1
|
Yen HY, Liko I, Song W, Kapoor P, Almeida F, Toporowska J, Gherbi K, Hopper JTS, Charlton SJ, Politis A, Sansom MSP, Jazayeri A, Robinson CV. Mass spectrometry captures biased signalling and allosteric modulation of a G-protein-coupled receptor. Nat Chem 2022; 14:1375-1382. [PMID: 36357787 PMCID: PMC9758051 DOI: 10.1038/s41557-022-01041-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 08/09/2022] [Indexed: 11/12/2022]
Abstract
G-protein-coupled receptors signal through cognate G proteins. Despite the widespread importance of these receptors, their regulatory mechanisms for G-protein selectivity are not fully understood. Here we present a native mass spectrometry-based approach to interrogate both biased signalling and allosteric modulation of the β1-adrenergic receptor in response to various ligands. By simultaneously capturing the effects of ligand binding and receptor coupling to different G proteins, we probed the relative importance of specific interactions with the receptor through systematic changes in 14 ligands, including isoprenaline derivatives, full and partial agonists, and antagonists. We observed enhanced dynamics of the intracellular loop 3 in the presence of isoprenaline, which is capable of acting as a biased agonist. We also show here that endogenous zinc ions augment the binding in receptor-Gs complexes and propose a zinc ion-binding hotspot at the TM5/TM6 intracellular interface of the receptor-Gs complex. Further interrogation led us to propose a mechanism in which zinc ions facilitate a structural transition of the intermediate complex towards the stable state.
Collapse
Affiliation(s)
- Hsin-Yung Yen
- Chemical Research Laboratory, University of Oxford, Oxford, UK.
- OMass Therapeutics, Oxford, UK.
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.
| | - Idlir Liko
- Chemical Research Laboratory, University of Oxford, Oxford, UK
- OMass Therapeutics, Oxford, UK
| | - Wanling Song
- Department of Biochemistry, University of Oxford, Oxford, UK
- Rahko, London, UK
| | | | | | | | | | | | - Steven J Charlton
- OMass Therapeutics, Oxford, UK
- School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, UK
| | - Argyris Politis
- Department of Chemistry, King's College London, London, UK
- Faculty of Biology, Medicine and Health, School of Biological Sciences, The University of Manchester, Manchester, UK
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, Oxford, UK
| | | | - Carol V Robinson
- Chemical Research Laboratory, University of Oxford, Oxford, UK.
- Kavli Institute for Nanoscience Discovery, Oxford, UK.
| |
Collapse
|
2
|
Abramsson ML, Sahin C, Hopper JTS, Branca RMM, Danielsson J, Xu M, Chandler SA, Österlund N, Ilag LL, Leppert A, Costeira-Paulo J, Lang L, Teilum K, Laganowsky A, Benesch JLP, Oliveberg M, Robinson CV, Marklund EG, Allison TM, Winther JR, Landreh M. Charge Engineering Reveals the Roles of Ionizable Side Chains in Electrospray Ionization Mass Spectrometry. JACS Au 2021; 1:2385-2393. [PMID: 34977906 PMCID: PMC8717373 DOI: 10.1021/jacsau.1c00458] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Indexed: 05/03/2023]
Abstract
In solution, the charge of a protein is intricately linked to its stability, but electrospray ionization distorts this connection, potentially limiting the ability of native mass spectrometry to inform about protein structure and dynamics. How the behavior of intact proteins in the gas phase depends on the presence and distribution of ionizable surface residues has been difficult to answer because multiple chargeable sites are present in virtually all proteins. Turning to protein engineering, we show that ionizable side chains are completely dispensable for charging under native conditions, but if present, they are preferential protonation sites. The absence of ionizable side chains results in identical charge state distributions under native-like and denaturing conditions, while coexisting conformers can be distinguished using ion mobility separation. An excess of ionizable side chains, on the other hand, effectively modulates protein ion stability. In fact, moving a single ionizable group can dramatically alter the gas-phase conformation of a protein ion. We conclude that although the sum of the charges is governed solely by Coulombic terms, their locations affect the stability of the protein in the gas phase.
Collapse
Affiliation(s)
- Mia L. Abramsson
- Department
of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Tomtebodavägen 23A, 171 65 Stockholm, Sweden
| | - Cagla Sahin
- Department
of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Tomtebodavägen 23A, 171 65 Stockholm, Sweden
- Linderstrøm-Lang
Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes vej 5, 2200 Copenhagen, Denmark
| | - Jonathan T. S. Hopper
- Department
of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K.
| | - Rui M. M. Branca
- Department
of Oncology-Pathology, Science for Life
Laboratory and Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Jens Danielsson
- Department
of Biochemistry and Biophysics, Stockholm
University, 106 91 Stockholm, Sweden
| | - Mingming Xu
- Department
of Biochemistry and Biophysics, Stockholm
University, 106 91 Stockholm, Sweden
| | - Shane A. Chandler
- Department
of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K.
