1
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Mallis RJ, Lee JJ, den Berg AV, Brazin KN, Viennet T, Zmuda J, Cross M, Radeva D, Rodriguez‐Mias R, Villén J, Gelev V, Reinherz EL, Arthanari H. Efficient and economic protein labeling for NMR in mammalian expression systems: Application to a preT-cell and T-cell receptor protein. Protein Sci 2024; 33:e4950. [PMID: 38511503 PMCID: PMC10955624 DOI: 10.1002/pro.4950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/05/2024] [Accepted: 02/16/2024] [Indexed: 03/22/2024]
Abstract
Protein nuclear magnetic resonance (NMR) spectroscopy relies on the ability to isotopically label polypeptides, which is achieved through heterologous expression in various host organisms. Most commonly, Escherichia coli is employed by leveraging isotopically substituted ammonium and glucose to uniformly label proteins with 15N and 13C, respectively. Moreover, E. coli can grow and express proteins in uniformly deuterium-substituted water (D2O), a strategy useful for experiments targeting high molecular weight proteins. Unfortunately, many proteins, particularly those requiring specific posttranslational modifications like disulfide bonding or glycosylation for proper folding and/or function, cannot be readily expressed in their functional forms using E. coli-based expression systems. One such class of proteins includes T-cell receptors and their related preT-cell receptors. In this study, we present an expression system for isotopic labeling of proteins using a nonadherent human embryonic kidney cell line, Expi293F, and a specially designed media. We demonstrate the application of this platform to the β subunit common to both receptors. In addition, we show that this expression system and media can be used to specifically label amino acids Phe, Ile, Val, and Leu in this system, utilizing an amino acid-specific labeling protocol that allows targeted incorporation at high efficiency without significant isotopic scrambling. We demonstrate that this system can also be used to express proteins with fluorinated amino acids. We were routinely able to obtain an NMR sample with a concentration of 200 μM from 30 mL of culture media, utilizing less than 20 mg of the labeled amino acids.
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Affiliation(s)
- Robert J. Mallis
- Laboratory of ImmunobiologyDana‐Farber Cancer InstituteBostonMassachusettsUSA
- Department of Medical OncologyDana‐Farber Cancer InstituteBostonMassachusettsUSA
- Department of DermatologyHarvard Medical SchoolBostonMassachusettsUSA
| | - Jonathan J. Lee
- Laboratory of ImmunobiologyDana‐Farber Cancer InstituteBostonMassachusettsUSA
- Department of Medical OncologyDana‐Farber Cancer InstituteBostonMassachusettsUSA
| | | | - Kristine N. Brazin
- Laboratory of ImmunobiologyDana‐Farber Cancer InstituteBostonMassachusettsUSA
- Department of Medical OncologyDana‐Farber Cancer InstituteBostonMassachusettsUSA
- Department of MedicineHarvard Medical SchoolBostonMassachusettsUSA
| | - Thibault Viennet
- Department of Cancer BiologyDana‐Farber Cancer InstituteBostonMassachusettsUSA
- Department of Biological Chemistry and Molecular PharmacologyHarvard Medical SchoolBostonMassachusettsUSA
| | | | | | - Denitsa Radeva
- Faculty of Chemistry and PharmacySofia UniversitySofiaBulgaria
| | | | - Judit Villén
- Department of Genome SciencesUniversity of WashingtonSeattleWashingtonUSA
| | - Vladimir Gelev
- Faculty of Chemistry and PharmacySofia UniversitySofiaBulgaria
| | - Ellis L. Reinherz
- Laboratory of ImmunobiologyDana‐Farber Cancer InstituteBostonMassachusettsUSA
- Department of Medical OncologyDana‐Farber Cancer InstituteBostonMassachusettsUSA
- Department of MedicineHarvard Medical SchoolBostonMassachusettsUSA
| | - Haribabu Arthanari
- Department of Cancer BiologyDana‐Farber Cancer InstituteBostonMassachusettsUSA
- Department of Biological Chemistry and Molecular PharmacologyHarvard Medical SchoolBostonMassachusettsUSA
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2
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Jin B, Thakur N, Wijesekara AV, Eddy MT. Illuminating GPCR signaling mechanisms by NMR spectroscopy with stable-isotope labeled receptors. Curr Opin Pharmacol 2023; 72:102364. [PMID: 37612173 DOI: 10.1016/j.coph.2023.102364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 02/06/2023] [Accepted: 02/20/2023] [Indexed: 08/25/2023]
Abstract
G protein-coupled receptors (GPCRs) exhibit remarkable structural plasticity, which underlies their capacity to recognize a wide range of extracellular molecules and interact with intracellular partner proteins. Nuclear magnetic resonance (NMR) spectroscopy is uniquely well-suited to investigate GPCR structural plasticity, enabled by stable-isotope "probes" incorporated into receptors that inform on structure and dynamics. Progress with stable-isotope labeling methods in Eukaryotic expression systems has enabled production of native or nearly-native human receptors with varied and complementary distributions of NMR probes. These advances have opened up new avenues for investigating the roles of conformational dynamics in signaling processes, including by mapping allosteric communication networks, understanding the specificity of GPCR interactions with partner proteins and exploring the impact of membrane environments on GPCR function.
