1
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Bower JB, Robson SA, Ziarek JJ. Insights on the G protein-coupled receptor helix 8 solution structure and orientation using a neurotensin receptor 1 peptide. Protein Sci 2024; 33:e4976. [PMID: 38757374 PMCID: PMC11099793 DOI: 10.1002/pro.4976] [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: 02/02/2024] [Revised: 03/12/2024] [Accepted: 03/14/2024] [Indexed: 05/18/2024]
Abstract
G-protein coupled receptors (GPCRs) are the largest class of membrane proteins encoded in the human genome with high pharmaceutical relevance and implications to human health. These receptors share a prevalent architecture of seven transmembrane helices followed by an intracellular, amphipathic helix 8 (H8) and a disordered C-terminal tail (Ctail). Technological advancements have led to over 1000 receptor structures in the last two decades, yet frequently H8 and the Ctail are conformationally heterogeneous or altogether absent. Here we synthesize a peptide comprising the neurotensin receptor 1 (NTS1) H8 and Ctail (H8-Ctail) to investigate its structural stability, conformational dynamics, and orientation in the presence of detergent and phospholipid micelles, which mimic the membrane. Circular dichroism (CD) and nuclear magnetic resonance (NMR) measurements confirm that zwitterionic 1,2-diheptanoyl-sn-glycero-3-phosphocholine is a potent stabilizer of H8 structure, whereas the commonly-used branched detergent lauryl maltose neopentyl glycol (LMNG) is unable to completely stabilize the helix - even at amounts four orders of magnitude greater than its critical micellar concentration. We then used NMR spectroscopy to assign the backbone chemical shifts. A series of temperature and lipid titrations were used to define the H8 boundaries as F376-R392 from chemical shift perturbations, changes in resonance intensity, and chemical-shift-derived phi/psi angles. Finally, the H8 azimuthal and tilt angles, defining the helix orientation relative of the membrane normal were measured using paramagnetic relaxation enhancement NMR. Taken together, our studies reveal the H8-Ctail region is sensitive to membrane physicochemical properties and is capable of more adaptive behavior than previously suggested by static structural techniques.
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Affiliation(s)
- James B. Bower
- Molecular and Cellular Biochemistry DepartmentIndiana UniversityBloomingtonIndianaUSA
| | - Scott A. Robson
- Department of PharmacologyNorthwestern University Feinberg School of MedicineChicagoIllinoisUSA
| | - Joshua J. Ziarek
- Molecular and Cellular Biochemistry DepartmentIndiana UniversityBloomingtonIndianaUSA
- Department of PharmacologyNorthwestern University Feinberg School of MedicineChicagoIllinoisUSA
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2
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Asadollahi K, Rajput S, de Zhang LA, Ang CS, Nie S, Williamson NA, Griffin MDW, Bathgate RAD, Scott DJ, Weikl TR, Jameson GNL, Gooley PR. Unravelling the mechanism of neurotensin recognition by neurotensin receptor 1. Nat Commun 2023; 14:8155. [PMID: 38071229 PMCID: PMC10710507 DOI: 10.1038/s41467-023-44010-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 11/26/2023] [Indexed: 12/18/2023] Open
Abstract
The conformational ensembles of G protein-coupled receptors (GPCRs) include inactive and active states. Spectroscopy techniques, including NMR, show that agonists, antagonists and other ligands shift the ensemble toward specific states depending on the pharmacological efficacy of the ligand. How receptors recognize ligands and the kinetic mechanism underlying this population shift is poorly understood. Here, we investigate the kinetic mechanism of neurotensin recognition by neurotensin receptor 1 (NTS1) using 19F-NMR, hydrogen-deuterium exchange mass spectrometry and stopped-flow fluorescence spectroscopy. Our results indicate slow-exchanging conformational heterogeneity on the extracellular surface of ligand-bound NTS1. Numerical analysis of the kinetic data of neurotensin binding to NTS1 shows that ligand recognition follows an induced-fit mechanism, in which conformational changes occur after neurotensin binding. This approach is applicable to other GPCRs to provide insight into the kinetic regulation of ligand recognition by GPCRs.
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Affiliation(s)
- Kazem Asadollahi
- Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC, 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia
- The Florey, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Sunnia Rajput
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Lazarus Andrew de Zhang
- The Florey, University of Melbourne, Parkville, VIC, 3010, Australia
- Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
| | - Ching-Seng Ang
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Shuai Nie
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Nicholas A Williamson
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Michael D W Griffin
- Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC, 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Ross A D Bathgate
- Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC, 3010, Australia
- The Florey, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Daniel J Scott
- Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC, 3010, Australia
- The Florey, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Thomas R Weikl
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14476, Potsdam, Germany
| | - Guy N L Jameson
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia
- School of Chemistry, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Paul R Gooley
- Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC, 3010, Australia.
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia.
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3
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Borgini M, Wieteska Ł, Hinck CS, Krzysiak T, Hinck AP, Wipf P. Synthesis of 13C-methyl-labeled amino acids and their incorporation into proteins in mammalian cells. Org Biomol Chem 2023; 21:9216-9229. [PMID: 37964666 PMCID: PMC10825848 DOI: 10.1039/d3ob01320k] [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: 08/17/2023] [Accepted: 11/06/2023] [Indexed: 11/16/2023]
Abstract
Isotopic labeling of methyl-substituted proteinogenic amino acids with 13C has transformed applications of solution-based NMR spectroscopy and allowed the study of much larger and more complex proteins than previously possible with 15N labeling. Procedures are well-established for producing methyl-labeled proteins expressed in bacteria, with efficient incorporation of 13C-methyl labeled metabolic precursors to enable the isotopic labeling of Ile, Val, and Leu methyl groups. Recently, similar methodology has been applied to enable 13C-methyl labeling of Ile, Val, and Leu in yeast, extending the approach to proteins that do not readily fold when produced in bacteria. Mammalian or insect cells are nonetheless preferable for production of many human proteins, yet 13C-methyl labeling using similar metabolic precursors is not feasible as these cells lack the requisite biosynthetic machinery. Herein, we report versatile and high-yielding synthetic routes to 13C methyl-labeled amino acids based on palladium-catalyzed C(sp3)-H functionalization. We demonstrate the efficient incorporation of two of the synthesized amino acids, 13C-γ2-Ile and 13C-γ1,γ2-Val, into human receptor extracellular domains with multiple disulfides using suspension-cultured HEK293 cells. Production costs are reasonable, even at moderate expression levels of 2-3 mg purified protein per liter of medium, and the method can be extended to label other methyl groups, such as 13C-δ1-Ile and 13C-δ1,δ2-Leu. In summary, we demonstrate the cost-effective production of methyl-labeled proteins in mammalian cells by incorporation of 13C methyl-labeled amino acids generated de novo by a versatile synthetic route.
