1
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Hoare BL, Tippett DN, Kaur A, Cullum SA, Miljuš T, Koers EJ, Harwood CR, Dijon N, Holliday ND, Sykes DA, Veprintsev DB. ThermoBRET: A Ligand-Engagement Nanoscale Thermostability Assay Applied to GPCRs. Chembiochem 2024; 25:e202300459. [PMID: 37872746 DOI: 10.1002/cbic.202300459] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 06/22/2023] [Revised: 10/18/2023] [Accepted: 10/19/2023] [Indexed: 10/25/2023]
Abstract
Measurements of membrane protein thermostability reflect ligand binding. Current thermostability assays often require protein purification or rely on pre-existing radiolabelled or fluorescent ligands, limiting their application to established targets. Alternative methods, such as fluorescence-detection size exclusion chromatography thermal shift, detect protein aggregation but are not amenable to high-throughput screening. Here, we present a ThermoBRET method to quantify the relative thermostability of G protein coupled receptors (GPCRs), using cannabinoid receptors (CB1 and CB2 ) and the β2 -adrenoceptor (β2 AR) as model systems. ThermoBRET reports receptor unfolding, does not need labelled ligands and can be used with non-purified proteins. It uses Bioluminescence Resonance Energy Transfer (BRET) between Nanoluciferase (Nluc) and a thiol-reactive fluorescent dye that binds cysteines exposed by unfolding. We demonstrate that the melting point (Tm ) of Nluc-fused GPCRs can be determined in non-purified detergent solubilised membrane preparations or solubilised whole cells, revealing differences in thermostability for different solubilising conditions and in the presence of stabilising ligands. We extended the range of the assay by developing the thermostable tsNLuc by incorporating mutations from the fragments of split-Nluc (Tm of 87 °C versus 59 °C). ThermoBRET allows the determination of GPCR thermostability, which is useful for protein purification optimisation and drug discovery screening.
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Affiliation(s)
- Bradley L Hoare
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
- Current address, Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC 3052, Australia
| | - David N Tippett
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
- Current address, Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Amandeep Kaur
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Sean A Cullum
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Tamara Miljuš
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Eline J Koers
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Clare R Harwood
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Nicola Dijon
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Nicholas D Holliday
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - David A Sykes
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Dmitry B Veprintsev
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
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2
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Avellaneda MJ, Koers EJ, Sunderlikova V, Tans SJ. Protein Tethering for Single-Molecule Force Spectroscopy. Methods Mol Biol 2024; 2694:57-67. [PMID: 37823999 DOI: 10.1007/978-1-0716-3377-9_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Molecular manipulation by optical tweezers is a central technique to study the folded states of individual proteins and how they depend on interactions with molecules including DNA, ligands, and other proteins. One of the key challenges of this approach is to stably attach DNA handles in an efficient manner. Here, we provide detailed descriptions of a universal approach to covalently link long DNA tethers of up to 5000 base pairs to proteins with or without native cysteines.
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3
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Gusach A, Lee Y, Khoshgrudi AN, Mukhaleva E, Ma N, Koers EJ, Chen Q, Edwards PC, Huang F, Kim J, Mancia F, Verprintsev DB, Vaidehi N, Weyand SN, Tate CG. Molecular recognition of an aversive odorant by the murine trace amine-associated receptor TAAR7f. bioRxiv 2023:2023.07.07.547762. [PMID: 37461561 PMCID: PMC10350033 DOI: 10.1101/2023.07.07.547762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
There are two main families of G protein-coupled receptors that detect odours in humans, the odorant receptors (ORs) and the trace amine-associated receptors (TAARs). Their amino acid sequences are distinct, with the TAARs being most similar to the aminergic receptors such as those activated by adrenaline, serotonin and histamine. To elucidate the structural determinants of ligand recognition by TAARs, we have determined the cryo-EM structure of a murine receptor, mTAAR7f, coupled to the heterotrimeric G protein Gs and bound to the odorant N,N-dimethylcyclohexylamine (DMCH) to an overall resolution of 2.9 Å. DMCH is bound in a hydrophobic orthosteric binding site primarily through van der Waals interactions and a strong charge-charge interaction between the tertiary amine of the ligand and an aspartic acid residue. This site is distinct and non-overlapping with the binding site for the odorant propionate in the odorant receptor OR51E2. The structure, in combination with mutagenesis data and molecular dynamics simulations suggests that the activation of the receptor follows a similar pathway to that of the β-adrenoceptors, with the significant difference that DMCH interacts directly with one of the main activation microswitch residues.