| | - Nicklas Österlund
- Department
of Biochemistry and Biophysics, Stockholm
University, 106 91 Stockholm, Sweden
| | - Leopold L. Ilag
- Department
of Material and Environmental Chemistry, Stockholm University, 106 91 Stockholm, Sweden
| | - Axel Leppert
- Department
of Biosciences and Nutrition, Karolinska
Institutet, Neo, 141 83 Huddinge, Sweden
| | - Joana Costeira-Paulo
- Department
of Chemistry−BMC, Uppsala University, Box 576, 751 23 Uppsala, Sweden
| | - Lisa Lang
- Department
of Biochemistry and Biophysics, Stockholm
University, 106 91 Stockholm, Sweden
| | - Kaare Teilum
- Linderstrøm-Lang
Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes vej 5, 2200 Copenhagen, Denmark
| | - Arthur Laganowsky
- Department
of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Justin L. P. Benesch
- Department
of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K.
| | - Mikael Oliveberg
- Department
of Biochemistry and Biophysics, Stockholm
University, 106 91 Stockholm, Sweden
| | - Carol V. Robinson
- Department
of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K.
| | - Erik G. Marklund
- Department
of Chemistry−BMC, Uppsala University, Box 576, 751 23 Uppsala, Sweden
| | - Timothy M. Allison
- Biomolecular
Interaction Centre, School of Physical and Chemical Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Jakob R. Winther
- Linderstrøm-Lang
Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes vej 5, 2200 Copenhagen, Denmark
| | - Michael Landreh
- Department
of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Tomtebodavägen 23A, 171 65 Stockholm, Sweden
| |
Collapse
|
3
|
Jansen KB, Inns PG, Housden NG, Hopper JTS, Kaminska R, Lee S, Robinson CV, Bayley H, Kleanthous C. Bifurcated binding of the OmpF receptor underpins import of the bacteriocin colicin N into Escherichia coli. J Biol Chem 2020; 295:9147-9156. [PMID: 32398259 PMCID: PMC7335789 DOI: 10.1074/jbc.ra120.013508] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 05/04/2020] [Indexed: 11/14/2022] Open
Abstract
Colicins are Escherichia coli-specific bacteriocins that translocate across the outer bacterial membrane by a poorly understood mechanism. Group A colicins typically parasitize the proton-motive force-linked Tol system in the inner membrane via porins after first binding an outer membrane protein receptor. Recent studies have suggested that the pore-forming group A colicin N (ColN) instead uses lipopolysaccharide as a receptor. Contrary to this prevailing view, using diffusion-precipitation assays, native state MS, isothermal titration calorimetry, single-channel conductance measurements in planar lipid bilayers, and in vivo fluorescence imaging, we demonstrate here that ColN uses OmpF both as its receptor and translocator. This dual function is achieved by ColN having multiple distinct OmpF-binding sites, one located within its central globular domain and another within its disordered N terminus. We observed that the ColN globular domain associates with the extracellular surface of OmpF and that lipopolysaccharide (LPS) enhances this binding. Approximately 90 amino acids of ColN then translocate through the porin, enabling the ColN N terminus to localize within the lumen of an OmpF subunit from the periplasmic side of the membrane, a binding mode reminiscent of that observed for the nuclease colicin E9. We conclude that bifurcated engagement of porins is intrinsic to the import mechanism of group A colicins.
Collapse
Affiliation(s)
| | | | | | | | - Renata Kaminska
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Sejeong Lee
- Chemistry Research laboratory, University of Oxford, Oxford, United Kingdom
| | - Carol V Robinson
- Chemistry Research laboratory, University of Oxford, Oxford, United Kingdom
| | - Hagan Bayley
- Chemistry Research laboratory, University of Oxford, Oxford, United Kingdom
| | - Colin Kleanthous
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom.
| |
Collapse
|
4
|
Bolla JR, Corey RA, Sahin C, Gault J, Hummer A, Hopper JTS, Lane DP, Drew D, Allison TM, Stansfeld PJ, Robinson CV, Landreh M. A Mass‐Spectrometry‐Based Approach to Distinguish Annular and Specific Lipid Binding to Membrane Proteins. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201914411] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Jani Reddy Bolla
- Department of ChemistryUniversity of Oxford South Parks Road Oxford OX1 3QZ UK
| | - Robin A. Corey
- Department of BiochemistryUniversity of Oxford South Parks Road Oxford OX1 3QU UK
| | - Cagla Sahin
- Department of Microbiology, Tumor and Cell BiologyKarolinska Institutet 17165 Solna Sweden
- Department of BiologyUniversity of Copenhagen Copenhagen N 2200 Denmark
| | - Joseph Gault
- Department of ChemistryUniversity of Oxford South Parks Road Oxford OX1 3QZ UK
| | - Alissa Hummer
- Department of BiochemistryUniversity of Oxford South Parks Road Oxford OX1 3QU UK
| | - Jonathan T. S. Hopper
- OMass Therapeutics The Oxford Science Park, The Schrödinger Building Kidlington OX4 4GE UK
| | - David P. Lane
- Department of Microbiology, Tumor and Cell BiologyKarolinska Institutet 17165 Solna Sweden
| | - David Drew
- Department of Biochemistry and BiophysicsStockholm University 10691 Stockholm Sweden
| | - Timothy M. Allison
- Biomolecular Interaction Centre and School of Physical and Chemical SciencesUniversity of Canterbury Christchurch 8140 New Zealand
| | - Phillip J. Stansfeld
- Department of BiochemistryUniversity of Oxford South Parks Road Oxford OX1 3QU UK
- School of Life Sciences & Department of ChemistryUniversity of Warwick Coventry CV4 7AL UK
| | - Carol V. Robinson
- Department of ChemistryUniversity of Oxford South Parks Road Oxford OX1 3QZ UK
| | - Michael Landreh
- Department of Microbiology, Tumor and Cell BiologyKarolinska Institutet 17165 Solna Sweden
| |
Collapse
|
5
|
Bolla JR, Corey RA, Sahin C, Gault J, Hummer A, Hopper JTS, Lane DP, Drew D, Allison TM, Stansfeld PJ, Robinson CV, Landreh M. A Mass-Spectrometry-Based Approach to Distinguish Annular and Specific Lipid Binding to Membrane Proteins. Angew Chem Int Ed Engl 2020; 59:3523-3528. [PMID: 31886601 PMCID: PMC7065234 DOI: 10.1002/anie.201914411] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 12/29/2019] [Indexed: 01/21/2023]
Abstract
Membrane proteins engage in a variety of contacts with their surrounding lipids, but distinguishing between specifically bound lipids, and non‐specific, annular interactions is a challenging problem. Applying native mass spectrometry to three membrane protein complexes with different lipid‐binding properties, we explore the ability of detergents to compete with lipids bound in different environments. We show that lipids in annular positions on the presenilin homologue protease are subject to constant exchange with detergent. By contrast, detergent‐resistant lipids bound at the dimer interface in the leucine transporter show decreased koff rates in molecular dynamics simulations. Turning to the lipid flippase MurJ, we find that addition of the natural substrate lipid‐II results in the formation of a 1:1 protein–lipid complex, where the lipid cannot be displaced by detergent from the highly protected active site. In summary, we distinguish annular from non‐annular lipids based on their exchange rates in solution.