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Affiliation(s)
- Beining Jin
- Department of Chemistry; University of Florida; Gainesville, FL, 32611, USA
| | - Naveen Thakur
- Department of Chemistry; University of Florida; Gainesville, FL, 32611, USA
| | | | - Matthew T Eddy
- Department of Chemistry; University of Florida; Gainesville, FL, 32611, USA.
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3
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Pintér G, Hohmann K, Grün J, Wirmer-Bartoschek J, Glaubitz C, Fürtig B, Schwalbe H. Real-time nuclear magnetic resonance spectroscopy in the study of biomolecular kinetics and dynamics. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2021; 2:291-320. [PMID: 37904763 PMCID: PMC10539803 DOI: 10.5194/mr-2-291-2021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 04/07/2021] [Indexed: 11/01/2023]
Abstract
The review describes the application of nuclear magnetic resonance (NMR) spectroscopy to study kinetics of folding, refolding and aggregation of proteins, RNA and DNA. Time-resolved NMR experiments can be conducted in a reversible or an irreversible manner. In particular, irreversible folding experiments pose large requirements for (i) signal-to-noise due to the time limitations and (ii) synchronising of the refolding steps. Thus, this contribution discusses the application of methods for signal-to-noise increases, including dynamic nuclear polarisation, hyperpolarisation and photo-CIDNP for the study of time-resolved NMR studies. Further, methods are reviewed ranging from pressure and temperature jump, light induction to rapid mixing to induce rapidly non-equilibrium conditions required to initiate folding.
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Affiliation(s)
- György Pintér
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang
Goethe-Universität Frankfurt, Frankfurt 60438, Germany
| | - Katharina F. Hohmann
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang
Goethe-Universität Frankfurt, Frankfurt 60438, Germany
| | - J. Tassilo Grün
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang
Goethe-Universität Frankfurt, Frankfurt 60438, Germany
| | - Julia Wirmer-Bartoschek
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang
Goethe-Universität Frankfurt, Frankfurt 60438, Germany
| | - Clemens Glaubitz
- Institute for Biophysical Chemistry, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität Frankfurt, Frankfurt 60438, Germany
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang
Goethe-Universität Frankfurt, Frankfurt 60438, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang
Goethe-Universität Frankfurt, Frankfurt 60438, Germany
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4
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Krug U, Gloge A, Schmidt P, Becker‐Baldus J, Bernhard F, Kaiser A, Montag C, Gauglitz M, Vishnivetskiy SA, Gurevich VV, Beck‐Sickinger AG, Glaubitz C, Huster D. The Conformational Equilibrium of the Neuropeptide Y2 Receptor in Bilayer Membranes. Angew Chem Int Ed Engl 2020; 59:23854-23861. [PMID: 32790043 PMCID: PMC7736470 DOI: 10.1002/anie.202006075] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/13/2020] [Indexed: 12/23/2022]
Abstract
Dynamic structural transitions within the seven-transmembrane bundle represent the mechanism by which G-protein-coupled receptors convert an extracellular chemical signal into an intracellular biological function. Here, the conformational dynamics of the neuropeptide Y receptor type 2 (Y2R) during activation was investigated. The apo, full agonist-, and arrestin-bound states of Y2R were prepared by cell-free expression, functional refolding, and reconstitution into lipid membranes. To study conformational transitions between these states, all six tryptophans of Y2R were 13 C-labeled. NMR-signal assignment was achieved by dynamic-nuclear-polarization enhancement and the individual functional states of the receptor were characterized by monitoring 13 C NMR chemical shifts. Activation of Y2R is mediated by molecular switches involving the toggle switch residue Trp2816.48 of the highly conserved SWLP motif and Trp3277.55 adjacent to the NPxxY motif. Furthermore, a conformationally preserved "cysteine lock"-Trp11623.50 was identified.