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Affiliation(s)
- Matteo Borgini
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA.
| | - Łukasz Wieteska
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA.
| | - Cynthia S Hinck
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA.
| | - Troy Krzysiak
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA.
| | - Andrew P Hinck
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA.
| | - Peter Wipf
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA.
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4
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Asadollahi K, Rajput S, Jameson GNL, Scott DJ, Gooley PR. Encounter Complexes Between the N-terminal of Neurotensin with the Extracellular Loop 2 of the Neurotensin Receptor 1 Steer Neurotensin to the Orthosteric Binding Pocket. J Mol Biol 2023; 435:168244. [PMID: 37625583 DOI: 10.1016/j.jmb.2023.168244] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 08/08/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023]
Abstract
Neurotensin (NT) is a linear disordered peptide that activates two different class A GPCRs, neurotensin receptor 1 (NTS1) and NTS2. Resolved structures of the complex of the C-terminal fragment of NT, NT8-13, with NTS1 shows the peptide takes a well-defined structure in the bound state. However, the mechanisms underlying NT recognition of NTS1, and the conformational transition of NT upon binding NTS1 is an open question that if answered may aid discovery of highly selective drugs and reveal potential secondary binding sites on the surface of the receptor. Herein we investigated the interactions guiding NT to the orthosteric binding pocket of NTS1 by combining NMR experiments with kinetic analysis of the binding pathway using stopped-flow fluorescence and mutagenesis on both NT and NTS1. We show the presence of transient structures in the middle part of NT that kinetically regulate the binding of NT to NTS1. Moreover, our results indicate that the binding pathway of NT onto NTS1 is mediated via electrostatic interactions between the N-terminal region of NT with the extracellular loop 2 of NTS1. These interactions induce backbone conformational changes in neurotensin similar to the bound-state neurotensin, suggesting that the N-terminal region of NT and these interactions should be considered for development of selective drugs against NTS1.
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Affiliation(s)
- Kazem Asadollahi
- Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC 3010, Australia; Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia; The Florey, University of Melbourne, Parkville, VIC 3010, Australia. https://twitter.com/@KazemAsadollahi
| | - Sunnia Rajput
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia
| | - Guy N L Jameson
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia; School of Chemistry, University of Melbourne, Parkville, VIC 3010, Australia
| | - Daniel J Scott
- Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC 3010, Australia; The Florey, University of Melbourne, Parkville, VIC 3010, Australia
| | - Paul R Gooley
- Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC 3010, Australia; Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia.
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5
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Prosser RS, Alonzi NA. Discerning conformational dynamics and binding kinetics of GPCRs by 19F NMR. Curr Opin Pharmacol 2023; 72:102377. [PMID: 37612172 DOI: 10.1016/j.coph.2023.102377] [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: 01/25/2023] [Revised: 03/08/2023] [Accepted: 03/13/2023] [Indexed: 08/25/2023]
Abstract
19F NMR provides a way of monitoring conformational dynamics of G-protein coupled receptors (GPCRs) from the perspective of an ensemble. While X-ray crystallography provides exquisitely resolved high-resolution structures of specific states, it generally does not recapitulate the true ensemble of functional states. Fluorine (19F) NMR provides a highly sensitive spectroscopic window into the conformational ensemble, generally permitting the direct quantification of resolvable states. Moreover, straightforward T1- and T2-based relaxation experiments allow for the study of fluctuations within a given state and exchange between states, on timescales spanning nanoseconds to seconds. Conveniently, most biological systems are free of fluorine. Thus, via fluorinated amino acid analogues or thiol-reactive fluorinated tags, F or CF3 reporters can be site specifically incorporated into proteins of interest. In this review, fluorine labeling protocols and 19F NMR experiments will be presented, from the perspective of small molecule NMR (i.e. drug or small molecule interactions with receptors) or macromolecular NMR (i.e. conformational dynamics of receptors and receptor-G-protein complexes).
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Affiliation(s)
- R S Prosser
- Chemistry Department, University of Toronto, CPS UTM, Davis Building, Rm 4052, 3359 Mississauga Rd North, Mississauga, Ontario, L5L 1C6, Canada; Biochemistry Department, University of Toronto, CPS UTM, Davis Building, Rm 4052, 3359 Mississauga Rd North, Mississauga, Ontario, L5L 1C6, Canada.
