1
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Kogut-Günthel MM, Zara Z, Nicoli A, Steuer A, Lopez-Balastegui M, Selent J, Karanth S, Koehler M, Ciancetta A, Abiko LA, Hagn F, Di Pizio A. The path to the G protein-coupled receptor structural landscape: Major milestones and future directions. Br J Pharmacol 2024. [PMID: 39209310 DOI: 10.1111/bph.17314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 06/14/2024] [Accepted: 06/28/2024] [Indexed: 09/04/2024] Open
Abstract
G protein-coupled receptors (GPCRs) play a crucial role in cell function by transducing signals from the extracellular environment to the inside of the cell. They mediate the effects of various stimuli, including hormones, neurotransmitters, ions, photons, food tastants and odorants, and are renowned drug targets. Advancements in structural biology techniques, including X-ray crystallography and cryo-electron microscopy (cryo-EM), have driven the elucidation of an increasing number of GPCR structures. These structures reveal novel features that shed light on receptor activation, dimerization and oligomerization, dichotomy between orthosteric and allosteric modulation, and the intricate interactions underlying signal transduction, providing insights into diverse ligand-binding modes and signalling pathways. However, a substantial portion of the GPCR repertoire and their activation states remain structurally unexplored. Future efforts should prioritize capturing the full structural diversity of GPCRs across multiple dimensions. To do so, the integration of structural biology with biophysical and computational techniques will be essential. We describe in this review the progress of nuclear magnetic resonance (NMR) to examine GPCR plasticity and conformational dynamics, of atomic force microscopy (AFM) to explore the spatial-temporal dynamics and kinetic aspects of GPCRs, and the recent breakthroughs in artificial intelligence for protein structure prediction to characterize the structures of the entire GPCRome. In summary, the journey through GPCR structural biology provided in this review illustrates how far we have come in decoding these essential proteins architecture and function. Looking ahead, integrating cutting-edge biophysics and computational tools offers a path to navigating the GPCR structural landscape, ultimately advancing GPCR-based applications.
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Affiliation(s)
| | - Zeenat Zara
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
- Faculty of Science, University of South Bohemia in Ceske Budejovice, České Budějovice, Czech Republic
| | - Alessandro Nicoli
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
- Professorship for Chemoinformatics and Protein Modelling, Department of Molecular Life Science, School of Life Science, Technical University of Munich, Freising, Germany
| | - Alexandra Steuer
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
- Professorship for Chemoinformatics and Protein Modelling, Department of Molecular Life Science, School of Life Science, Technical University of Munich, Freising, Germany
| | - Marta Lopez-Balastegui
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute & Pompeu Fabra University, Barcelona, Spain
| | - Jana Selent
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute & Pompeu Fabra University, Barcelona, Spain
| | - Sanjai Karanth
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
| | - Melanie Koehler
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
- TUM Junior Fellow at the Chair of Nutritional Systems Biology, Technical University of Munich, Freising, Germany
| | - Antonella Ciancetta
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Ferrara, Italy
| | - Layara Akemi Abiko
- Focal Area Structural Biology and Biophysics, Biozentrum, University of Basel, Basel, Switzerland
| | - Franz Hagn
- Structural Membrane Biochemistry, Bavarian NMR Center, Dept. Bioscience, School of Natural Sciences, Technical University of Munich, Munich, Germany
- Institute of Structural Biology (STB), Helmholtz Munich, Neuherberg, Germany
| | - Antonella Di Pizio
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
- Professorship for Chemoinformatics and Protein Modelling, Department of Molecular Life Science, School of Life Science, Technical University of Munich, Freising, Germany
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2
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van Aalst EJ, Yekefallah M, A M van Beekveld R, Breukink E, Weingarth M, Wylie BJ. Coordination of bilayer properties by an inward-rectifier K + channel is a cooperative process driven by protein-lipid interaction. J Struct Biol X 2024; 9:100101. [PMID: 38883399 PMCID: PMC11176924 DOI: 10.1016/j.yjsbx.2024.100101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 05/27/2024] [Indexed: 06/18/2024] Open
Abstract
Physical properties of biological membranes directly or indirectly govern biological processes. Yet, the interplay between membrane and integral membrane proteins is difficult to assess due to reciprocal effects between membrane proteins, individual lipids, and membrane architecture. Using solid-state NMR (SSNMR) we previously showed that KirBac1.1, a bacterial Inward-Rectifier K+ channel, nucleates bilayer ordering and microdomain formation through tethering anionic lipids. Conversely, these lipids cooperatively bind cationic residues to activate the channel and initiate K+ flux. The mechanistic details governing the relationship between cooperative lipid loading and bilayer ordering are, however, unknown. To investigate, we generated KirBac1.1 samples with different concentrations of 13C-lableded phosphatidyl glycerol (PG) lipids and acquired a full suite of SSNMR 1D temperature series experiments using the ordered all-trans (AT) and disordered trans-gauche (TG) acyl conformations as markers of bilayer dynamics. We observed increased AT ordered signal, decreased TG disordered signal, and increased bilayer melting temperature with increased PG concentration. Further, we identified cooperativity between ordering and direct binding of PG lipids, indicating KirBac1.1-driven bilayer ordering and microdomain formation is a classically cooperative Hill-type process driven by and predicated upon direct binding of PG lipids. Our results provide unique mechanistic insight into how proteins and lipids in tandem contribute to supramolecular bilayer heterogeneity in the lipid membrane.