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Affiliation(s)
- Ulrike Krug
- Institute of Medical Physics and BiophysicsUniversity of LeipzigHärtelstr. 16–1804107LeipzigGermany
| | - Anika Gloge
- Institute of Medical Physics and BiophysicsUniversity of LeipzigHärtelstr. 16–1804107LeipzigGermany
| | - Peter Schmidt
- Institute of Medical Physics and BiophysicsUniversity of LeipzigHärtelstr. 16–1804107LeipzigGermany
| | - Johanna Becker‐Baldus
- Institute of Biophysical ChemistryGoethe University FrankfurtGermany
- Center for Biomolecular Magnetic ResonanceGoethe University FrankfurtGermany
| | - Frank Bernhard
- Institute of Biophysical ChemistryGoethe University FrankfurtGermany
- Center for Biomolecular Magnetic ResonanceGoethe University FrankfurtGermany
| | - Anette Kaiser
- Institute of BiochemistryUniversity of LeipzigLeipzigGermany
| | - Cindy Montag
- Institute of Medical Physics and BiophysicsUniversity of LeipzigHärtelstr. 16–1804107LeipzigGermany
| | - Marcel Gauglitz
- Institute of Medical Physics and BiophysicsUniversity of LeipzigHärtelstr. 16–1804107LeipzigGermany
- Berlin Joint Electron Paramagnetic Resonance LaboratoryFree University BerlinGermany
| | | | | | | | - Clemens Glaubitz
- Institute of Biophysical ChemistryGoethe University FrankfurtGermany
- Center for Biomolecular Magnetic ResonanceGoethe University FrankfurtGermany
| | - Daniel Huster
- Institute of Medical Physics and BiophysicsUniversity of LeipzigHärtelstr. 16–1804107LeipzigGermany
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5
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Krug U, Gloge A, Schmidt P, Becker‐Baldus J, Bernhard F, Kaiser A, Montag C, Gauglitz M, Vishnivetskiy SA, Gurevich VV, Beck‐Sickinger AG, Glaubitz C, Huster D. Das Konformationsgleichgewicht des Neuropeptid‐Y2‐Rezeptors in Lipidmembranen. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202006075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Ulrike Krug
- Institut für Medizinische Physik und Biophysik Universität Leipzig Härtelstr. 16–18 04107 Leipzig Deutschland
| | - Anika Gloge
- Institut für Medizinische Physik und Biophysik Universität Leipzig Härtelstr. 16–18 04107 Leipzig Deutschland
| | - Peter Schmidt
- Institut für Medizinische Physik und Biophysik Universität Leipzig Härtelstr. 16–18 04107 Leipzig Deutschland
| | - Johanna Becker‐Baldus
- Institut für Biophysikalische Chemie Goethe-Universität Frankfurt am Main Deutschland
- Zentrum für Biomolekulare Magnetresonanz Goethe-Universität Frankfurt am Main Deutschland
| | - Frank Bernhard
- Institut für Biophysikalische Chemie Goethe-Universität Frankfurt am Main Deutschland
- Zentrum für Biomolekulare Magnetresonanz Goethe-Universität Frankfurt am Main Deutschland
| | - Anette Kaiser
- Institut für Biochemie Universität Leipzig Deutschland
| | - Cindy Montag
- Institut für Medizinische Physik und Biophysik Universität Leipzig Härtelstr. 16–18 04107 Leipzig Deutschland
| | - Marcel Gauglitz
- Institut für Medizinische Physik und Biophysik Universität Leipzig Härtelstr. 16–18 04107 Leipzig Deutschland
- Berlin Joint Electron Paramagnetic Resonance Laboratory Freie Universität Berlin Deutschland
| | | | | | | | - Clemens Glaubitz
- Institut für Biophysikalische Chemie Goethe-Universität Frankfurt am Main Deutschland
- Zentrum für Biomolekulare Magnetresonanz Goethe-Universität Frankfurt am Main Deutschland
| | - Daniel Huster
- Institut für Medizinische Physik und Biophysik Universität Leipzig Härtelstr. 16–18 04107 Leipzig Deutschland
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6
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Capturing Peptide-GPCR Interactions and Their Dynamics. Molecules 2020; 25:molecules25204724. [PMID: 33076289 PMCID: PMC7587574 DOI: 10.3390/molecules25204724] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/08/2020] [Accepted: 10/09/2020] [Indexed: 12/16/2022] Open
Abstract
Many biological functions of peptides are mediated through G protein-coupled receptors (GPCRs). Upon ligand binding, GPCRs undergo conformational changes that facilitate the binding and activation of multiple effectors. GPCRs regulate nearly all physiological processes and are a favorite pharmacological target. In particular, drugs are sought after that elicit the recruitment of selected effectors only (biased ligands). Understanding how ligands bind to GPCRs and which conformational changes they induce is a fundamental step toward the development of more efficient and specific drugs. Moreover, it is emerging that the dynamic of the ligand–receptor interaction contributes to the specificity of both ligand recognition and effector recruitment, an aspect that is missing in structural snapshots from crystallography. We describe here biochemical and biophysical techniques to address ligand–receptor interactions in their structural and dynamic aspects, which include mutagenesis, crosslinking, spectroscopic techniques, and mass-spectrometry profiling. With a main focus on peptide receptors, we present methods to unveil the ligand–receptor contact interface and methods that address conformational changes both in the ligand and the GPCR. The presented studies highlight a wide structural heterogeneity among peptide receptors, reveal distinct structural changes occurring during ligand binding and a surprisingly high dynamics of the ligand–GPCR complexes.