| | - Nicholas A Alonzi
- Chemistry Department, University of Toronto, CPS UTM, Davis Building, Rm 4052, 3359 Mississauga Rd North, Mississauga, Ontario, L5L 1C6, Canada
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6
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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 PMCID: PMC11221349 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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7
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Bumbak F, Bower JB, Zemmer SC, Inoue A, Pons M, Paniagua JC, Yan F, Ford J, Wu H, Robson SA, Bathgate RAD, Scott DJ, Gooley PR, Ziarek JJ. Stabilization of pre-existing neurotensin receptor conformational states by β-arrestin-1 and the biased allosteric modulator ML314. Nat Commun 2023; 14:3328. [PMID: 37286565 PMCID: PMC10247727 DOI: 10.1038/s41467-023-38894-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 05/19/2023] [Indexed: 06/09/2023] Open
Abstract
The neurotensin receptor 1 (NTS1) is a G protein-coupled receptor (GPCR) with promise as a drug target for the treatment of pain, schizophrenia, obesity, addiction, and various cancers. A detailed picture of the NTS1 structural landscape has been established by X-ray crystallography and cryo-EM and yet, the molecular determinants for why a receptor couples to G protein versus arrestin transducers remain poorly defined. We used 13CεH3-methionine NMR spectroscopy to show that binding of phosphatidylinositol-4,5-bisphosphate (PIP2) to the receptor's intracellular surface allosterically tunes the timescale of motions at the orthosteric pocket and conserved activation motifs - without dramatically altering the structural ensemble. β-arrestin-1 further remodels the receptor ensemble by reducing conformational exchange kinetics for a subset of resonances, whereas G protein coupling has little to no effect on exchange rates. A β-arrestin biased allosteric modulator transforms the NTS1:G protein complex into a concatenation of substates, without triggering transducer dissociation, suggesting that it may function by stabilizing signaling incompetent G protein conformations such as the non-canonical state. Together, our work demonstrates the importance of kinetic information to a complete picture of the GPCR activation landscape.
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Affiliation(s)
- Fabian Bumbak
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, 47405, USA.
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins and Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia.
| | - James B Bower
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, 47405, USA
| | - Skylar C Zemmer
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, 47405, USA
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi, 980-8578, Japan
| | - Miquel Pons
- Biomolecular NMR laboratory, Department of Inorganic and Organic Chemistry, Universitat de Barcelona (UB), 08028, Barcelona, Spain
| | - Juan Carlos Paniagua
- Department of Materials Science and Physical Chemistry & Institute of Theoretical and Computational Chemistry (IQTCUB), Universitat de Barcelona (UB), 08028, Barcelona, Spain
| | - Fei Yan
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia
| | - James Ford
- Department of Chemistry, Indiana University, Bloomington, IN, 47405-7102, USA
| | - Hongwei Wu
- Department of Chemistry, Indiana University, Bloomington, IN, 47405-7102, USA
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Scott A Robson
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, 47405, USA
| | - Ross A D Bathgate
- The Florey Institute of Neuroscience and Mental Health and Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Daniel J Scott
- The Florey Institute of Neuroscience and Mental Health and Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Paul R Gooley
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Joshua J Ziarek
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, 47405, USA.
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8
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Ayikpoe R, Zhu L, Chen JY, Ting CP, van der Donk WA. Macrocyclization and Backbone Rearrangement During RiPP Biosynthesis by a SAM-Dependent Domain-of-Unknown-Function 692. ACS CENTRAL SCIENCE 2023; 9:1008-1018. [PMID: 37252350 PMCID: PMC10214503 DOI: 10.1021/acscentsci.3c00160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Indexed: 05/31/2023]
Abstract
The domain of unknown function 692 (DUF692) is an emerging family of post-translational modification enzymes involved in the biosynthesis of ribosomally synthesized and post-translationally modified peptide (RiPP) natural products. Members of this family are multinuclear iron-containing enzymes, and only two members have been functionally characterized to date: MbnB and TglH. Here, we used bioinformatics to select another member of the DUF692 family, ChrH, that is encoded in the genomes of the Chryseobacterium genus along with a partner protein ChrI. We structurally characterized the ChrH reaction product and show that the enzyme complex catalyzes an unprecedented chemical transformation that results in the formation of a macrocycle, an imidazolidinedione heterocycle, two thioaminals, and a thiomethyl group. Based on isotopic labeling studies, we propose a mechanism for the four-electron oxidation and methylation of the substrate peptide. This work identifies the first SAM-dependent reaction catalyzed by a DUF692 enzyme complex, further expanding the repertoire of remarkable reactions catalyzed by these enzymes. Based on the three currently characterized DUF692 family members, we suggest the family be called multinuclear non-heme iron dependent oxidative enzymes (MNIOs).
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Affiliation(s)
- Richard
S. Ayikpoe
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, Urbana, 61801, Illinois, United States
- Carl
R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, 61801, Illinois, United States
| | - Lingyang Zhu
- School
of Chemical Sciences NMR Laboratory, University
of Illinois at Urbana−Champaign, Urbana, 61801, Illinois, United States
| | - Jeff Y. Chen
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, Urbana, 61801, Illinois, United States
- Carl
R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, 61801, Illinois, United States
| | - Chi P. Ting
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, Urbana, 61801, Illinois, United States
- Carl
R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, 61801, Illinois, United States
| | - Wilfred A. van der Donk
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, Urbana, 61801, Illinois, United States
- Carl
R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, 61801, Illinois, United States
- Howard
Hughes Medical Institute at the University of Illinois at Urbana−Champaign, Urbana, 61801, Illinois, United States
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9
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Asadollahi K, Huang K, Yan F, de Zhang LA, Scott DJ, Gooley PR. High yield expression and purification of full-length Neurotensin with pyroglutamate modification. Protein Expr Purif 2023; 204:106227. [PMID: 36574939 DOI: 10.1016/j.pep.2022.106227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/17/2022] [Accepted: 12/21/2022] [Indexed: 12/25/2022]
Abstract
Neurotensin (NT) is a 13-residue endogenous peptide found in mammals, with neurotransmission and hormonal roles in the central nervous system and gastrointestinal tract, respectively. The first residue of NT is a pyroglutamate (pGlu) that makes the expression and purification of large amounts of NT with native modification challenging. Here, we describe a simple and efficient procedure for expression and purification of large amounts of NT based on using the small ubiquitin-like modifier (SUMO) as a fusion partner and subsequent enzymatic conversion of the N-terminal glutamine to pGlu. Yields of 13 mg/L and 8 mg/L of pure peptide were obtained from expression in rich and minimal media, respectively. The method is adaptable to expression and purification of proteins and peptides with pGlu modification in a wide range of eukaryotic and prokaryotic expression hosts.
