass spectra, called PeakSeeker. Overlapped peaks are detected by examination of the second derivative of the raw mass spectrum. Charge state distributions of the molecular species are determined by fitting linear combinations of charge envelopes to the overall experimental mass spectrum. This software is capable of deconvoluting heterogeneous, complex, and noisy native mass spectra of large protein assemblies as demonstrated by analysis of (1) synthetic mononucleosomes containing severely overlapping peaks, (2) an RNA polymerase II/α-amanitin complex with many closely interleaved ion signals, and (3) human TriC complex containing high levels of background noise. Graphical Abstract ᅟ.
Collapse
Affiliation(s)
- Jonathan Lu
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, 94158, USA
- Princeton University, Princeton, NJ, 08544, USA
| | - Michael J Trnka
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, 94158, USA
| | - Soung-Hun Roh
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Philip J J Robinson
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Carrie Shiau
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, 94158, USA
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, CA, 94158, USA
| | - Danica Galonic Fujimori
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, 94158, USA
| | - Wah Chiu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Alma L Burlingame
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, 94158, USA
| | - Shenheng Guan
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, 94158, USA.
- Institute for Neurodegenerative Diseases, University of California, San Francisco, CA, 94143, USA.
| |
Collapse
|
597
|
Laszlo KJ, Bush MF. Analysis of Native-Like Proteins and Protein Complexes Using Cation to Anion Proton Transfer Reactions (CAPTR). JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:2152-61. [PMID: 26323617 PMCID: PMC4655144 DOI: 10.1007/s13361-015-1245-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 07/23/2015] [Accepted: 08/01/2015] [Indexed: 05/08/2023]
Abstract
Mass spectra of native-like protein complexes often exhibit narrow charge-state distributions, broad peaks, and contributions from multiple, coexisting species. These factors can make it challenging to interpret those spectra, particularly for mixtures with significant heterogeneity. Here we demonstrate the use of ion/ion proton transfer reactions to reduce the charge states of m/z-selected, native-like ions of proteins and protein complexes, a technique that we refer to as cation to anion proton transfer reactions (CAPTR). We then demonstrate that CAPTR can increase the accuracy of charge state assignments and the resolution of interfering species in native mass spectrometry. The CAPTR product ion spectra for pyruvate kinase exhibit ~30 peaks and enable unambiguous determination of the charge state of each peak, whereas the corresponding precursor spectra exhibit ~6 peaks and the assigned charge states have an uncertainty of ±3%. 15+ bovine serum albumin and 21+ yeast enolase dimer both appear near m/z 4450 and are completely unresolved in a mixture. After a single CAPTR event, the resulting product ions are baseline resolved. The separation of the product ions increases dramatically after each subsequent CAPTR event; 12 events resulted in a 3000-fold improvement in separation relative to the precursor ions. Finally, we introduce a framework for interpreting and predicting the figures of merit for CAPTR experiments. More generally, these results suggest that CAPTR strongly complements other mass spectrometry tools for analyzing proteins and protein complexes, particularly those in mixtures. Graphical Abstract ᅟ.
Collapse
Affiliation(s)
- Kenneth J Laszlo
- Department of Chemistry, University of Washington, Seattle, WA, 98195-1700, USA
| | - Matthew F Bush
- Department of Chemistry, University of Washington, Seattle, WA, 98195-1700, USA.
| |
Collapse
|
598
|
Cai W, Guner H, Gregorich ZR, Chen AJ, Ayaz-Guner S, Peng Y, Valeja SG, Liu X, Ge Y. MASH Suite Pro: A Comprehensive Software Tool for Top-Down Proteomics. Mol Cell Proteomics 2015; 15:703-14. [PMID: 26598644 DOI: 10.1074/mcp.o115.054387] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Indexed: 12/25/2022] Open
Abstract
Top-down mass spectrometry (MS)-based proteomics is arguably a disruptive technology for the comprehensive analysis of all proteoforms arising from genetic variation, alternative splicing, and posttranslational modifications (PTMs). However, the complexity of top-down high-resolution mass spectra presents a significant challenge for data analysis. In contrast to the well-developed software packages available for data analysis in bottom-up proteomics, the data analysis tools in top-down proteomics remain underdeveloped. Moreover, despite recent efforts to develop algorithms and tools for the deconvolution of top-down high-resolution mass spectra and the identification of proteins from complex mixtures, a multifunctional software platform, which allows for the identification, quantitation, and characterization of proteoforms with visual validation, is still lacking. Herein, we have developed MASH Suite Pro, a comprehensive software tool for top-down proteomics with multifaceted functionality. MASH Suite Pro is capable of processing high-resolution MS and tandem MS (MS/MS) data using two deconvolution algorithms to optimize protein identification results. In addition, MASH Suite Pro allows for the characterization of PTMs and sequence variations, as well as the relative quantitation of multiple proteoforms in different experimental conditions. The program also provides visualization components for validation and correction of the computational outputs. Furthermore, MASH Suite Pro facilitates data reporting and presentation via direct output of the graphics. Thus, MASH Suite Pro significantly simplifies and speeds up the interpretation of high-resolution top-down proteomics data by integrating tools for protein identification, quantitation, characterization, and visual validation into a customizable and user-friendly interface. We envision that MASH Suite Pro will play an integral role in advancing the burgeoning field of top-down proteomics.