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7
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Kubatova N, Mao J, Eckert CE, Saxena K, Gande SL, Wachtveitl J, Glaubitz C, Schwalbe H. Light Dynamics of the Retinal-Disease-Relevant G90D Bovine Rhodopsin Mutant. Angew Chem Int Ed Engl 2020; 59:15656-15664. [PMID: 32602600 PMCID: PMC7496284 DOI: 10.1002/anie.202003671] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 06/25/2020] [Indexed: 12/11/2022]
Abstract
The RHO gene encodes the G-protein-coupled receptor (GPCR) rhodopsin. Numerous mutations associated with impaired visual cycle have been reported; the G90D mutation leads to a constitutively active mutant form of rhodopsin that causes CSNB disease. We report on the structural investigation of the retinal configuration and conformation in the binding pocket in the dark and light-activated state by solution and MAS-NMR spectroscopy. We found two long-lived dark states for the G90D mutant with the 11-cis retinal bound as Schiff base in both populations. The second minor population in the dark state is attributed to a slight shift in conformation of the covalently bound 11-cis retinal caused by the mutation-induced distortion on the salt bridge formation in the binding pocket. Time-resolved UV/Vis spectroscopy was used to monitor the functional dynamics of the G90D mutant rhodopsin for all relevant time scales of the photocycle. The G90D mutant retains its conformational heterogeneity during the photocycle.
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Affiliation(s)
- Nina Kubatova
- Center for Biomolecular Magnetic ResonanceGoethe University FrankfurtMax-von-Laue-Strasse 760438FrankfurtGermany
- Institute for Organic Chemistry and Chemical BiologyGoethe University FrankfurtMax-von-Laue-Strasse 760438FrankfurtGermany
| | - Jiafei Mao
- Center for Biomolecular Magnetic ResonanceGoethe University FrankfurtMax-von-Laue-Strasse 760438FrankfurtGermany
- Institute of Biophysical ChemistryGoethe University FrankfurtMax-von-Laue-Strasse 960438FrankfurtGermany
| | - Carl Elias Eckert
- Institute of Physical and Theoretical ChemistryGoethe University FrankfurtMax-von-Laue-Strasse 760438FrankfurtGermany
| | - Krishna Saxena
- Center for Biomolecular Magnetic ResonanceGoethe University FrankfurtMax-von-Laue-Strasse 760438FrankfurtGermany
- Institute for Organic Chemistry and Chemical BiologyGoethe University FrankfurtMax-von-Laue-Strasse 760438FrankfurtGermany
| | - Santosh L. Gande
- Center for Biomolecular Magnetic ResonanceGoethe University FrankfurtMax-von-Laue-Strasse 760438FrankfurtGermany
- Institute for Organic Chemistry and Chemical BiologyGoethe University FrankfurtMax-von-Laue-Strasse 760438FrankfurtGermany
| | - Josef Wachtveitl
- Institute of Physical and Theoretical ChemistryGoethe University FrankfurtMax-von-Laue-Strasse 760438FrankfurtGermany
| | - Clemens Glaubitz
- Center for Biomolecular Magnetic ResonanceGoethe University FrankfurtMax-von-Laue-Strasse 760438FrankfurtGermany
- Institute of Biophysical ChemistryGoethe University FrankfurtMax-von-Laue-Strasse 960438FrankfurtGermany
| | - Harald Schwalbe
- Center for Biomolecular Magnetic ResonanceGoethe University FrankfurtMax-von-Laue-Strasse 760438FrankfurtGermany
- Institute for Organic Chemistry and Chemical BiologyGoethe University FrankfurtMax-von-Laue-Strasse 760438FrankfurtGermany
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8
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Kögler LM, Stichel J, Beck-Sickinger AG. Structural investigations of cell-free expressed G protein-coupled receptors. Biol Chem 2020; 401:97-116. [PMID: 31539345 DOI: 10.1515/hsz-2019-0292] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 09/02/2019] [Indexed: 12/11/2022]
Abstract
G protein-coupled receptors (GPCRs) are of great pharmaceutical interest and about 35% of the commercial drugs target these proteins. Still there is huge potential left in finding molecules that target new GPCRs or that modulate GPCRs differentially. For a rational drug design, it is important to understand the structure, binding and activation of the protein of interest. Structural investigations of GPCRs remain challenging, although huge progress has been made in the last 20 years, especially in the generation of crystal structures of GPCRs. This is mostly caused by issues with the expression yield, purity or labeling. Cell-free protein synthesis (CFPS) is an efficient alternative for recombinant expression systems that can potentially address many of these problems. In this article the use of CFPS for structural investigations of GPCRs is reviewed. We compare different CFPS systems, including the cellular basis and reaction configurations, and strategies for an efficient solubilization. Next, we highlight recent advances in the structural investigation of cell-free expressed GPCRs, with special emphasis on the role of photo-crosslinking approaches to investigate ligand binding sites on GPCRs.