Collapse
Affiliation(s)
- Jani Reddy Bolla
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK
| | - Robin A Corey
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Cagla Sahin
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17165, Solna, Sweden.,Department of Biology, University of Copenhagen, Copenhagen N, 2200, Denmark
| | - Joseph Gault
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK
| | - Alissa Hummer
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Jonathan T S Hopper
- OMass Therapeutics, The Oxford Science Park, The Schrödinger Building, Kidlington, OX4 4GE, UK
| | - David P Lane
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17165, Solna, Sweden
| | - David Drew
- Department of Biochemistry and Biophysics, Stockholm University, 10691, Stockholm, Sweden
| | - Timothy M Allison
- Biomolecular Interaction Centre and School of Physical and Chemical Sciences, University of Canterbury, Christchurch, 8140, New Zealand
| | - Phillip J Stansfeld
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.,School of Life Sciences & Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
| | - Carol V Robinson
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK
| | - Michael Landreh
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17165, Solna, Sweden
| |
Collapse
|
6
|
Gupta K, Li J, Liko I, Gault J, Bechara C, Wu D, Hopper JTS, Giles K, Benesch JLP, Robinson CV. Identifying key membrane protein lipid interactions using mass spectrometry. Nat Protoc 2018; 13:1106-1120. [PMID: 29700483 PMCID: PMC6049616 DOI: 10.1038/nprot.2018.014] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
With the recent success in determining membrane protein structures, further detailed understanding of the identity and function of the bound lipidome is essential. Using an approach that combines high-energy native mass spectrometry (HE-nMS) and solution-phase lipid profiling, this protocol can be used to determine the identity of the endogenous lipids that directly interact with a protein. Furthermore, this method can identify systems in which such lipid binding has a major role in regulating the oligomeric assembly of membrane proteins. The protocol begins with recording of the native mass spectrum of the protein of interest, under successive delipidation conditions, to determine whether delipidation leads to disruption of the oligomeric state. Subsequently, we propose using a bipronged strategy: first, an HE-nMS platform is used that allows dissociation of the detergent micelle at the front end of the instrument. This allows for isolation of the protein-lipid complex at the quadrupole and successive fragmentation at the collision cell, which leads to identification of the bound lipid masses. Next, simultaneous coupling of this with in-solution LC-MS/MS-based identification of extracted lipids reveals the complete identity of the interacting lipidome that copurifies with the proteins. Assimilation of the results of these two sets of experiments divulges the complete identity of the set of lipids that directly interact with the membrane protein of interest, and can further delineate its role in maintaining the oligomeric state of the protein. The entire procedure takes 2 d to complete.
Collapse
Affiliation(s)
- Kallol Gupta
- Department of Chemistry, University of Oxford, Oxford, UK
| | - Jingwen Li
- Department of Chemistry, University of Oxford, Oxford, UK
| | - Idlir Liko
- Department of Chemistry, University of Oxford, Oxford, UK
| | - Joseph Gault
- Department of Chemistry, University of Oxford, Oxford, UK
| | - Cherine Bechara
- Department of Chemistry, University of Oxford, Oxford, UK
- Institut de Genomique Fonctionnelle, CNRS UMR-5203, INSERM U1191, University of Montpellier, Montpellier, France
| | - Di Wu
- Department of Chemistry, University of Oxford, Oxford, UK
| | | | | | | | | |
Collapse
|
7
|
Natan E, Endoh T, Haim-Vilmovsky L, Flock T, Chalancon G, Hopper JTS, Kintses B, Horvath P, Daruka L, Fekete G, Pál C, Papp B, Oszi E, Magyar Z, Marsh JA, Elcock AH, Babu MM, Robinson CV, Sugimoto N, Teichmann SA. Cotranslational protein assembly imposes evolutionary constraints on homomeric proteins. Nat Struct Mol Biol 2018; 25:279-288. [PMID: 29434345 PMCID: PMC5995306 DOI: 10.1038/s41594-018-0029-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 01/10/2018] [Indexed: 01/11/2023]
Abstract
Cotranslational protein folding can facilitate rapid formation of functional structures. However, it can also cause premature assembly of protein complexes, if two interacting nascent chains are in close proximity. By analyzing known protein structures, we show that homomeric protein contacts are enriched toward the C termini of polypeptide chains across diverse proteomes. We hypothesize that this is the result of evolutionary constraints for folding to occur before assembly. Using high-throughput imaging of protein homomers in Escherichia coli and engineered protein constructs with N- and C-terminal oligomerization domains, we show that, indeed, proteins with C-terminal homomeric interface residues consistently assemble more efficiently than those with N-terminal interface residues. Using in vivo, in vitro and in silico experiments, we identify features that govern successful assembly of homomers, which have implications for protein design and expression optimization.