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Affiliation(s)
- Kazem Asadollahi
- Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC, 3052, Australia; Bio21 Molecular Sciences and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3052, Australia; The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Katherine Huang
- Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC, 3052, Australia; Bio21 Molecular Sciences and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Fei Yan
- Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC, 3052, Australia; Bio21 Molecular Sciences and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Lazarus A de Zhang
- Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC, 3052, Australia; The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC, 3052, Australia; Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
| | - Daniel J Scott
- Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC, 3052, Australia; The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Paul R Gooley
- Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC, 3052, Australia; Bio21 Molecular Sciences and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3052, Australia.
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10
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Ayikpoe RS, Zhu L, Chen JY, Ting CP, van der Donk WA. A remarkable transformation catalyzed by a domain-of-unknown-function 692 during the biosynthesis of a new RiPP natural product. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.06.527370. [PMID: 36798408 PMCID: PMC9934569 DOI: 10.1101/2023.02.06.527370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
The domain of unknown function 692 (DUF692) is an emerging family of posttranslational modification enzymes involved in the biosynthesis of ribosomally-synthesized and posttranslationally modified peptide (RiPP) natural products. Members of this family are multinuclear iron-containing enzymes and only two members have been functionally characterized to date: MbnB and TglH. Here, we used bioinformatics to select another member of the DUF692 family, ChrH, that is ubiquitously encoded in the genomes of the Chryseobacterium genus along with a partner protein ChrI. We structurally characterized the ChrH reaction product and show that the enzyme catalyzes an unprecedented chemical transformation that results in the formation of a macrocycle, an imidazolidinedione heterocycle, two thioaminals, and a thiomethylation. Based on isotopic labeling studies, we propose a mechanism for the four-electron oxidation and methylation of the substrate peptide. This work identifies the first SAM-dependent DUF692 enzyme, further expanding the repertoire of remarkable reactions catalyzed by these enzymes.
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Affiliation(s)
- Richard S. Ayikpoe
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
| | - Lingyang Zhu
- School of Chemical Sciences NMR Laboratory, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
| | - Jeff Y. Chen
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
| | - Chi P. Ting
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
| | - Wilfred A. van der Donk
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
- Howard Hughes Medical Institute at the University of Illinois at Urbana-Champaign, Urbana, 61801, IL, USA
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11
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Ligands selectively tune the local and global motions of neurotensin receptor 1 (NTS 1). Cell Rep 2023; 42:112015. [PMID: 36680775 PMCID: PMC9930568 DOI: 10.1016/j.celrep.2023.112015] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/05/2022] [Accepted: 01/05/2023] [Indexed: 01/21/2023] Open
Abstract
Nuclear magnetic resonance (NMR) studies have revealed that fast methyl sidechain dynamics can report on entropically-driven allostery. Yet, NMR applications have been largely limited to the super-microsecond motional regimes of G protein-coupled receptors (GPCRs). We use 13Cε-methionine chemical shift-based global order parameters to test if ligands affect the fast dynamics of a thermostabilized GPCR, neurotensin receptor 1 (NTS1). We establish that the NTS1 solution ensemble includes substates with lifetimes on several, discrete timescales. The longest-lived states reflect those captured in agonist- and inverse agonist-bound crystal structures, separated by large energy barriers. We observe that the rapid fluctuations of individual methionine residues, superimposed on these long-lived states, respond collectively with the degree of fast, global dynamics correlating with ligand pharmacology. This approach lends confidence to interpreting spectra in terms of local structure and methyl dihedral angle geometry. The results suggest a role for sub-microsecond dynamics and conformational entropy in GPCR ligand discrimination.
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12
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Ye L, Wang X, McFarland A, Madsen JJ. 19F NMR: A promising tool for dynamic conformational studies of G protein-coupled receptors. Structure 2022; 30:1372-1384. [PMID: 36130592 DOI: 10.1016/j.str.2022.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 07/31/2022] [Accepted: 08/23/2022] [Indexed: 10/14/2022]
Abstract
Advances in X-ray crystallography and cryoelectron microscopy enabled unprecedented insights into the activation processes of G protein-coupled receptors (GPCRs). However, these static receptor structures provide limited information about dynamics and conformational transitions that play pivotal roles in mediating signaling diversity through the multifaceted interactions between ligands, receptors, and transducers. Developing NMR approaches to probe the dynamics of conformational transitions will push the frontier of receptor science toward a more comprehensive understanding of these signaling processes. Although much progress has been made during the last decades, it remains challenging to delineate receptor conformational states and interrogate the functions of the individual states at a quantitative level. Here we cover the progress of 19F NMR applications in GPCR conformational and dynamic studies during the past 20 years. Current challenges and limitations of 19F NMR for studying GPCR dynamics are also discussed, along with experimental strategies that will drive this field forward.
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Affiliation(s)
- Libin Ye
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL 33620, USA; H. Lee Moffitt Cancer Center & Research Institute, 12902 USF Magnolia Drive, Tampa, FL 33612, USA.