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Affiliation(s)
- Anastasiia Gusach
- MRC Laboratory of Molecular Biology, Francis Crick Avenue,
Cambridge CB2 0QH, UK
| | - Yang Lee
- MRC Laboratory of Molecular Biology, Francis Crick Avenue,
Cambridge CB2 0QH, UK
| | - Armin Nikpour Khoshgrudi
- Centre of Membrane Proteins and Receptors (COMPARE), University
of Birmingham and University of Nottingham, Midlands, NG7 2RD, UK
- Division of Physiology, Pharmacology & Neuroscience, School
of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Elizaveta Mukhaleva
- Department of Computational and Quantitative Medicine, Beckman
Research Institute of the City of Hope, 1500 E Duarte Road, Duarte, CA-91006, USA
| | - Ning Ma
- Department of Computational and Quantitative Medicine, Beckman
Research Institute of the City of Hope, 1500 E Duarte Road, Duarte, CA-91006, USA
| | - Eline J. Koers
- Centre of Membrane Proteins and Receptors (COMPARE), University
of Birmingham and University of Nottingham, Midlands, NG7 2RD, UK
- Division of Physiology, Pharmacology & Neuroscience, School
of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Qingchao Chen
- MRC Laboratory of Molecular Biology, Francis Crick Avenue,
Cambridge CB2 0QH, UK
| | - Patricia C. Edwards
- MRC Laboratory of Molecular Biology, Francis Crick Avenue,
Cambridge CB2 0QH, UK
| | - Fanglu Huang
- Department of Biochemistry, University of Cambridge, Tennis Court
Road, Cambridge, UK
| | - Jonathan Kim
- Department of Physiology and Cellular Biophysics, Columbia
University, Irving Medical Center, New York, NY 10032, USA
| | - Filippo Mancia
- Department of Physiology and Cellular Biophysics, Columbia
University, Irving Medical Center, New York, NY 10032, USA
| | - Dmitry B. Verprintsev
- Centre of Membrane Proteins and Receptors (COMPARE), University
of Birmingham and University of Nottingham, Midlands, NG7 2RD, UK
- Division of Physiology, Pharmacology & Neuroscience, School
of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Nagarajan Vaidehi
- Department of Computational and Quantitative Medicine, Beckman
Research Institute of the City of Hope, 1500 E Duarte Road, Duarte, CA-91006, USA
| | - Simone N. Weyand
- Department of Biochemistry, University of Cambridge, Tennis Court
Road, Cambridge, UK
- Department of Medicine, University of Cambridge, Victor Phillip
Dahdaleh Building, Heart & Lung Research Institute, Papworth Road, Cambridge Biomedical
Campus, Cambridge, CB2 0BB, UK
- Cambridge Institute for Medical Research, Keith Peters Building,
Biomedical Campus, Hills Rd, Cambridge CB2 0XY, UK
- EMBL’s European Bioinformatics Institute (EMBL-EBI),
Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Christopher G. Tate
- MRC Laboratory of Molecular Biology, Francis Crick Avenue,
Cambridge CB2 0QH, UK
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4
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Jiménez-Rosés M, Morgan BA, Jimenez Sigstad M, Tran TDZ, Srivastava R, Bunsuz A, Borrega-Román L, Hompluem P, Cullum SA, Harwood CR, Koers EJ, Sykes DA, Styles IB, Veprintsev DB. Combined docking and machine learning identify key molecular determinants of ligand pharmacological activity on β2 adrenoceptor. Pharmacol Res Perspect 2022; 10:e00994. [PMID: 36029004 PMCID: PMC9418666 DOI: 10.1002/prp2.994] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 05/09/2022] [Accepted: 06/21/2022] [Indexed: 11/06/2022] Open
Abstract
G protein‐coupled receptors (GPCRs) are valuable therapeutic targets for many diseases. A central question of GPCR drug discovery is to understand what determines the agonism or antagonism of ligands that bind them. Ligands exert their action via the interactions in the ligand binding pocket. We hypothesized that there is a common set of receptor interactions made by ligands of diverse structures that mediate their action and that among a large dataset of different ligands, the functionally important interactions will be over‐represented. We computationally docked ~2700 known β2AR ligands to multiple β2AR structures, generating ca 75 000 docking poses and predicted all atomic interactions between the receptor and the ligand. We used machine learning (ML) techniques to identify specific interactions that correlate with the agonist or antagonist activity of these ligands. We demonstrate with the application of ML methods that it is possible to identify the key interactions associated with agonism or antagonism of ligands. The most representative interactions for agonist ligands involve K972.68×67, F194ECL2, S2035.42×43, S2045.43×44, S2075.46×641, H2966.58×58, and K3057.32×31. Meanwhile, the antagonist ligands made interactions with W2866.48×48 and Y3167.43×42, both residues considered to be important in GPCR activation. The interpretation of ML analysis in human understandable form allowed us to construct an exquisitely detailed structure‐activity relationship that identifies small changes to the ligands that invert their pharmacological activity and thus helps to guide the drug discovery process. This approach can be readily applied to any drug target.