Collapse
Affiliation(s)
| | - Tamaki Endoh
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, Kobe, Japan
| | - Liora Haim-Vilmovsky
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Tilman Flock
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | | | | | - Bálint Kintses
- Synthetic and System Biology Unit, Biological Research Center of the Hungarian Academia of Sciences, Szeged, Hungary
| | - Peter Horvath
- Synthetic and System Biology Unit, Biological Research Center of the Hungarian Academia of Sciences, Szeged, Hungary
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Lejla Daruka
- Synthetic and System Biology Unit, Biological Research Center of the Hungarian Academia of Sciences, Szeged, Hungary
| | - Gergely Fekete
- Synthetic and System Biology Unit, Biological Research Center of the Hungarian Academia of Sciences, Szeged, Hungary
| | - Csaba Pál
- Synthetic and System Biology Unit, Biological Research Center of the Hungarian Academia of Sciences, Szeged, Hungary
| | - Balázs Papp
- Synthetic and System Biology Unit, Biological Research Center of the Hungarian Academia of Sciences, Szeged, Hungary
| | - Erika Oszi
- Institute of Plant Biology, Biological Research Center of the Hungarian Academia of Sciences, Szeged, Hungary
| | - Zoltán Magyar
- Institute of Plant Biology, Biological Research Center of the Hungarian Academia of Sciences, Szeged, Hungary
| | - Joseph A Marsh
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Adrian H Elcock
- Department of Biochemistry, University of Iowa, Iowa City, IA, USA
| | - M Madan Babu
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | | | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, Kobe, Japan
- Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Kobe, Japan
| | - Sarah A Teichmann
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
- Cavendish Laboratory, University of Cambridge, Cambridge, UK.
| |
Collapse
|
8
|
Ambrose S, Housden NG, Gupta K, Fan J, White P, Yen H, Marcoux J, Kleanthous C, Hopper JTS, Robinson CV. Native Desorption Electrospray Ionization Liberates Soluble and Membrane Protein Complexes from Surfaces. Angew Chem Int Ed Engl 2017; 56:14463-14468. [PMID: 28884954 PMCID: PMC5813186 DOI: 10.1002/anie.201704849] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 08/07/2017] [Indexed: 12/19/2022]
Abstract
Mass spectrometry (MS) applications for intact protein complexes typically require electrospray (ES) ionization and have not been achieved via direct desorption from surfaces. Desorption ES ionization (DESI) MS has however transformed the study of tissue surfaces through release and characterisation of small molecules. Motivated by the desire to screen for ligand binding to intact protein complexes we report the development of a native DESI platform. By establishing conditions that preserve non-covalent interactions we exploit the surface to capture a rapid turnover enzyme-substrate complex and to optimise detergents for membrane protein study. We demonstrate binding of lipids and drugs to membrane proteins deposited on surfaces and selectivity from a mix of related agonists for specific binding to a GPCR. Overall therefore we introduce this native DESI platform with the potential for high-throughput ligand screening of some of the most challenging drug targets including GPCRs.