| | - Xudong Wang
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL 33620, USA
| | - Aidan McFarland
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL 33620, USA
| | - Jesper J Madsen
- Global and Planetary Health, College of Public Health, University of South Florida, Tampa, FL 33612, USA; Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
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13
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Dixon AD, Inoue A, Robson SA, Culhane KJ, Trinidad JC, Sivaramakrishnan S, Bumbak F, Ziarek JJ. Effect of Ligands and Transducers on the Neurotensin Receptor 1 Conformational Ensemble. J Am Chem Soc 2022; 144:10241-10250. [PMID: 35647863 PMCID: PMC9936889 DOI: 10.1021/jacs.2c00828] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Using a discrete, intracellular 19F nuclear magnetic resonance (NMR) probe on transmembrane helix 6 of the neurotensin receptor 1 (NTS1), we aim to understand how ligands and transducers modulate the receptor's structural ensemble in a solution. For apo NTS1, 19F NMR spectra reveal an ensemble of at least three conformational substates (one inactive and two active-like) in equilibrium that exchange on the millisecond to second timescale. Dynamic NMR experiments reveal that these substates follow a linear three-site exchange process that is both thermodynamically and kinetically remodeled by orthosteric ligands. As previously observed in other G protein-coupled receptors (GPCRs), the full agonist is insufficient to completely stabilize the active-like state. The inactive substate is abolished upon coupling to β-arrestin-1 (βArr1) or the C-terminal helix of Gαq, which comprises ≳60% of the GPCR/G protein interface surface area. Whereas βArr1 exclusively selects for pre-existing active-like substates, the Gαq peptide induces a new substate. Both transducer molecules promote substantial line broadening of active-like states, suggesting contributions from additional microsecond to millisecond exchange processes. Together, our study suggests that (i) the NTS1 allosteric activation mechanism may be alternatively dominated by induced fit or conformational selection depending on the coupled transducer, and (ii) the available static structures do not represent the entire conformational ensemble observed in a solution.
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Affiliation(s)
- Austin D. Dixon
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578 Miyagi, Japan
| | - Scott A. Robson
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Kelly J. Culhane
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55455, United States,Present Address: Department of Chemistry, Lawrence University, Appleton, Wisconsin, 54911, United States
| | - Jonathan C. Trinidad
- Laboratory for Biological Mass Spectrometry, Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Sivaraj Sivaramakrishnan
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Fabian Bumbak
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States,Present Address: Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Joshua J. Ziarek
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
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14
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G Protein-coupled Receptor (GPCR) Reconstitution and Labeling for Solution Nuclear Magnetic Resonance (NMR) Studies of the Structural Basis of Transmembrane Signaling. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27092658. [PMID: 35566006 PMCID: PMC9101874 DOI: 10.3390/molecules27092658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/14/2022] [Accepted: 04/14/2022] [Indexed: 11/17/2022]
Abstract
G protein-coupled receptors (GPCRs) are a large membrane protein family found in higher organisms, including the human body. GPCRs mediate cellular responses to diverse extracellular stimuli and thus control key physiological functions, which makes them important targets for drug design. Signaling by GPCRs is related to the structure and dynamics of these proteins, which are modulated by extrinsic ligands as well as by intracellular binding partners such as G proteins and arrestins. Here, we review some basics of using nuclear magnetic resonance (NMR) spectroscopy in solution for the characterization of GPCR conformations and intermolecular interactions that relate to transmembrane signaling.
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15
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Waltenspühl Y, Ehrenmann J, Klenk C, Plückthun A. Engineering of Challenging G Protein-Coupled Receptors for Structure Determination and Biophysical Studies. Molecules 2021; 26:molecules26051465. [PMID: 33800379 PMCID: PMC7962830 DOI: 10.3390/molecules26051465] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/27/2021] [Accepted: 03/01/2021] [Indexed: 01/14/2023] Open
Abstract
Membrane proteins such as G protein-coupled receptors (GPCRs) exert fundamental biological functions and are involved in a multitude of physiological responses, making these receptors ideal drug targets. Drug discovery programs targeting GPCRs have been greatly facilitated by the emergence of high-resolution structures and the resulting opportunities to identify new chemical entities through structure-based drug design. To enable the determination of high-resolution structures of GPCRs, most receptors have to be engineered to overcome intrinsic hurdles such as their poor stability and low expression levels. In recent years, multiple engineering approaches have been developed to specifically address the technical difficulties of working with GPCRs, which are now beginning to make more challenging receptors accessible to detailed studies. Importantly, successfully engineered GPCRs are not only valuable in X-ray crystallography, but further enable biophysical studies with nuclear magnetic resonance spectroscopy, surface plasmon resonance, native mass spectrometry, and fluorescence anisotropy measurements, all of which are important for the detailed mechanistic understanding, which is the prerequisite for successful drug design. Here, we summarize engineering strategies based on directed evolution to reduce workload and enable biophysical experiments of particularly challenging GPCRs.
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16
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Deluigi M, Klipp A, Klenk C, Merklinger L, Eberle SA, Morstein L, Heine P, Mittl PRE, Ernst P, Kamenecka TM, He Y, Vacca S, Egloff P, Honegger A, Plückthun A. Complexes of the neurotensin receptor 1 with small-molecule ligands reveal structural determinants of full, partial, and inverse agonism. SCIENCE ADVANCES 2021; 7:7/5/eabe5504. [PMID: 33571132 PMCID: PMC7840143 DOI: 10.1126/sciadv.abe5504] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 12/09/2020] [Indexed: 05/15/2023]
Abstract
Neurotensin receptor 1 (NTSR1) and related G protein-coupled receptors of the ghrelin family are clinically unexploited, and several mechanistic aspects of their activation and inactivation have remained unclear. Enabled by a new crystallization design, we present five new structures: apo-state NTSR1 as well as complexes with nonpeptide inverse agonists SR48692 and SR142948A, partial agonist RTI-3a, and the novel full agonist SRI-9829, providing structural rationales on how ligands modulate NTSR1. The inverse agonists favor a large extracellular opening of helices VI and VII, undescribed so far for NTSR1, causing a constriction of the intracellular portion. In contrast, the full and partial agonists induce a binding site contraction, and their efficacy correlates with the ability to mimic the binding mode of the endogenous agonist neurotensin. Providing evidence of helical and side-chain rearrangements modulating receptor activation, our structural and functional data expand the mechanistic understanding of NTSR1 and potentially other peptidergic receptors.