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Affiliation(s)
- Mireia Jiménez-Rosés
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK.,Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Bradley Angus Morgan
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK.,School of Computer Science, University of Birmingham, Birmingham, UK.,The Alan Turing Institute, London, UK.,MRC IMPACT Doctoral Training Programme, Universities of Birmingham, Leicester and Nottingham, Midlands, UK
| | - Maria Jimenez Sigstad
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK.,Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Thuy Duong Zoe Tran
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK.,MSc Programme in Drug Discovery & Pharmaceutical Sciences, University of Nottingham, Nottingham, UK
| | - Rohini Srivastava
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK.,MSc Programme in Drug Discovery & Pharmaceutical Sciences, University of Nottingham, Nottingham, UK
| | - Asuman Bunsuz
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK.,Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Leire Borrega-Román
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK.,Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, UK.,Department of Pharmacology, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain.,Bioaraba, Neurofarmacología Celular y Molecular, Vitoria-Gasteiz, Spain
| | - Pattarin Hompluem
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK.,Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Sean A Cullum
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK.,Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, UK.,MRC IMPACT Doctoral Training Programme, Universities of Birmingham, Leicester and Nottingham, Midlands, UK
| | - Clare R Harwood
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK.,Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, UK.,MRC IMPACT Doctoral Training Programme, Universities of Birmingham, Leicester and Nottingham, Midlands, UK
| | - Eline J Koers
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK.,Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, UK
| | - David A Sykes
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK.,Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Iain B Styles
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK.,School of Computer Science, University of Birmingham, Birmingham, UK.,The Alan Turing Institute, London, UK
| | - Dmitry B Veprintsev
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK.,Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, UK
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5
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Gazzi T, Brennecke B, Atz K, Korn C, Sykes D, Forn-Cuni G, Pfaff P, Sarott RC, Westphal MV, Mostinski Y, Mach L, Wasinska-Kalwa M, Weise M, Hoare BL, Miljuš T, Mexi M, Roth N, Koers EJ, Guba W, Alker A, Rufer AC, Kusznir EA, Huber S, Raposo C, Zirwes EA, Osterwald A, Pavlovic A, Moes S, Beck J, Nettekoven M, Benito-Cuesta I, Grande T, Drawnel F, Widmer G, Holzer D, van der Wel T, Mandhair H, Honer M, Fingerle J, Scheffel J, Broichhagen J, Gawrisch K, Romero J, Hillard CJ, Varga ZV, van der Stelt M, Pacher P, Gertsch J, Ullmer C, McCormick PJ, Oddi S, Spaink HP, Maccarrone M, Veprintsev DB, Carreira EM, Grether U, Nazaré M. Detection of cannabinoid receptor type 2 in native cells and zebrafish with a highly potent, cell-permeable fluorescent probe. Chem Sci 2022; 13:5539-5545. [PMID: 35694350 PMCID: PMC9116301 DOI: 10.1039/d1sc06659e] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 01/22/2022] [Indexed: 12/16/2022] Open
Abstract
Despite its essential role in the (patho)physiology of several diseases, CB2R tissue expression profiles and signaling mechanisms are not yet fully understood. We report the development of a highly potent, fluorescent CB2R agonist probe employing structure-based reverse design. It commences with a highly potent, preclinically validated ligand, which is conjugated to a silicon-rhodamine fluorophore, enabling cell permeability. The probe is the first to preserve interspecies affinity and selectivity for both mouse and human CB2R. Extensive cross-validation (FACS, TR-FRET and confocal microscopy) set the stage for CB2R detection in endogenously expressing living cells along with zebrafish larvae. Together, these findings will benefit clinical translatability of CB2R based drugs. Detection and visualization of the cannabinoid receptor type 2 by a cell-permeable high affinity fluorescent probe platform enables tracing receptor trafficking in live cells and in zebrafish.![]()