Collapse
Affiliation(s)
- Stephen Ambrose
- Department of Chemistry, Physical & Theoretical Chemistry LaboratoryUniversity of OxfordOxfordOX1 3QZUK
| | | | - Kallol Gupta
- Department of Chemistry, Physical & Theoretical Chemistry LaboratoryUniversity of OxfordOxfordOX1 3QZUK
| | - Jieyuan Fan
- Department of Chemistry, Physical & Theoretical Chemistry LaboratoryUniversity of OxfordOxfordOX1 3QZUK
| | - Paul White
- Department of BiochemistryUniversity of OxfordOxfordUK
| | - Hsin‐Yung Yen
- Department of Chemistry, Physical & Theoretical Chemistry LaboratoryUniversity of OxfordOxfordOX1 3QZUK
| | - Julien Marcoux
- Department of Chemistry, Physical & Theoretical Chemistry LaboratoryUniversity of OxfordOxfordOX1 3QZUK
- Current address: IPBSCNRS, UMR 5089205 Route de Narbonne31077ToulouseFrance
| | | | - Jonathan T. S. Hopper
- Department of Chemistry, Physical & Theoretical Chemistry LaboratoryUniversity of OxfordOxfordOX1 3QZUK
| | - Carol V. Robinson
- Department of Chemistry, Physical & Theoretical Chemistry LaboratoryUniversity of OxfordOxfordOX1 3QZUK
| |
Collapse
|
9
|
Ambrose S, Housden NG, Gupta K, Fan J, White P, Yen HY, Marcoux J, Kleanthous C, Hopper JTS, Robinson CV. Inside Back Cover: Native Desorption Electrospray Ionization Liberates Soluble and Membrane Protein Complexes from Surfaces (Angew. Chem. Int. Ed. 46/2017). Angew Chem Int Ed Engl 2017. [DOI: 10.1002/anie.201710562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Stephen Ambrose
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory; University of Oxford; Oxford OX1 3QZ UK
| | | | - Kallol Gupta
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory; University of Oxford; Oxford OX1 3QZ UK
| | - Jieyuan Fan
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory; University of Oxford; Oxford OX1 3QZ UK
| | - Paul White
- Department of Biochemistry; University of Oxford; Oxford UK
| | - Hsin-Yung Yen
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory; University of Oxford; Oxford OX1 3QZ UK
| | - Julien Marcoux
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory; University of Oxford; Oxford OX1 3QZ UK
- Current address: IPBS; CNRS, UMR 5089; 205 Route de Narbonne 31077 Toulouse France
| | | | - Jonathan T. S. Hopper
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory; University of Oxford; Oxford OX1 3QZ UK
| | - Carol V. Robinson
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory; University of Oxford; Oxford OX1 3QZ UK
| |
Collapse
|
10
|
Ambrose S, Housden NG, Gupta K, Fan J, White P, Yen HY, Marcoux J, Kleanthous C, Hopper JTS, Robinson CV. Innenrücktitelbild: Native Desorption Electrospray Ionization Liberates Soluble and Membrane Protein Complexes from Surfaces (Angew. Chem. 46/2017). Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201710562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Stephen Ambrose
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory; University of Oxford; Oxford OX1 3QZ UK
| | | | - Kallol Gupta
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory; University of Oxford; Oxford OX1 3QZ UK
| | - Jieyuan Fan
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory; University of Oxford; Oxford OX1 3QZ UK
| | - Paul White
- Department of Biochemistry; University of Oxford; Oxford UK
| | - Hsin-Yung Yen
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory; University of Oxford; Oxford OX1 3QZ UK
| | - Julien Marcoux
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory; University of Oxford; Oxford OX1 3QZ UK
- Current address: IPBS; CNRS, UMR 5089; 205 Route de Narbonne 31077 Toulouse France
| | | | - Jonathan T. S. Hopper
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory; University of Oxford; Oxford OX1 3QZ UK
| | - Carol V. Robinson
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory; University of Oxford; Oxford OX1 3QZ UK
| |
Collapse
|
11
|
Manzi L, Barrow AS, Hopper JTS, Kaminska R, Kleanthous C, Robinson CV, Moses JE, Oldham NJ. Carbene Footprinting Reveals Binding Interfaces of a Multimeric Membrane-Spanning Protein. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201708254] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Lucio Manzi
- School of Chemistry; University of Nottingham; University Park Nottingham NG7 2RD UK
| | - Andrew S. Barrow
- School of Chemistry; University of Nottingham; University Park Nottingham NG7 2RD UK
- Current address: La Trobe Institute for Molecular Science; La Trobe University; Melbourne Victoria 3086 Australia
| | - Jonathan T. S. Hopper
- OMass Technologies Ltd.; Centre for Innovation and Enterprise; Begbroke Science Park, Woodstock Road Oxford OX5 1PF UK
| | - Renata Kaminska
- Department of Biochemistry; University of Oxford; South Parks Road Oxford OX1 3QU UK
| | - Colin Kleanthous
- Department of Biochemistry; University of Oxford; South Parks Road Oxford OX1 3QU UK
| | - Carol V. Robinson
- Chemistry Research Laboratory; University of Oxford; South Parks Road Oxford OX1 3QZ UK
| | - John E. Moses
- School of Chemistry; University of Nottingham; University Park Nottingham NG7 2RD UK
- Current address: La Trobe Institute for Molecular Science; La Trobe University; Melbourne Victoria 3086 Australia
| | - Neil J. Oldham
- School of Chemistry; University of Nottingham; University Park Nottingham NG7 2RD UK
| |
Collapse
|
12
|
Manzi L, Barrow AS, Hopper JTS, Kaminska R, Kleanthous C, Robinson CV, Moses JE, Oldham NJ. Carbene Footprinting Reveals Binding Interfaces of a Multimeric Membrane-Spanning Protein. Angew Chem Int Ed Engl 2017; 56:14873-14877. [DOI: 10.1002/anie.201708254] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Indexed: 12/28/2022]
Affiliation(s)
- Lucio Manzi
- School of Chemistry; University of Nottingham; University Park Nottingham NG7 2RD UK
| | - Andrew S. Barrow
- School of Chemistry; University of Nottingham; University Park Nottingham NG7 2RD UK
- Current address: La Trobe Institute for Molecular Science; La Trobe University; Melbourne Victoria 3086 Australia
| | - Jonathan T. S. Hopper
- OMass Technologies Ltd.; Centre for Innovation and Enterprise; Begbroke Science Park, Woodstock Road Oxford OX5 1PF UK
| | - Renata Kaminska
- Department of Biochemistry; University of Oxford; South Parks Road Oxford OX1 3QU UK
| | - Colin Kleanthous
- Department of Biochemistry; University of Oxford; South Parks Road Oxford OX1 3QU UK
| | - Carol V. Robinson
- Chemistry Research Laboratory; University of Oxford; South Parks Road Oxford OX1 3QZ UK
| | - John E. Moses