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Affiliation(s)
- Lisa Maria Kögler
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, Leipzig University, Brüderstr. 34, D-04103 Leipzig, Germany
| | - Jan Stichel
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, Leipzig University, Brüderstr. 34, D-04103 Leipzig, Germany
| | - Annette G Beck-Sickinger
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, Leipzig University, Brüderstr. 34, D-04103 Leipzig, Germany
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9
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Kubatova N, Mao J, Eckert CE, Saxena K, Gande SL, Wachtveitl J, Glaubitz C, Schwalbe H. Light Dynamics of the Retinal‐Disease‐Relevant G90D Bovine Rhodopsin Mutant. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202003671] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Nina Kubatova
- Center for Biomolecular Magnetic Resonance Goethe University Frankfurt Max-von-Laue-Strasse 7 60438 Frankfurt Germany
- Institute for Organic Chemistry and Chemical Biology Goethe University Frankfurt Max-von-Laue-Strasse 7 60438 Frankfurt Germany
| | - Jiafei Mao
- Center for Biomolecular Magnetic Resonance Goethe University Frankfurt Max-von-Laue-Strasse 7 60438 Frankfurt Germany
- Institute of Biophysical Chemistry Goethe University Frankfurt Max-von-Laue-Strasse 9 60438 Frankfurt Germany
| | - Carl Elias Eckert
- Institute of Physical and Theoretical Chemistry Goethe University Frankfurt Max-von-Laue-Strasse 7 60438 Frankfurt Germany
| | - Krishna Saxena
- Center for Biomolecular Magnetic Resonance Goethe University Frankfurt Max-von-Laue-Strasse 7 60438 Frankfurt Germany
- Institute for Organic Chemistry and Chemical Biology Goethe University Frankfurt Max-von-Laue-Strasse 7 60438 Frankfurt Germany
| | - Santosh L. Gande
- Center for Biomolecular Magnetic Resonance Goethe University Frankfurt Max-von-Laue-Strasse 7 60438 Frankfurt Germany
- Institute for Organic Chemistry and Chemical Biology Goethe University Frankfurt Max-von-Laue-Strasse 7 60438 Frankfurt Germany
| | - Josef Wachtveitl
- Institute of Physical and Theoretical Chemistry Goethe University Frankfurt Max-von-Laue-Strasse 7 60438 Frankfurt Germany
| | - Clemens Glaubitz
- Center for Biomolecular Magnetic Resonance Goethe University Frankfurt Max-von-Laue-Strasse 7 60438 Frankfurt Germany
- Institute of Biophysical Chemistry Goethe University Frankfurt Max-von-Laue-Strasse 9 60438 Frankfurt Germany
| | - Harald Schwalbe
- Center for Biomolecular Magnetic Resonance Goethe University Frankfurt Max-von-Laue-Strasse 7 60438 Frankfurt Germany
- Institute for Organic Chemistry and Chemical Biology Goethe University Frankfurt Max-von-Laue-Strasse 7 60438 Frankfurt Germany
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10
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Kleist AB, Peterson F, Tyler RC, Gustavsson M, Handel TM, Volkman BF. Solution NMR spectroscopy of GPCRs: Residue-specific labeling strategies with a focus on 13C-methyl methionine labeling of the atypical chemokine receptor ACKR3. Methods Cell Biol 2018; 149:259-288. [PMID: 30616824 DOI: 10.1016/bs.mcb.2018.09.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The past decade has witnessed remarkable progress in the determination of G protein-coupled receptor (GPCR) structures, profoundly expanding our understanding of how GPCRs recognize ligands, become activated, and interact with intracellular signaling components. In recent years, numerous studies have used solution nuclear magnetic resonance (NMR) spectroscopy to investigate GPCRs, providing fundamental insights into GPCR conformational changes, allostery, dynamics, and other facets of GPCR function are challenging to study using other structural techniques. Despite these advantages, NMR-based studies of GPCRs are few relative to the number of published structures, due in part to the challenges and limitations of NMR for the characterization of large membrane proteins. Several studies have circumvented these challenges using a variety of isotopic labeling strategies, including side chain derivatization and metabolic incorporation of NMR-active nuclei. In this chapter, we provide an overview of different isotopic labeling strategies and describe an in-depth protocol for the expression, purification, and NMR studies of the chemokine GPCR atypical chemokine receptor 3 (ACKR3) via 13CH3-methionine incorporation. The goal of this chapter is to provide a resource to the GPCR community for those interested in pursuing NMR studies of GPCRs.