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Affiliation(s)
- Thais Gazzi
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Campus Berlin-Buch 13125 Berlin Germany
| | - Benjamin Brennecke
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Campus Berlin-Buch 13125 Berlin Germany
| | - Kenneth Atz
- Roche Pharma Research & Early Development, Roche Innovation Center Basel F. Hoffmann-La Roche Ltd. 4070 Basel Switzerland
| | - Claudia Korn
- Roche Pharma Research & Early Development, Roche Innovation Center Basel F. Hoffmann-La Roche Ltd. 4070 Basel Switzerland
| | - David Sykes
- Faculty of Medicine & Health Sciences, University of Nottingham Nottingham NG7 2UH England UK.,United Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham Midlands England UK
| | | | - Patrick Pfaff
- Laboratorium für Organische Chemie, Eidgenössische Technische Hochschule Zürich Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
| | - Roman C Sarott
- Laboratorium für Organische Chemie, Eidgenössische Technische Hochschule Zürich Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
| | - Matthias V Westphal
- Laboratorium für Organische Chemie, Eidgenössische Technische Hochschule Zürich Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
| | - Yelena Mostinski
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Campus Berlin-Buch 13125 Berlin Germany
| | - Leonard Mach
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Campus Berlin-Buch 13125 Berlin Germany
| | - Malgorzata Wasinska-Kalwa
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Campus Berlin-Buch 13125 Berlin Germany
| | - Marie Weise
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Campus Berlin-Buch 13125 Berlin Germany
| | - Bradley L Hoare
- Faculty of Medicine & Health Sciences, University of Nottingham Nottingham NG7 2UH England UK.,United Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham Midlands England UK
| | - Tamara Miljuš
- Faculty of Medicine & Health Sciences, University of Nottingham Nottingham NG7 2UH England UK.,United Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham Midlands England UK
| | - Maira Mexi
- Faculty of Medicine & Health Sciences, University of Nottingham Nottingham NG7 2UH England UK.,United Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham Midlands England UK
| | - Nicolas Roth
- William Harvey Research Institute, Barts and the London School of Medicine, Queen Mary University of London London EC1M 6BQ England UK
| | - Eline J Koers
- Faculty of Medicine & Health Sciences, University of Nottingham Nottingham NG7 2UH England UK.,United Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham Midlands England UK
| | - Wolfgang Guba
- Roche Pharma Research & Early Development, Roche Innovation Center Basel F. Hoffmann-La Roche Ltd. 4070 Basel Switzerland
| | - André Alker
- Roche Pharma Research & Early Development, Roche Innovation Center Basel F. Hoffmann-La Roche Ltd. 4070 Basel Switzerland
| | - Arne C Rufer
- Roche Pharma Research & Early Development, Roche Innovation Center Basel F. Hoffmann-La Roche Ltd. 4070 Basel Switzerland
| | - Eric A Kusznir
- Roche Pharma Research & Early Development, Roche Innovation Center Basel F. Hoffmann-La Roche Ltd. 4070 Basel Switzerland
| | - Sylwia Huber
- Roche Pharma Research & Early Development, Roche Innovation Center Basel F. Hoffmann-La Roche Ltd. 4070 Basel Switzerland
| | - Catarina Raposo
- Roche Pharma Research & Early Development, Roche Innovation Center Basel F. Hoffmann-La Roche Ltd. 4070 Basel Switzerland
| | - Elisabeth A Zirwes
- Roche Pharma Research & Early Development, Roche Innovation Center Basel F. Hoffmann-La Roche Ltd. 4070 Basel Switzerland
| | - Anja Osterwald
- Roche Pharma Research & Early Development, Roche Innovation Center Basel F. Hoffmann-La Roche Ltd. 4070 Basel Switzerland
| | - Anto Pavlovic
- Roche Pharma Research & Early Development, Roche Innovation Center Basel F. Hoffmann-La Roche Ltd. 4070 Basel Switzerland
| | - Svenja Moes
- Roche Pharma Research & Early Development, Roche Innovation Center Basel F. Hoffmann-La Roche Ltd. 4070 Basel Switzerland
| | - Jennifer Beck