- School of Chemistry; University of Nottingham; University Park Nottingham NG7 2RD UK
- Current address: La Trobe Institute for Molecular Science; La Trobe University; Melbourne Victoria 3086 Australia
| | - Neil J. Oldham
- School of Chemistry; University of Nottingham; University Park Nottingham NG7 2RD UK
| |
Collapse
|
13
|
Ambrose S, Housden NG, Gupta K, Fan J, White P, Yen HY, Marcoux J, Kleanthous C, Hopper JTS, Robinson CV. Native Desorption Electrospray Ionization Liberates Soluble and Membrane Protein Complexes from Surfaces. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201704849] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Stephen Ambrose
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory; University of Oxford; Oxford OX1 3QZ UK
| | | | - Kallol Gupta
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory; University of Oxford; Oxford OX1 3QZ UK
| | - Jieyuan Fan
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory; University of Oxford; Oxford OX1 3QZ UK
| | - Paul White
- Department of Biochemistry; University of Oxford; Oxford UK
| | - Hsin-Yung Yen
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory; University of Oxford; Oxford OX1 3QZ UK
| | - Julien Marcoux
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory; University of Oxford; Oxford OX1 3QZ UK
- Current address: IPBS; CNRS, UMR 5089; 205 Route de Narbonne 31077 Toulouse France
| | | | - Jonathan T. S. Hopper
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory; University of Oxford; Oxford OX1 3QZ UK
| | - Carol V. Robinson
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory; University of Oxford; Oxford OX1 3QZ UK
| |
Collapse
|
14
|
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. Sci Adv 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] [What about the content of this article? (0)] [Affiliation(s)] [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
|
15
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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
|
16
|
Liko I, Hopper JTS, Allison TM, Benesch JLP, Robinson CV. Negative Ions Enhance Survival of Membrane Protein Complexes. J Am Soc Mass Spectrom 2016; 27:1099-104. [PMID: 27106602 PMCID: PMC4869745 DOI: 10.1007/s13361-016-1381-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 03/07/2016] [Accepted: 03/08/2016] [Indexed: 05/08/2023]
Abstract
Membrane protein complexes are commonly introduced to the mass spectrometer solubilized in detergent micelles. The collisional activation used to remove the detergent, however, often causes protein unfolding and dissociation. As in the case for soluble proteins, electrospray in the positive ion mode is most commonly used for the study of membrane proteins. Here we show several distinct advantages of employing the negative ion mode. Negative polarity can yield lower average charge states for membrane proteins solubilized in saccharide detergents, with enhanced peak resolution and reduced adduct formation. Most importantly, we demonstrate that negative ion mode electrospray ionization (ESI) minimizes subunit dissociation in the gas phase, allowing access to biologically relevant oligomeric states. Together, these properties mean that intact membrane protein ions can be generated in a greater range of solubilizing detergents. The formation of negative ions, therefore, greatly expands the possibilities of using mass spectrometry on this intractable class of protein. Graphical Abstract ᅟ.
Collapse
Affiliation(s)
- Idlir Liko
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 5QY, UK
| | - Jonathan T S Hopper
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 5QY, UK
| | - Timothy M Allison
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 5QY, UK
| | - Justin L P Benesch
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 5QY, UK
| | - Carol V Robinson
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 5QY, UK.
| |
Collapse
|
17
|
Bugge K, Papaleo E, Haxholm GW, Hopper JTS, Robinson CV, Olsen JG, Lindorff-Larsen K, Kragelund BB. A combined computational and structural model of the full-length human prolactin receptor. Nat Commun 2016; 7:11578. [PMID: 27174498 PMCID: PMC4869255 DOI: 10.1038/ncomms11578] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 04/11/2016] [Indexed: 12/13/2022] Open
Abstract
The prolactin receptor is an archetype member of the class I cytokine receptor family, comprising receptors with fundamental functions in biology as well as key drug targets. Structurally, each of these receptors represent an intriguing diversity, providing an exceptionally challenging target for structural biology. Here, we access the molecular architecture of the monomeric human prolactin receptor by combining experimental and computational efforts. We solve the NMR structure of its transmembrane domain in micelles and collect structural data on overlapping fragments of the receptor with small-angle X-ray scattering, native mass spectrometry and NMR spectroscopy. Along with previously published data, these are integrated by molecular modelling to generate a full receptor structure. The result provides the first full view of a class I cytokine receptor, exemplifying the architecture of more than 40 different receptor chains, and reveals that the extracellular domain is merely the tip of a molecular iceberg.
Collapse
Affiliation(s)
- Katrine Bugge
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Elena Papaleo
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Gitte W. Haxholm
- 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
| | - Johan G. Olsen
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, 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
|
18
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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
|
19
|
Landreh M, Liko I, Uzdavinys P, Coincon M, Hopper JTS, Drew D, Robinson CV. Controlling release, unfolding and dissociation of membrane protein complexes in the gas phase through collisional cooling. Chem Commun (Camb) 2016; 51:15582-4. [PMID: 26356172 DOI: 10.1039/c5cc07045g] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Mass spectrometry of intact membrane protein complexes requires removal of the detergent micelle by collisional activation. We demonstrate that the necessary energy can be obtained by adjusting the degree of collisional cooling in the ion source. This enables us to extend the energy regime for dissociation of membrane protein complexes.