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Affiliation(s)
- Andrew B Kleist
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Francis Peterson
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Robert C Tyler
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Martin Gustavsson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, United States
| | - Tracy M Handel
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, United States
| | - Brian F Volkman
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, United States.
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11
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Mattle D, Kuhn B, Aebi J, Bedoucha M, Kekilli D, Grozinger N, Alker A, Rudolph MG, Schmid G, Schertler GFX, Hennig M, Standfuss J, Dawson RJP. Ligand channel in pharmacologically stabilized rhodopsin. Proc Natl Acad Sci U S A 2018; 115:3640-3645. [PMID: 29555765 PMCID: PMC5889642 DOI: 10.1073/pnas.1718084115] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
In the degenerative eye disease retinitis pigmentosa (RP), protein misfolding leads to fatal consequences for cell metabolism and rod and cone cell survival. To stop disease progression, a therapeutic approach focuses on stabilizing inherited protein mutants of the G protein-coupled receptor (GPCR) rhodopsin using pharmacological chaperones (PC) that improve receptor folding and trafficking. In this study, we discovered stabilizing nonretinal small molecules by virtual and thermofluor screening and determined the crystal structure of pharmacologically stabilized opsin at 2.4 Å resolution using one of the stabilizing hits (S-RS1). Chemical modification of S-RS1 and further structural analysis revealed the core binding motif of this class of rhodopsin stabilizers bound at the orthosteric binding site. Furthermore, previously unobserved conformational changes are visible at the intradiscal side of the seven-transmembrane helix bundle. A hallmark of this conformation is an open channel connecting the ligand binding site with the membrane and the intradiscal lumen of rod outer segments. Sufficient in size, the passage permits the exchange of hydrophobic ligands such as retinal. The results broaden our understanding of rhodopsin's conformational flexibility and enable therapeutic drug intervention against rhodopsin-related retinitis pigmentosa.
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Affiliation(s)
- Daniel Mattle
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Bernd Kuhn
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
| | - Johannes Aebi
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
| | - Marc Bedoucha
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
| | - Demet Kekilli
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Nathalie Grozinger
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
| | - Andre Alker
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
| | - Markus G Rudolph
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
| | - Georg Schmid
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
| | - Gebhard F X Schertler
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
- Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Michael Hennig
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
| | - Jörg Standfuss
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland;
| | - Roger J P Dawson
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland;
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12
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Woods KN, Pfeffer J, Klein-Seetharaman J. Chlorophyll-Derivative Modulation of Rhodopsin Signaling Properties through Evolutionarily Conserved Interaction Pathways. Front Mol Biosci 2017; 4:85. [PMID: 29312953 PMCID: PMC5733091 DOI: 10.3389/fmolb.2017.00085] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 11/28/2017] [Indexed: 01/04/2023] Open
Abstract
Retinal is the light-absorbing chromophore that is responsible for the activation of visual pigments and light-driven ion pumps. Evolutionary changes in the intermolecular interactions of the retinal with specific amino acids allow for adaptation of the spectral characteristics, referred to as spectral tuning. However, it has been proposed that a specific species of dragon fish has bypassed the adaptive evolutionary process of spectral tuning and replaced it with a single evolutionary event: photosensitization of rhodopsin by chlorophyll derivatives. Here, by using a combination of experimental measurements and computational modeling to probe retinal-receptor interactions in rhodopsin, we show how the binding of the chlorophyll derivative, chlorin-e6 (Ce6) in the intracellular domain (ICD) of the receptor allosterically excites G-protein coupled receptor class A (GPCR-A) conserved long-range correlated fluctuations that connect distant parts of the receptor. These long-range correlated motions are associated with regulating the dynamics and intermolecular interactions of specific amino acids in the retinal ligand-binding pocket that have been associated with shifts in the absorbance peak maximum (λmax) and hence, spectral sensitivity of the visual system. Moreover, the binding of Ce6 affects the overall global properties of the receptor. Specifically, we find that Ce6-induced dynamics alter the thermal stability of rhodopsin by adjusting hydrogen-bonding interactions near the receptor active-site that consequently also influences the intrinsic conformational equilibrium of the receptor. Due to the conservation of the ICD residues amongst different receptors in this class and the fact that all GPCR-A receptors share a common mechanism of activation, it is possible that the allosteric associations excited in rhodopsin with Ce6 binding are a common feature in all class A GPCRs.