- Roche Pharma Research & Early Development, Roche Innovation Center Basel F. Hoffmann-La Roche Ltd. 4070 Basel Switzerland
| | - Matthias Nettekoven
- Roche Pharma Research & Early Development, Roche Innovation Center Basel F. Hoffmann-La Roche Ltd. 4070 Basel Switzerland
| | - Irene Benito-Cuesta
- Faculty of Experimental Sciences, Universidad Francisco de Vitoria Pozuelo de Alarcón 28223 Madrid Spain
| | - Teresa Grande
- Faculty of Experimental Sciences, Universidad Francisco de Vitoria Pozuelo de Alarcón 28223 Madrid Spain
| | - Faye Drawnel
- Roche Pharma Research & Early Development, Roche Innovation Center Basel F. Hoffmann-La Roche Ltd. 4070 Basel Switzerland
| | - Gabriella Widmer
- Roche Pharma Research & Early Development, Roche Innovation Center Basel F. Hoffmann-La Roche Ltd. 4070 Basel Switzerland
| | - Daniela Holzer
- Roche Pharma Research & Early Development, Roche Innovation Center Basel F. Hoffmann-La Roche Ltd. 4070 Basel Switzerland
| | - Tom van der Wel
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University 2333 CC Leiden the Netherlands
| | - Harpreet Mandhair
- Institute of Biochemistry and Molecular Medicine, University of Bern 3012 Bern Switzerland
| | - Michael Honer
- Roche Pharma Research & Early Development, Roche Innovation Center Basel F. Hoffmann-La Roche Ltd. 4070 Basel Switzerland
| | - Jürgen Fingerle
- Roche Pharma Research & Early Development, Roche Innovation Center Basel F. Hoffmann-La Roche Ltd. 4070 Basel Switzerland
| | - Jörg Scheffel
- Dermatological Allergology, Allergie-Centrum-Charité, Department of Dermatology and Allergy, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin Berlin Germany.,Allergology, Fraunhofer Institute for Translational Medicine and Pharmacology ITMP Berlin Germany
| | - Johannes Broichhagen
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Campus Berlin-Buch 13125 Berlin Germany
| | - Klaus Gawrisch
- National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health Rockville MD 20852 USA
| | - Julián Romero
- Faculty of Experimental Sciences, Universidad Francisco de Vitoria Pozuelo de Alarcón 28223 Madrid Spain
| | - Cecilia J Hillard
- Department of Pharmacology and Toxicology, Neuroscience Research Center, Medical College of Wisconsin Milwaukee WI 53226 USA
| | - Zoltan V Varga
- National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health Rockville MD 20852 USA.,HCEMM-SU Cardiometabolic Immunology Research Group, Department of Pharmacology and Pharmacotherapy, Semmelweis University 1085 Budapest Hungary
| | - Mario van der Stelt
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University 2333 CC Leiden the Netherlands
| | - Pal Pacher
- National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health Rockville MD 20852 USA
| | - Jürg Gertsch
- Institute of Biochemistry and Molecular Medicine, University of Bern 3012 Bern Switzerland
| | - Christoph Ullmer
- Roche Pharma Research & Early Development, Roche Innovation Center Basel F. Hoffmann-La Roche Ltd. 4070 Basel Switzerland
| | - Peter J McCormick
- William Harvey Research Institute, Barts and the London School of Medicine, Queen Mary University of London London EC1M 6BQ England UK
| | - Sergio Oddi
- Faculty of Veterinary Medicine, University of Teramo 64100 Teramo European Italy.,European Center for Brain Research (CERC), Santa Lucia Foundation 00179 Rome Italy
| | - Herman P Spaink
- Leiden University Einsteinweg 55 2333 CC Leiden the Netherlands
| | - Mauro Maccarrone
- European Center for Brain Research (CERC), Santa Lucia Foundation 00179 Rome Italy.,Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila 67100 L'Aquila Italy
| | - Dmitry B Veprintsev
- Faculty of Medicine & Health Sciences, University of Nottingham Nottingham NG7 2UH England UK.,United Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham Midlands England UK
| | - Erick M Carreira
- Laboratorium für Organische Chemie, Eidgenössische Technische Hochschule Zürich Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
| | - Uwe Grether
- Roche Pharma Research & Early Development, Roche Innovation Center Basel F. Hoffmann-La Roche Ltd. 4070 Basel Switzerland
| | - Marc Nazaré
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) Campus Berlin-Buch 13125 Berlin Germany
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6