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Affiliation(s)
- Mattia Deluigi
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Alexander Klipp
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Christoph Klenk
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Lisa Merklinger
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Stefanie A Eberle
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Lena Morstein
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Philipp Heine
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Peer R E Mittl
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Patrick Ernst
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Theodore M Kamenecka
- Department of Molecular Medicine, The Scripps Research Institute, Scripps Florida, 130 Scripps Way #A2A, Jupiter, FL 33458, USA
| | - Yuanjun He
- Department of Molecular Medicine, The Scripps Research Institute, Scripps Florida, 130 Scripps Way #A2A, Jupiter, FL 33458, USA
| | - Santiago Vacca
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Pascal Egloff
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Annemarie Honegger
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
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17
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Jones AJY, Gabriel F, Tandale A, Nietlispach D. Structure and Dynamics of GPCRs in Lipid Membranes: Physical Principles and Experimental Approaches. Molecules 2020; 25:E4729. [PMID: 33076366 PMCID: PMC7587580 DOI: 10.3390/molecules25204729] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/11/2020] [Accepted: 10/12/2020] [Indexed: 02/06/2023] Open
Abstract
Over the past decade, the vast amount of information generated through structural and biophysical studies of GPCRs has provided unprecedented mechanistic insight into the complex signalling behaviour of these receptors. With this recent information surge, it has also become increasingly apparent that in order to reproduce the various effects that lipids and membranes exert on the biological function for these allosteric receptors, in vitro studies of GPCRs need to be conducted under conditions that adequately approximate the native lipid bilayer environment. In the first part of this review, we assess some of the more general effects that a membrane environment exerts on lipid bilayer-embedded proteins such as GPCRs. This is then followed by the consideration of more specific effects, including stoichiometric interactions with specific lipid subtypes. In the final section, we survey a range of different membrane mimetics that are currently used for in vitro studies, with a focus on NMR applications.
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Affiliation(s)
| | | | | | - Daniel Nietlispach
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK; (A.J.Y.J.); (F.G.); (A.T.)
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18
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Bumbak F, Thomas T, Noonan-Williams BJ, Vaid TM, Yan F, Whitehead AR, Bruell S, Kocan M, Tan X, Johnson MA, Bathgate RAD, Chalmers DK, Gooley PR, Scott DJ. Conformational Changes in Tyrosine 11 of Neurotensin Are Required to Activate the Neurotensin Receptor 1. ACS Pharmacol Transl Sci 2020; 3:690-705. [PMID: 32832871 PMCID: PMC7432660 DOI: 10.1021/acsptsci.0c00026] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Indexed: 12/12/2022]
Abstract
Cell-cell communication via endogenous peptides and their receptors is vital for controlling all aspects of human physiology and most peptides signal through G protein-coupled receptors (GPCRs). Disordered peptides bind GPCRs through complex modes for which there are few representative crystal structures. The disordered peptide neurotensin (NT) is a neuromodulator of classical neurotransmitters such as dopamine and glutamate, through activation of neurotensin receptor 1 (NTS1). While several experimental structures show how NT binds NTS1, details about the structural dynamics of NT during and after binding NTS1, or the role of peptide dynamics on receptor activation, remain obscure. Here saturation transfer difference (STD) NMR revealed that the binding mode of NT fragment NT10-13 is heterogeneous. Epitope maps of NT10-13 at NTS1 suggested that tyrosine 11 (Y11) samples other conformations to those observed in crystal structures of NT-bound NTS1. Molecular dynamics (MD) simulations confirmed that when NT is bound to NTS1, residue Y11 can exist in two χ1 rotameric states, gauche plus (g+) or gauche minus (g-). Since only the g+ Y11 state is observed in all the structures solved to date, we asked if the g- state is important for receptor activation. NT analogues with Y11 replaced with 7-OH-Tic were synthesized to restrain the dynamics of the side chain. P(OH-TIC)IL bound NTS1 with the same affinity as NT10-13 but did not activate NTS1, instead acted as an antagonist. This study highlights that flexibility of Y11 in NT may be required for NT activation of NTS1.
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Affiliation(s)
- Fabian Bumbak
- The
Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria 3010, Australia
- Department
of Biochemistry and Molecular Biology, The
University of Melbourne, Parkville, Victoria 3010, Australia
- Bio21
Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Trayder Thomas
- Monash
Institute of Pharmaceutical Sciences, Monash
University, Parkville, Victoria 3052, Australia
| | - Billy J. Noonan-Williams
- Monash
Institute of Pharmaceutical Sciences, Monash
University, Parkville, Victoria 3052, Australia
| | - Tasneem M. Vaid
- The
Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria 3010, Australia
- Department
of Biochemistry and Molecular Biology, The
University of Melbourne, Parkville, Victoria 3010, Australia
- Bio21
Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Fei Yan
- Department
of Biochemistry and Molecular Biology, The
University of Melbourne, Parkville, Victoria 3010, Australia
- Bio21
Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Alice R. Whitehead
- The
Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Shoni Bruell
- The
Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Martina Kocan
- The
Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria 3010, Australia
- The School
of BioSciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Xuan Tan
- Department
of Chemistry, The University of Alabama
at Birmingham, Birmingham, Alabama 35294-1240, United States
| | - Margaret A. Johnson
- Department
of Chemistry, The University of Alabama
at Birmingham, Birmingham, Alabama 35294-1240, United States
| | - Ross A. D. Bathgate
- The
Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria 3010, Australia
- Department
of Biochemistry and Molecular Biology, The
University of Melbourne, Parkville, Victoria 3010, Australia
| | - David K. Chalmers
- Monash
Institute of Pharmaceutical Sciences, Monash
University, Parkville, Victoria 3052, Australia
| | - Paul R. Gooley
- Department
of Biochemistry and Molecular Biology, The
University of Melbourne, Parkville, Victoria 3010, Australia
- Bio21
Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Daniel J. Scott
- The
Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria 3010, Australia
- Department
of Biochemistry and Molecular Biology, The
University of Melbourne, Parkville, Victoria 3010, Australia
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19
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Wu FJ, Williams LM, Abdul-Ridha A, Gunatilaka A, Vaid TM, Kocan M, Whitehead AR, Griffin MDW, Bathgate RAD, Scott DJ, Gooley PR. Probing the correlation between ligand efficacy and conformational diversity at the α 1A-adrenoreceptor reveals allosteric coupling of its microswitches. J Biol Chem 2020; 295:7404-7417. [PMID: 32303636 PMCID: PMC7247315 DOI: 10.1074/jbc.ra120.012842] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 04/14/2020] [Indexed: 12/11/2022] Open
Abstract
G protein-coupled receptors (GPCRs) use a series of conserved microswitches to transmit signals across the cell membrane via an allosteric network encompassing the ligand-binding site and the G protein-binding site. Crystal structures of GPCRs provide snapshots of their inactive and active states, but poorly describe the conformational dynamics of the allosteric network that underlies GPCR activation. Here, we analyzed the correlation between ligand binding and receptor conformation of the α1A-adrenoreceptor, a GPCR that stimulates smooth muscle contraction in response to binding noradrenaline. NMR of [13CϵH3]methionine-labeled α1A-adrenoreceptor variants, each exhibiting differing signaling capacities, revealed how different classes of ligands modulate the conformational equilibria of this receptor. [13CϵH3]Methionine residues near the microswitches exhibited distinct states that correlated with ligand efficacies, supporting a conformational selection mechanism. We propose that allosteric coupling among the microswitches controls the conformation of the α1A-adrenoreceptor and underlies the mechanism of ligand modulation of GPCR signaling in cells.