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Affiliation(s)
- Kristina N. Woods
- Lehrstuhl für BioMolekulare Optik, Ludwig-Maximilians-Universität, München, Germany
- *Correspondence: Kristina N. Woods
| | - Jürgen Pfeffer
- Bavarian School of Public Policy, Technical University of Munich, München, Germany
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13
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Gozem S, Luk HL, Schapiro I, Olivucci M. Theory and Simulation of the Ultrafast Double-Bond Isomerization of Biological Chromophores. Chem Rev 2017; 117:13502-13565. [DOI: 10.1021/acs.chemrev.7b00177] [Citation(s) in RCA: 175] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Samer Gozem
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Hoi Ling Luk
- Chemistry
Department, Bowling Green State University, Overman Hall, Bowling Green, Ohio 43403, United States
| | - Igor Schapiro
- Fritz
Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Massimo Olivucci
- Chemistry
Department, Bowling Green State University, Overman Hall, Bowling Green, Ohio 43403, United States
- Dipartimento
di Biotecnologie, Chimica e Farmacia, Università di Siena, via A. Moro
2, 53100 Siena, Italy
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14
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Chatterjee D, Eckert CE, Slavov C, Saxena K, Fürtig B, Sanders CR, Gurevich VV, Wachtveitl J, Schwalbe H. Influence of Arrestin on the Photodecay of Bovine Rhodopsin. Angew Chem Int Ed Engl 2015; 54:13555-60. [PMID: 26383645 PMCID: PMC4685475 DOI: 10.1002/anie.201505798] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 08/11/2015] [Indexed: 11/07/2022]
Abstract
Continued activation of the photocycle of the dim-light receptor rhodopsin leads to the accumulation of all-trans-retinal in the rod outer segments (ROS). This accumulation can damage the photoreceptor cell. For retinal homeostasis, deactivation processes are initiated in which the release of retinal is delayed. One of these processes involves the binding of arrestin to rhodopsin. Here, the interaction of pre-activated truncated bovine visual arrestin (Arr(Tr)) with rhodopsin in 1,2-diheptanoyl-sn-glycero-3-phosphocholine (DHPC) micelles is investigated by solution NMR techniques and flash photolysis spectroscopy. Our results show that formation of the rhodopsin-arrestin complex markedly influences partitioning in the decay kinetics of rhodopsin, which involves the simultaneous formation of a meta II and a meta III state from the meta I state. Binding of Arr(Tr) leads to an increase in the population of the meta III state and consequently to an approximately twofold slower release of all-trans-retinal from rhodopsin.
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Affiliation(s)
- Deep Chatterjee
- Institute of Organic Chemistry and Chemical Biology, Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt/Main, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main (Germany)
| | - Carl Elias Eckert
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt/Main, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main (Germany)
| | - Chavdar Slavov
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt/Main, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main (Germany)
| | - Krishna Saxena
- Institute of Organic Chemistry and Chemical Biology, Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt/Main, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main (Germany)
| | - Boris Fürtig
- Institute of Organic Chemistry and Chemical Biology, Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt/Main, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main (Germany)
| | - Charles R Sanders
- Department of Biochemistry, Center for Structural Biology, Institute of Chemical Biology, Vanderbilt University School of Medicine, Nashville, TN 37232 (USA)
| | - Vsevolod V Gurevich
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN 37232 (USA)
| | - Josef Wachtveitl
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt/Main, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main (Germany).
| | - Harald Schwalbe
- Institute of Organic Chemistry and Chemical Biology, Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt/Main, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main (Germany).
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15
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Chatterjee D, Eckert CE, Slavov C, Saxena K, Fürtig B, Sanders CR, Gurevich VV, Wachtveitl J, Schwalbe H. Influence of Arrestin on the Photodecay of Bovine Rhodopsin. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201505798] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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16
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Enlightening the photoactive site of channelrhodopsin-2 by DNP-enhanced solid-state NMR spectroscopy. Proc Natl Acad Sci U S A 2015. [PMID: 26216996 DOI: 10.1073/pnas.1507713112] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Channelrhodopsin-2 from Chlamydomonas reinhardtii is a light-gated ion channel. Over recent years, this ion channel has attracted considerable interest because of its unparalleled role in optogenetic applications. However, despite considerable efforts, an understanding of how molecular events during the photocycle, including the retinal trans-cis isomerization and the deprotonation/reprotonation of the Schiff base, are coupled to the channel-opening mechanism remains elusive. To elucidate this question, changes of conformation and configuration of several photocycle and conducting/nonconducting states need to be determined at atomic resolution. Here, we show that such data can be obtained by solid-state NMR enhanced by dynamic nuclear polarization applied to (15)N-labeled channelrhodopsin-2 carrying 14,15-(13)C2 retinal reconstituted into lipid bilayers. In its dark state, a pure all-trans retinal conformation with a stretched C14-C15 bond and a significant out-of-plane twist of the H-C14-C15-H dihedral angle could be observed. Using a combination of illumination, freezing, and thermal relaxation procedures, a number of intermediate states was generated and analyzed by DNP-enhanced solid-state NMR. Three distinct intermediates could be analyzed with high structural resolution: the early [Formula: see text] K-like state, the slowly decaying late intermediate [Formula: see text], and a third intermediate populated only under continuous illumination conditions. Our data provide novel insight into the photoactive site of channelrhodopsin-2 during the photocycle. They further show that DNP-enhanced solid-state NMR fills the gap for challenging membrane proteins between functional studies and X-ray-based structure analysis, which is required for resolving molecular mechanisms.