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Naqvi MM, Avellaneda MJ, Roth A, Koers EJ, Roland A, Sunderlikova V, Kramer G, Rye HS, Tans SJ. Protein chain collapse modulation and folding stimulation by GroEL-ES. Sci Adv 2022; 8:eabl6293. [PMID: 35245117 PMCID: PMC8896798 DOI: 10.1126/sciadv.abl6293] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 01/11/2022] [Indexed: 06/14/2023]
Abstract
The collapse of polypeptides is thought important to protein folding, aggregation, intrinsic disorder, and phase separation. However, whether polypeptide collapse is modulated in cells to control protein states is unclear. Here, using integrated protein manipulation and imaging, we show that the chaperonin GroEL-ES can accelerate the folding of proteins by strengthening their collapse. GroEL induces contractile forces in substrate chains, which draws them into the cavity and triggers a general compaction and discrete folding transitions, even for slow-folding proteins. This collapse enhancement is strongest in the nucleotide-bound states of GroEL and is aided by GroES binding to the cavity rim and by the amphiphilic C-terminal tails at the cavity bottom. Collapse modulation is distinct from other proposed GroEL-ES folding acceleration mechanisms, including steric confinement and misfold unfolding. Given the prevalence of collapse throughout the proteome, we conjecture that collapse modulation is more generally relevant within the protein quality control machinery.
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Affiliation(s)
| | | | - Andrew Roth
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77845, USA
| | | | | | | | - Günter Kramer
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, Heidelberg D-69120, Germany
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 282, Heidelberg D-69120, Germany
| | - Hays S. Rye
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77845, USA
| | - Sander J. Tans
- AMOLF, Science Park 104, 1098 XG Amsterdam, Netherlands
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, Netherlands
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7
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Wruck F, Avellaneda MJ, Koers EJ, Minde DP, Mayer MP, Kramer G, Mashaghi A, Tans SJ. Protein Folding Mediated by Trigger Factor and Hsp70: New Insights from Single-Molecule Approaches. J Mol Biol 2017; 430:438-449. [PMID: 28911846 DOI: 10.1016/j.jmb.2017.09.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 08/26/2017] [Accepted: 09/04/2017] [Indexed: 01/01/2023]
Abstract
Chaperones assist in protein folding, but what this common phrase means in concrete terms has remained surprisingly poorly understood. We can readily measure chaperone binding to unfolded proteins, but how they bind and affect proteins along folding trajectories has remained obscure. Here we review recent efforts by our labs and others that are beginning to pry into this issue, with a focus on the chaperones trigger factor and Hsp70. Single-molecule methods are central, as they allow the stepwise process of folding to be followed directly. First results have already revealed contrasts with long-standing paradigms: rather than acting only "early" by stabilizing unfolded chain segments, these chaperones can bind and stabilize partially folded structures as they grow to their native state. The findings suggest a fundamental redefinition of the protein folding problem and a more extensive functional repertoire of chaperones than previously assumed.
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Affiliation(s)
- Florian Wruck
- AMOLF, Science Park 104, 1098 XG Amsterdam, the Netherlands
| | | | - Eline J Koers
- AMOLF, Science Park 104, 1098 XG Amsterdam, the Netherlands
| | - David P Minde
- AMOLF, Science Park 104, 1098 XG Amsterdam, the Netherlands
| | - Matthias P Mayer
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, D-69120 Heidelberg, Germany; German Cancer Research Center (DKFZ), Im Neuenheimer Feld 282, D-69120 Heidelberg, Germany
| | - Günter Kramer
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, D-69120 Heidelberg, Germany; German Cancer Research Center (DKFZ), Im Neuenheimer Feld 282, D-69120 Heidelberg, Germany
| | - Alireza Mashaghi
- Leiden Academic Centre for Drug Research, Faculty of Mathematics and Natural Sciences, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands
| | - Sander J Tans
- AMOLF, Science Park 104, 1098 XG Amsterdam, the Netherlands.