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Affiliation(s)
- Feng-Jie Wu
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville 3052, VIC, Australia; Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville 3052, VIC, Australia; The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville 3052, VIC, Australia
| | - Lisa M Williams
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville 3052, VIC, Australia
| | - Alaa Abdul-Ridha
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville 3052, VIC, Australia
| | - Avanka Gunatilaka
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville 3052, VIC, Australia
| | - Tasneem M Vaid
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville 3052, VIC, Australia; Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville 3052, VIC, Australia; The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville 3052, VIC, Australia
| | - Martina Kocan
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville 3052, VIC, Australia
| | - Alice R Whitehead
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville 3052, VIC, Australia
| | - Michael D W Griffin
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville 3052, VIC, Australia; Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville 3052, VIC, Australia
| | - Ross A D Bathgate
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville 3052, VIC, Australia; The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville 3052, VIC, Australia
| | - Daniel J Scott
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville 3052, VIC, Australia; The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville 3052, VIC, Australia.
| | - Paul R Gooley
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville 3052, VIC, Australia; Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville 3052, VIC, Australia.
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20
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Schuster M, Deluigi M, Pantić M, Vacca S, Baumann C, Scott DJ, Plückthun A, Zerbe O. Optimizing the α 1B-adrenergic receptor for solution NMR studies. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183354. [PMID: 32413443 DOI: 10.1016/j.bbamem.2020.183354] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 05/01/2020] [Accepted: 05/09/2020] [Indexed: 12/14/2022]
Abstract
Sample preparation for NMR studies of G protein-coupled receptors faces special requirements: Proteins need to be stable for prolonged measurements at elevated temperatures, they should ideally be uniformly labeled with the stable isotopes 13C, 15N, and all carbon-bound protons should be replaced by deuterons. In addition, certain NMR experiments require protonated methyl groups in the presence of a perdeuterated background. All these requirements are most easily satisfied when using Escherichia coli as the expression host. Here we describe a workflow, starting from a temperature-stabilized mutant of the α1B-adrenergic receptor, obtained using the CHESS methodology, into an even more stable species, in which flexible parts from termini were removed and the intracellular loop 3 (ICL3) was stabilized against proteolytic cleavage. The yield after purification corresponds to 1-2 mg/L of D2O culture. The final purification step is ligand-affinity chromatography to ensure that only well-folded ligand-binding protein is isolated. Proper selection of detergent has a remarkable influence on the quality of NMR spectra. All optimization steps of sequence and detergent are monitored on a small scale by monitoring the melting temperature and long-term thermal stability to allow for screening of many conditions. The stabilized mutant of the α1B-adrenergic receptor was additionally incorporated in nanodiscs, but displayed slightly inferior spectra compared to a sample in detergent micelles. Finally, both [15N,1H]- as well as [13C,1H]-HSQC spectra are shown highlighting the high quality of the final NMR sample. Importantly, the quality of [13C,1H]-HSQC spectra indicates that the so prepared receptor could be used for studying side-chain dynamics.
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Affiliation(s)
- Matthias Schuster
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Mattia Deluigi
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Milica Pantić
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Santiago Vacca
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Christian Baumann
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Daniel J Scott
- Florey Institute of Neuroscience and Mental Health, Department of Biochemistry and Molecular Biology, The University of Melbourne, 30 Royal Parade Parkville, 3052, Victoria, Australia
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Oliver Zerbe
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
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21
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Bostock MJ, Solt AS, Nietlispach D. The role of NMR spectroscopy in mapping the conformational landscape of GPCRs. Curr Opin Struct Biol 2019; 57:145-156. [PMID: 31075520 DOI: 10.1016/j.sbi.2019.03.030] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 03/19/2019] [Accepted: 03/27/2019] [Indexed: 11/26/2022]
Abstract
Over recent years, nuclear magnetic resonance (NMR) spectroscopy has developed into a powerful mechanistic tool for the investigation of G protein-coupled receptors (GPCRs). NMR provides insights which underpin the dynamic nature of these important receptors and reveals experimental evidence for a complex conformational energy landscape that is explored during receptor activation resulting in signalling. NMR studies have highlighted both the dynamic properties of different receptor states as well as the exchange pathways and intermediates formed during activation, extending the static view of GPCRs obtained from other techniques. NMR studies can be undertaken in realistic membrane-like phospholipid environments and an ever-increasing choice of labelling strategies provides comprehensive, receptor-wide information. Combined with other structural methods, NMR is contributing to our understanding of allosteric signal propagation and the interaction of GPCRs with intracellular binding partners (IBP), crucial to explaining cellular signalling.