Collapse
Affiliation(s)
- Michael Landreh
- Department of Chemistry, Theoretical and Physical Chemistry Laboratory, University of Oxford, Oxford OX1 3TA, UK.
| | | | | | | | | | | | | |
Collapse
|
20
|
Wojdyla JA, Cutts E, Kaminska R, Papadakos G, Hopper JTS, Stansfeld PJ, Staunton D, Robinson CV, Kleanthous C. Structure and function of the Escherichia coli Tol-Pal stator protein TolR. J Biol Chem 2015; 290:26675-87. [PMID: 26354441 PMCID: PMC4646322 DOI: 10.1074/jbc.m115.671586] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Indexed: 12/31/2022] Open
Abstract
TolR is a 15-kDa inner membrane protein subunit of the Tol-Pal complex in Gram-negative bacteria, and its function is poorly understood. Tol-Pal is recruited to cell division sites where it is involved in maintaining the integrity of the outer membrane. TolR is related to MotB, the peptidoglycan (PG)-binding stator protein from the flagellum, suggesting it might serve a similar role in Tol-Pal. The only structure thus far reported for TolR is of the periplasmic domain from Haemophilus influenzae in which N- and C-terminal residues had been deleted (TolR(62–133), Escherichia coli numbering). H. influenzae TolR(62–133) is a symmetrical dimer with a large deep cleft at the dimer interface. Here, we present the 1.7-Å crystal structure of the intact periplasmic domain of E. coli TolR (TolR(36–142)). E. coli TolR(36–142) is also dimeric, but the architecture of the dimer is radically different from that of TolR(62–133) due to the intertwining of its N and C termini. TolR monomers are rotated ∼180° relative to each other as a result of this strand swapping, obliterating the putative PG-binding groove seen in TolR(62–133). We found that removal of the strand-swapped regions (TolR(60–133)) exposes cryptic PG binding activity that is absent in the full-length domain. We conclude that to function as a stator in the Tol-Pal complex dimeric TolR must undergo large scale structural remodeling reminiscent of that proposed for MotB, where the N- and C-terminal sequences unfold in order for the protein to both reach and bind the PG layer ∼90 Å away from the inner membrane.
Collapse
Affiliation(s)
- Justyna A Wojdyla
- From the Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU and
| | - Erin Cutts
- From the Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU and
| | - Renata Kaminska
- From the Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU and
| | - Grigorios Papadakos
- From the Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU and
| | - Jonathan T S Hopper
- the Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Phillip J Stansfeld
- From the Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU and
| | - David Staunton
- From the Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU and
| | - Carol V Robinson
- the Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Colin Kleanthous
- From the Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU and
| |
Collapse
|
21
|
Hopper JTS, Robinson CV. Mass spectrometry quantifies protein interactions--from molecular chaperones to membrane porins. Angew Chem Int Ed Engl 2014; 53:14002-15. [PMID: 25354304 DOI: 10.1002/anie.201403741] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Indexed: 12/16/2022]
Abstract
Proteins possess an intimate relationship between their structure and function, with folded protein structures generating recognition motifs for the binding of ligands and other proteins. Mass spectrometry (MS) can provide information on a number of levels of protein structure, from the primary amino acid sequence to its three-dimensional fold and quaternary interactions. Given that MS is a gas-phase technique, with its foundations in analytical chemistry, it is perhaps counter-intuitive to use it to study the structure and non-covalent interactions of proteins that form in solution. Herein we show, however, that MS can go beyond simply preserving protein interactions in the gas phase by providing new insight into dynamic interaction networks, dissociation mechanisms, and the cooperativity of ligand binding. We consider potential pitfalls in data interpretation and place particular emphasis on recent studies that revealed quantitative information about dynamic protein interactions, in both soluble and membrane-embedded assemblies.
Collapse
Affiliation(s)
- Jonathan T S Hopper
- Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ (UK)
| | | |
Collapse
|
22
|
Mehmood S, Marcoux J, Hopper JTS, Allison TM, Liko I, Borysik AJ, Robinson CV. Charge reduction stabilizes intact membrane protein complexes for mass spectrometry. J Am Chem Soc 2014; 136:17010-2. [PMID: 25402655 DOI: 10.1021/ja510283g] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The study of intact soluble protein assemblies by means of mass spectrometry is providing invaluable contributions to structural biology and biochemistry. A recent breakthrough has enabled similar study of membrane protein complexes, following their release from detergent micelles in the gas phase. Careful optimization of mass spectrometry conditions, particularly with respect to energy regimes, is essential for maintaining compact folded states as detergent is removed. However, many of the saccharide detergents widely employed in structural biology can cause unfolding of membrane proteins in the gas phase. Here, we investigate the potential of charge reduction by introducing three membrane protein complexes from saccharide detergents and show how reducing their overall charge enables generation of compact states, as evidenced by ion mobility mass spectrometry. We find that charge reduction stabilizes the oligomeric state and enhances the stability of lipid-bound complexes. This finding is significant since maintaining native-like membrane proteins enables ligand binding to be assessed from a range of detergents that retain solubility while protecting the overall fold.