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17
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Rinnenthal J, Wagner D, Marquardsen T, Krahn A, Engelke F, Schwalbe H. A temperature-jump NMR probe setup using rf heating optimized for the analysis of temperature-induced biomacromolecular kinetic processes. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 251:84-93. [PMID: 25616187 DOI: 10.1016/j.jmr.2014.11.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Revised: 11/24/2014] [Accepted: 11/25/2014] [Indexed: 06/04/2023]
Abstract
A novel temperature jump (T-jump) probe operational at B(0) fields of 600 MHz (14.1 Tesla) with an integrated cage radio-frequency (rf) coil for rapid (<1 s) heating in high-resolution (HR) liquid-state NMR-spectroscopy is presented and its performance investigated. The probe consists of an inner 2.5 mm "heating coil" designed for generating rf-electric fields of 190-220 MHz across a lossy dielectric sample and an outer two coil assembly for (1)H-, (2)H- and (15)N-nuclei. High B(0) field homogeneities (0.7 Hz at 600 MHz) are combined with high heating rates (20-25 K/s) and only small temperature gradients (<±1.5 K, 3s after 20 K T-jump). The heating coil is under control of a high power rf-amplifier within the NMR console and can therefore easily be accessed by the pulse programmer. Furthermore, implementation of a real-time setup including synchronization of the NMR spectrometer's air flow heater with the rf-heater used to maintain the temperature of the sample is described. Finally, the applicability of the real-time T-jump setup for the investigation of biomolecular kinetic processes in the second-to-minute timescale is demonstrated for samples of a model 14mer DNA hairpin and a (15)N-selectively labeled 40nt hsp17-RNA thermometer.
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Affiliation(s)
- Jörg Rinnenthal
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse 7, D-60438 Frankfurt/Main, Germany
| | - Dominic Wagner
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse 7, D-60438 Frankfurt/Main, Germany
| | | | - Alexander Krahn
- Bruker BioSpin GmbH, Am Silberstreifen, 76287 Rheinstetten, Germany
| | - Frank Engelke
- Bruker BioSpin GmbH, Am Silberstreifen, 76287 Rheinstetten, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse 7, D-60438 Frankfurt/Main, Germany.
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Sounier R, Bellot G, Chou JJ. Mapping Conformational Heterogeneity of Mitochondrial Nucleotide Transporter in Uninhibited States. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201408417] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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19
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Sounier R, Bellot G, Chou JJ. Mapping conformational heterogeneity of mitochondrial nucleotide transporter in uninhibited states. Angew Chem Int Ed Engl 2015; 54:2436-41. [PMID: 25605594 DOI: 10.1002/anie.201408417] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 11/09/2014] [Indexed: 12/18/2022]
Abstract
One of the less well understood aspects of membrane transporters is the dynamic coupling between conformational change and substrate transport. NMR approaches are used herein to investigate conformational heterogeneity of the GTP/GDP carrier (GGC) from yeast mitochondria. NMR residual dipolar coupling (RDC) analysis of GGC in a DNA-origami nanotube liquid crystal shows that several structured segments have different generalized degrees of order (GDO), thus indicating the presence of conformational heterogeneity. Complete GDO mapping reveals asymmetry between domains of the transporter and even within certain transmembrane helices. Nucleotide binding partially reduces local structural heterogeneity, and the substrate binds to multiple sites along the transport cavity. These observations suggest that mitochondrial carriers in the uninhibited states are intrinsically plastic and structural plasticity is asymmetrically distributed among the three homologous domains.
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Affiliation(s)
- Remy Sounier
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115 (USA); Present address: Institut de Génomique Fonctionnelle, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 5203, Institut National de la Santé et de la Recherche Médicale (INSERM) U1191, Université de Montpellier, F-34000 Montpellier (France)
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Neue Mitglieder der Deutschen Akademie der Naturforscher Leopoldina / Preis für den Dozenten des Jahres in den Naturwissenschaften: Stephan P. A. Sauer / Preis für den Wissenschaftler des Jahres an der Universität Frankfurt: H. Schwalbe / Lorenz-Oken-Meda. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201408895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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New Members of the Deutsche Akademie der Naturforscher Leopoldina / Teacher of the Year at SCIENCE Award: Stephan P. A. Sauer / Scientist of the Year Prize, University of Frankfurt: H. Schwalbe / Lorenz Oken Medal: H.-J. Quadbeck-Seeger / Normann Medal: U. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/anie.201408895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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22
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Harald Schwalbe. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201404174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Harald Schwalbe. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/anie.201404174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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