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8
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Avellaneda MJ, Koers EJ, Naqvi MM, Tans SJ. The chaperone toolbox at the single-molecule level: From clamping to confining. Protein Sci 2017; 26:1291-1302. [PMID: 28342267 DOI: 10.1002/pro.3161] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 03/17/2017] [Accepted: 03/17/2017] [Indexed: 11/09/2022]
Abstract
Protein folding is well known to be supervised by a dedicated class of proteins called chaperones. However, the core mode of action of these molecular machines has remained elusive due to several reasons including the promiscuous nature of the interactions between chaperones and their many clients, as well as the dynamics and heterogeneity of chaperone conformations and the folding process itself. While troublesome for traditional bulk techniques, these properties make an excellent case for the use of single-molecule approaches. In this review, we will discuss how force spectroscopy, fluorescence microscopy, FCS, and FRET methods are starting to zoom in on this intriguing and diverse molecular toolbox that is of direct importance for protein quality control in cells, as well as numerous degenerative conditions that depend on it.
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Affiliation(s)
| | - Eline J Koers
- AMOLF institute, Science Park 104, 1098XG Amsterdam, The Netherlands
| | - Mohsin M Naqvi
- AMOLF institute, Science Park 104, 1098XG Amsterdam, The Netherlands
| | - Sander J Tans
- AMOLF institute, Science Park 104, 1098XG Amsterdam, The Netherlands
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9
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van der Cruijsen EAW, Koers EJ, Sauvée C, Hulse RE, Weingarth M, Ouari O, Perozo E, Tordo P, Baldus M. Biomolecular DNP-Supported NMR Spectroscopy using Site-Directed Spin Labeling. Chemistry 2015; 21:12971-7. [DOI: 10.1002/chem.201501376] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Indexed: 12/24/2022]
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10
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Koers EJ, van der Cruijsen EAW, Rosay M, Weingarth M, Prokofyev A, Sauvée C, Ouari O, van der Zwan J, Pongs O, Tordo P, Maas WE, Baldus M. NMR-based structural biology enhanced by dynamic nuclear polarization at high magnetic field. J Biomol NMR 2014; 60:157-68. [PMID: 25284462 DOI: 10.1007/s10858-014-9865-8] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 09/23/2014] [Indexed: 05/04/2023]
Abstract
Dynamic nuclear polarization (DNP) has become a powerful method to enhance spectroscopic sensitivity in the context of magnetic resonance imaging and nuclear magnetic resonance spectroscopy. We show that, compared to DNP at lower field (400 MHz/263 GHz), high field DNP (800 MHz/527 GHz) can significantly enhance spectral resolution and allows exploitation of the paramagnetic relaxation properties of DNP polarizing agents as direct structural probes under magic angle spinning conditions. Applied to a membrane-embedded K(+) channel, this approach allowed us to refine the membrane-embedded channel structure and revealed conformational substates that are present during two different stages of the channel gating cycle. High-field DNP thus offers atomic insight into the role of molecular plasticity during the course of biomolecular function in a complex cellular environment.
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Affiliation(s)
- Eline J Koers
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, 3584 CH, Utrecht, The Netherlands
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11
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Sattler JJHB, Gonzalez-Jimenez ID, Luo L, Stears BA, Malek A, Barton DG, Kilos BA, Kaminsky MP, Verhoeven TWGM, Koers EJ, Baldus M, Weckhuysen BM. Platinum-promoted Ga/Al₂O₃ as highly active, selective, and stable catalyst for the dehydrogenation of propane. Angew Chem Int Ed Engl 2014; 53:9251-6. [PMID: 24989975 PMCID: PMC4499260 DOI: 10.1002/anie.201404460] [Citation(s) in RCA: 152] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Revised: 05/31/2014] [Indexed: 11/05/2022]
Abstract
A novel catalyst material for the selective dehydrogenation of propane is presented. The catalyst consists of 1000 ppm Pt, 3 wt% Ga, and 0.25 wt% K supported on alumina. We observed a synergy between Ga and Pt, resulting in a highly active and stable catalyst. Additionally, we propose a bifunctional active phase, in which coordinately unsaturated Ga(3+) species are the active species and where Pt functions as a promoter.