Collapse
Affiliation(s)
- Wenxuan Cai
- From the ‡Department of Cell and Regenerative Biology, §Molecular Pharmacology Training Program
| | - Huseyin Guner
- From the ‡Department of Cell and Regenerative Biology, ¶Human Proteomics Program
| | - Zachery R Gregorich
- From the ‡Department of Cell and Regenerative Biology, §Molecular Pharmacology Training Program
| | - Albert J Chen
- From the ‡Department of Cell and Regenerative Biology
| | | | - Ying Peng
- From the ‡Department of Cell and Regenerative Biology
| | | | - Xiaowen Liu
- **Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 410 West 10th Street, Indianapolis, IN 46202
| | - Ying Ge
- From the ‡Department of Cell and Regenerative Biology, ¶Human Proteomics Program, ‡‡Department of Chemistry, University of Wisconsin-Madison, 1300 University Ave., Madison, WI 53706,Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, 719 Indiana Ave., Indianapolis, IN 46202,
| |
Collapse
|
599
|
Marty MT, Hoi KK, Gault J, Robinson CV. Probing the Lipid Annular Belt by Gas-Phase Dissociation of Membrane Proteins in Nanodiscs. Angew Chem Int Ed Engl 2015; 55:550-4. [PMID: 26594028 PMCID: PMC4736441 DOI: 10.1002/anie.201508289] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 10/15/2015] [Indexed: 11/11/2022]
Abstract
Interactions between membrane proteins and lipids are often crucial for structure and function yet difficult to define because of their dynamic and heterogeneous nature. Here, we use mass spectrometry to demonstrate that membrane protein oligomers ejected from nanodiscs in the gas phase retain large numbers of lipid interactions. The complex mass spectra that result from gas-phase dissociation were assigned using a Bayesian deconvolution algorithm together with mass defect analysis, allowing us to count individual lipid molecules bound to membrane proteins. Comparison of the lipid distributions measured by mass spectrometry with molecular dynamics simulations reveals that the distributions correspond to distinct lipid shells that vary according to the type of protein-lipid interactions. Our results demonstrate that nanodiscs offer the potential for native mass spectrometry to probe interactions between membrane proteins and the wider lipid environment.
Collapse
Affiliation(s)
- Michael T Marty
- Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford OX1 3QZ (UK)
| | - Kin Kuan Hoi
- Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford OX1 3QZ (UK)
| | - Joseph Gault
- Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford OX1 3QZ (UK)
| | - Carol V Robinson
- Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford OX1 3QZ (UK).
| |
Collapse
|
600
|
Marty MT, Hoi KK, Gault J, Robinson CV. Probing the Lipid Annular Belt by Gas-Phase Dissociation of Membrane Proteins in Nanodiscs. ACTA ACUST UNITED AC 2015; 128:560-564. [PMID: 30416215 PMCID: PMC6213558 DOI: 10.1002/ange.201508289] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 10/15/2015] [Indexed: 12/21/2022]
Abstract
Interactions between membrane proteins and lipids are often crucial for structure and function yet difficult to define because of their dynamic and heterogeneous nature. Here, we use mass spectrometry to demonstrate that membrane protein oligomers ejected from nanodiscs in the gas phase retain large numbers of lipid interactions. The complex mass spectra that result from gas‐phase dissociation were assigned using a Bayesian deconvolution algorithm together with mass defect analysis, allowing us to count individual lipid molecules bound to membrane proteins. Comparison of the lipid distributions measured by mass spectrometry with molecular dynamics simulations reveals that the distributions correspond to distinct lipid shells that vary according to the type of protein–lipid interactions. Our results demonstrate that nanodiscs offer the potential for native mass spectrometry to probe interactions between membrane proteins and the wider lipid environment.
Collapse
Affiliation(s)
- Michael T Marty
- Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford OX1 3QZ (UK)
| | - Kin Kuan Hoi
- Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford OX1 3QZ (UK)
| | - Joseph Gault
- Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford OX1 3QZ (UK)
| | - Carol V Robinson
- Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford OX1 3QZ (UK)
| |
Collapse
|