Collapse
Affiliation(s)
- Shahid Mehmood
- Department of Chemistry, University of Oxford , Oxford, U.K
| | | | | | | | | | | | | |
Collapse
|
23
|
Hopper JTS, Robinson CV. Massenspektrometrie zur Quantifizierung von Wechselwirkungen zwischen Proteinen - von molekularen Chaperonen zu Membranporinen. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201403741] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
|
24
|
Hopper JTS, Rawlings A, Afonso JP, Channing D, Layfield R, Oldham NJ. Evidence for the preservation of native inter- and intra-molecular hydrogen bonds in the desolvated FK-binding protein·FK506 complex produced by electrospray ionization. J Am Soc Mass Spectrom 2012; 23:1757-1767. [PMID: 22797884 DOI: 10.1007/s13361-012-0430-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2012] [Revised: 06/06/2012] [Accepted: 06/06/2012] [Indexed: 06/01/2023]
Abstract
It is now well established that electrospray ionization (ESI) is capable of introducing noncovalent protein assemblies into a desolvated environment, thereby allowing their analysis by mass spectrometry. The degree to which native interactions from the solution phase are preserved in this environment is less clear. Site-directed mutagenesis of FK506-binding protein (FKBP) has been employed to probe specific intra- and inter-molecular interactions within the complex between FKBP and its ligand FK506. Collisional activation of wild-type and mutant-FKBP•FK506 ions, generated by ESI, demonstrated that removal of native protein-ligand interactions formed between residues Asp37, Tyr82, and FK506 significantly destabilized the complex. Mutation of Arg42 to Ala42, or Tyr26 to Phe26 also resulted in lower energy dissociation of the FKBP·FK506 complex. Although these residues do not form direct H-bonds to FK506, they interact with Asp37, ensuring its correct orientation to associate with the ligand. Comparison with solution-based affinity measurements of these mutants has been discussed, including the stabilization afforded by ordered water molecules. Ion mobility spectrometry (IMS) has been employed to provide gas-phase structural information on the unfolding of the complexes. The [M + 6H](6+) complexes of the wild-type and mutants have been shown to resist unfolding and retain compact conformations. However, removal of the basic Arg42 residue was found to induce significant structural weakening of the [M + 7H](7+) complex when raised to dissociation-level energies. Overall, destabilization of the FKBP·FK506 complex, resulting from targeted removal of specific H-bonds, provides evidence for the preservation of these interactions in the desolvated wild-type complex.
Collapse
|
25
|
Hopper JTS, Oldham NJ. Alkali metal cation-induced destabilization of gas-phase protein-ligand complexes: consequences and prevention. Anal Chem 2011; 83:7472-9. [PMID: 21863818 DOI: 10.1021/ac201686f] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Electrospray ionization, now a well established technique for studying noncovalent protein-ligand interactions, is prone to production of alkali metal adducts. Here it is shown that this adduction significantly destabilizes the interactions between two model proteins and their ligands and that destabilization correlates with cation size. For both the [FKBP·FK506] and [lysozyme·NAG(n)] systems, dissociation of the metalated complex occurs at markedly lower collision energies than their purely protonated equivalents. Dependency upon size of the metal(+) demonstrates the importance of electrostatic charge density during the dissociation process. Differences in the gas phase basicities (GBapp) of the multiply charged protein ions and proton and sodium affinities of the ligands explain the observed charge partitioning during dissociation of the complexes. Ion mobility-mass spectrometry measurements demonstrate that metal cation adduction does not induce a significant increase in unfolding of the polypeptides, indicating that this is not the principal mechanism responsible for destabilization. Destabilizing effects can be largely reduced by exposing the electrospray to solvent (e.g., acetonitrile) vapor, a method that acts to reduce the amount of adduct formation as well as decrease the charge states of the resulting ions. This approach leads to more accurate determination of apparent K(D)s in the presence of trace alkali metals.
Collapse
Affiliation(s)
- Jonathan T S Hopper
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD
| | | |
Collapse
|
26
|
Hopper JTS, Oldham NJ. Collision induced unfolding of protein ions in the gas phase studied by ion mobility-mass spectrometry: the effect of ligand binding on conformational stability. J Am Soc Mass Spectrom 2009; 20:1851-8. [PMID: 19643633 DOI: 10.1016/j.jasms.2009.06.010] [Citation(s) in RCA: 152] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2009] [Revised: 06/11/2009] [Accepted: 06/13/2009] [Indexed: 05/19/2023]
Abstract
Ion mobility spectrometry, with subsequent mass spectrometric detection, has been employed to study the stability of compact protein conformations of FK-binding protein, hen egg-white lysozyme, and horse heart myoglobin in the presence and absence of bound ligands. Protein ions, generated by electrospray ionization from ammonium acetate buffer, were activated by collision with argon gas to induce unfolding of their compact structures. The collisional cross sections (Omega) of folded and unfolded conformations were measured in the T-Wave mobility cell of a Waters Synapt HDMS (Waters, Altrincham, UK) employing a calibration against literature values for a range of protein standards. In the absence of activation, collisional cross section measurements were found to be consistent with those predicted for folded protein structures. Under conditions of defined collisional activation energies partially unfolded conformations were produced. The degree of unfolding and dissociation induced by these defined collision energies are related to the stability of noncovalent intra- and intermolecular interactions within protein complexes. These findings highlight the additional conformational stability of protein ions in the gas phase resulting from ligand binding.
Collapse
Affiliation(s)
- Jonathan T S Hopper
- School of Chemistry, University of Nottingham, University Park, Nottingham, United Kingdom
| | | |
Collapse
|