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Affiliation(s)
- Mark J Bostock
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Andras S Solt
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Daniel Nietlispach
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK.
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22
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Williams LM, He X, Vaid TM, Abdul‐Ridha A, Whitehead AR, Gooley PR, Bathgate RA, Williams SJ, Scott DJ. Diazepam is not a direct allosteric modulator of α 1-adrenoceptors, but modulates receptor signaling by inhibiting phosphodiesterase-4. Pharmacol Res Perspect 2019; 7:e00455. [PMID: 30619611 PMCID: PMC6306559 DOI: 10.1002/prp2.455] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 11/30/2018] [Accepted: 12/04/2018] [Indexed: 12/19/2022] Open
Abstract
α1A- and α1B-adrenoceptors (ARs) are G protein-coupled receptors (GPCRs) that are activated by adrenaline and noradrenaline to modulate smooth muscle contraction in the periphery, and neuronal outputs in the central nervous system (CNS). α1A- and α1B-AR are clinically targeted with antagonists for hypertension and benign prostatic hyperplasia and are emerging CNS targets for treating neurodegenerative diseases. The benzodiazepines midazolam, diazepam, and lorazepam are proposed to be positive allosteric modulators (PAMs) of α1-ARs. Here, using thermostabilized, purified, α1A- and α1B-ARs, we sought to identify the benzodiazepine binding site and modulatory mechanism to inform the design of selective PAMs. However, using a combination of biophysical approaches no evidence was found for direct binding of several benzodiazepines to purified, stabilized α1A- and α1B-ARs. Similarly, in cell-based assays expressing unmodified α1A- and α1B-ARs, benzodiazepine treatment had no effect on fluorescent ligand binding, agonist-stimulated Ca2+ release, or G protein activation. In contrast, several benzodiazepines positively modulated phenylephrine stimulation of a cAMP response element pathway by α1A- and α1B-ARs; however, this was shown to be caused by off-target inhibition of phosphodiesterases, known targets of diazepam. This study highlights how purified, stabilized GPCRs are useful for validating allosteric ligand binding and that care needs to be taken before assigning new targets to benzodiazepines.
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Affiliation(s)
- Lisa M. Williams
- The Florey Institute of Neuroscience and Mental HealthUniversity of MelbourneParkvilleVicAustralia
| | - Xiaoji He
- The Florey Institute of Neuroscience and Mental HealthUniversity of MelbourneParkvilleVicAustralia
- School of Chemistry and Bio21 Molecular Science and Biotechnology InstituteUniversity of MelbourneParkvilleVicAustralia
| | - Tasneem M. Vaid
- The Florey Institute of Neuroscience and Mental HealthUniversity of MelbourneParkvilleVicAustralia
- Department of Biochemistry and Molecular BiologyUniversity of MelbourneParkvilleVicAustralia
- The Bio21 Molecular Science and Biotechnology InstituteUniversity of MelbourneParkvilleVicAustralia
| | - Alaa Abdul‐Ridha
- The Florey Institute of Neuroscience and Mental HealthUniversity of MelbourneParkvilleVicAustralia
| | - Alice R. Whitehead
- The Florey Institute of Neuroscience and Mental HealthUniversity of MelbourneParkvilleVicAustralia
| | - Paul R. Gooley
- Department of Biochemistry and Molecular BiologyUniversity of MelbourneParkvilleVicAustralia
- The Bio21 Molecular Science and Biotechnology InstituteUniversity of MelbourneParkvilleVicAustralia
| | - Ross A.D. Bathgate
- The Florey Institute of Neuroscience and Mental HealthUniversity of MelbourneParkvilleVicAustralia
- Department of Biochemistry and Molecular BiologyUniversity of MelbourneParkvilleVicAustralia
| | - Spencer J. Williams
- School of Chemistry and Bio21 Molecular Science and Biotechnology InstituteUniversity of MelbourneParkvilleVicAustralia
- The Bio21 Molecular Science and Biotechnology InstituteUniversity of MelbourneParkvilleVicAustralia
| | - Daniel J. Scott
- The Florey Institute of Neuroscience and Mental HealthUniversity of MelbourneParkvilleVicAustralia
- Department of Biochemistry and Molecular BiologyUniversity of MelbourneParkvilleVicAustralia
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23
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Bumbak F, Bathgate RAD, Scott DJ, Gooley PR. Expression and Purification of a Functional E. coli 13CH 3-Methionine-Labeled Thermostable Neurotensin Receptor 1 Variant for Solution NMR Studies. Methods Mol Biol 2019; 1947:31-55. [PMID: 30969410 DOI: 10.1007/978-1-4939-9121-1_3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Escherichia coli (E. coli) is the most widely used expression host for recombinant proteins due to high expression yields and straightforward molecular cloning. Directed evolution of G protein-coupled receptors (GPCRs) has made several of these difficult to express membrane proteins amenable to prokaryotic expression. Here, we describe a protocol for near complete 13CH3-methionine labeling of a thermostable neurotensin receptor 1 (enNTS1) variant in E. coli for solution NMR-based dynamics studies. Our expression strategy utilizes methionine biosynthesis pathway inhibition forcing E. coli to incorporate exogenous methionine with 96% efficiency at expression levels of 2.6 mg enNTS1 per liter of expression culture containing 50 mg of 13CH3-methionine. We also provide a 3-step purification protocol that produces final yields of 0.6 mg of functional Apo-state enNTS1.
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Affiliation(s)
- Fabian Bumbak
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, VIC, Australia.,Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia.,The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, Australia
| | - Ross A D Bathgate
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, VIC, Australia.,The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, Australia
| | - Daniel J Scott
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, VIC, Australia.,The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, Australia
| | - Paul R Gooley
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, VIC, Australia. .,Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia.
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24
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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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