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Affiliation(s)
- Jesper J H B Sattler
- Inorganic Chemistry and Catalysis Group, Debye Institute for Nanomaterials Science, Utrecht UniversityUniversiteitsweg 99, 3584 CG Utrecht (The Netherlands)
| | - Ines D Gonzalez-Jimenez
- Inorganic Chemistry and Catalysis Group, Debye Institute for Nanomaterials Science, Utrecht UniversityUniversiteitsweg 99, 3584 CG Utrecht (The Netherlands)
| | - Lin Luo
- Hydrocarbons R&D, The Dow Chemical Company2301 N. Brazosport Blvd., Freeport, TX 77541 (USA)
| | - Brien A Stears
- Hydrocarbons R&D, The Dow Chemical Company2301 N. Brazosport Blvd., Freeport, TX 77541 (USA)
| | - Andrzej Malek
- Hydrocarbons R&D, The Dow Chemical Company2301 N. Brazosport Blvd., Freeport, TX 77541 (USA)
| | - David G Barton
- Core R&D, The Dow Chemical Company1776 Building, Midland, MI 48674 (USA)
| | - Beata A Kilos
- Core R&D, The Dow Chemical Company1776 Building, Midland, MI 48674 (USA)
| | - Mark P Kaminsky
- Hydrocarbons R&D, The Dow Chemical Company2301 N. Brazosport Blvd., Freeport, TX 77541 (USA)
| | - Tiny W G M Verhoeven
- Eindhoven University of TechnologyP.O. Box 513, 5600 MB Eindhoven (The Netherlands)
| | - Eline J Koers
- NMR Spectroscopy Research Group, Bijvoet Centre for Biomolecular Research Utrecht UniversityPadualaan 8, 3584 CH Utrecht (The Netherlands)
| | - Marc Baldus
- NMR Spectroscopy Research Group, Bijvoet Centre for Biomolecular Research Utrecht UniversityPadualaan 8, 3584 CH Utrecht (The Netherlands)
| | - Bert M Weckhuysen
- Inorganic Chemistry and Catalysis Group, Debye Institute for Nanomaterials Science, Utrecht UniversityUniversiteitsweg 99, 3584 CG Utrecht (The Netherlands)
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12
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Sattler JJHB, Gonzalez-Jimenez ID, Luo L, Stears BA, Malek A, Barton DG, Kilos BA, Kaminsky MP, Verhoeven TWGM, Koers EJ, Baldus M, Weckhuysen BM. Platinum-Promoted Ga/Al2O3as Highly Active, Selective, and Stable Catalyst for the Dehydrogenation of Propane. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201404460] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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13
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Koers EJ, López-Deber MP, Weingarth M, Nand D, Hickman DT, Mlaki Ndao D, Reis P, Granet A, Pfeifer A, Muhs A, Baldus M. NMR-Spektroskopie in Kombination mit dynamischer Kernpolarisation enthüllt mehrere Konformationen in Lipid-verankerten Peptid-Impfstoffen. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201303374] [Citation(s) in RCA: 7] [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: 11/09/2022]
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14
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Koers EJ, López-Deber MP, Weingarth M, Nand D, Hickman DT, Mlaki Ndao D, Reis P, Granet A, Pfeifer A, Muhs A, Baldus M. Dynamic nuclear polarization NMR spectroscopy: revealing multiple conformations in lipid-anchored peptide vaccines. Angew Chem Int Ed Engl 2013; 52:10905-8. [PMID: 24039018 DOI: 10.1002/anie.201303374] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2013] [Revised: 06/24/2013] [Indexed: 11/09/2022]
Affiliation(s)
- Eline J Koers
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht (The Netherlands)
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15
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Renault M, Pawsey S, Bos MP, Koers EJ, Nand D, Tommassen-van Boxtel R, Rosay M, Tommassen J, Maas WE, Baldus M. Solid-State NMR Spectroscopy on Cellular Preparations Enhanced by Dynamic Nuclear Polarization. Angew Chem Int Ed Engl 2012; 51:2998-3001. [DOI: 10.1002/anie.201105984] [Citation(s) in RCA: 155] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2011] [Revised: 11/02/2011] [Indexed: 11/05/2022]
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16
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Renault M, Pawsey S, Bos MP, Koers EJ, Nand D, Tommassen-van Boxtel R, Rosay M, Tommassen J, Maas WE, Baldus M. Festkörper-NMR-Spektroskopie an zellulären Proben: verbesserte Empfindlichkeit durch dynamische Kernpolarisation. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201105984] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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