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Affiliation(s)
- Evan J van Aalst
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
| | - Maryam Yekefallah
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
| | - Roy A M van Beekveld
- Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Eefjan Breukink
- Membrane Biochemistry and Biophysics, Department of Chemistry, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Markus Weingarth
- Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Benjamin J Wylie
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
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3
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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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4
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Shenol A, Lückmann M, Trauelsen M, Lambrughi M, Tiberti M, Papaleo E, Frimurer TM, Schwartz TW. Molecular dynamics-based identification of binding pathways and two distinct high-affinity sites for succinate in succinate receptor 1/GPR91. Mol Cell 2024; 84:955-966.e4. [PMID: 38325379 DOI: 10.1016/j.molcel.2024.01.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 11/30/2023] [Accepted: 01/16/2024] [Indexed: 02/09/2024]
Abstract
SUCNR1 is an auto- and paracrine sensor of the metabolic stress signal succinate. Using unsupervised molecular dynamics (MD) simulations (170.400 ns) and mutagenesis across human, mouse, and rat SUCNR1, we characterize how a five-arginine motif around the extracellular pole of TM-VI determines the initial capture of succinate in the extracellular vestibule (ECV) to either stay or move down to the orthosteric site. Metadynamics demonstrate low-energy succinate binding in both sites, with an energy barrier corresponding to an intermediate stage during which succinate, with an associated water cluster, unlocks the hydrogen-bond-stabilized conformationally constrained extracellular loop (ECL)-2b. Importantly, simultaneous binding of two succinate molecules through either a "sequential" or "bypassing" mode is a frequent endpoint. The mono-carboxylate NF-56-EJ40 antagonist enters SUCNR1 between TM-I and -II and does not unlock ECL-2b. It is proposed that occupancy of both high-affinity sites is required for selective activation of SUCNR1 by high local succinate concentrations.
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Affiliation(s)
- Aslihan Shenol
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Michael Lückmann
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mette Trauelsen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Matteo Lambrughi
- Cancer Structural Biology, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Matteo Tiberti
- Cancer Structural Biology, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Elena Papaleo
- Cancer Structural Biology, Danish Cancer Society Research Center, Copenhagen, Denmark; Cancer Systems Biology, Section for Bioinformatics, Department of Health and Technology, Technical University of Denmark, Lyngby, Denmark
| | - Thomas M Frimurer
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Thue W Schwartz
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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5
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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: 2] [Impact Index Per Article: 2.0] [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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6
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Lees JA, Dias JM, Rajamohan F, Fortin JP, O'Connor R, Kong JX, Hughes EAG, Fisher EL, Tuttle JB, Lovett G, Kormos BL, Unwalla RJ, Zhang L, Dechert Schmitt AM, Zhou D, Moran M, Stevens KA, Fennell KF, Varghese AE, Maxwell A, Cote EE, Zhang Y, Han S. An inverse agonist of orphan receptor GPR61 acts by a G protein-competitive allosteric mechanism. Nat Commun 2023; 14:5938. [PMID: 37741852 PMCID: PMC10517971 DOI: 10.1038/s41467-023-41646-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 09/11/2023] [Indexed: 09/25/2023] Open
Abstract
GPR61 is an orphan GPCR related to biogenic amine receptors. Its association with phenotypes relating to appetite makes it of interest as a druggable target to treat disorders of metabolism and body weight, such as obesity and cachexia. To date, the lack of structural information or a known biological ligand or tool compound has hindered comprehensive efforts to study GPR61 structure and function. Here, we report a structural characterization of GPR61, in both its active-like complex with heterotrimeric G protein and in its inactive state. Moreover, we report the discovery of a potent and selective small-molecule inverse agonist against GPR61 and structural elucidation of its allosteric binding site and mode of action. These findings offer mechanistic insights into an orphan GPCR while providing both a structural framework and tool compound to support further studies of GPR61 function and modulation.
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Affiliation(s)
- Joshua A Lees
- Discovery Sciences, Medicine Design, Pfizer Inc., Groton, CT, USA
| | - João M Dias
- Discovery Sciences, Medicine Design, Pfizer Inc., Groton, CT, USA
| | | | | | - Rebecca O'Connor
- Discovery Sciences, Medicine Design, Pfizer Inc., Groton, CT, USA
| | - Jimmy X Kong
- Internal Medicine Research Unit, Pfizer Inc., Cambridge, MA, USA
| | - Emily A G Hughes
- Internal Medicine Research Unit, Pfizer Inc., Cambridge, MA, USA
| | - Ethan L Fisher
- Internal Medicine, Medicine Design, Pfizer Inc., Groton, CT, USA
| | - Jamison B Tuttle
- Internal Medicine, Medicine Design, Pfizer Inc., Cambridge, MA, USA
| | - Gabrielle Lovett
- Internal Medicine, Medicine Design, Pfizer Inc., Cambridge, MA, USA
| | - Bethany L Kormos
- Internal Medicine, Medicine Design, Pfizer Inc., Cambridge, MA, USA
| | | | - Lei Zhang
- Internal Medicine, Medicine Design, Pfizer Inc., Cambridge, MA, USA
| | | | - Dahui Zhou
- Internal Medicine, Medicine Design, Pfizer Inc., Groton, CT, USA
| | - Michael Moran
- Internal Medicine, Medicine Design, Pfizer Inc., Groton, CT, USA
| | | | | | | | - Andrew Maxwell
- Discovery Sciences, Medicine Design, Pfizer Inc., Groton, CT, USA
| | - Emmaline E Cote
- Discovery Sciences, Medicine Design, Pfizer Inc., Groton, CT, USA
| | - Yuan Zhang
- Internal Medicine, Medicine Design, Pfizer Inc., Cambridge, MA, USA
| | - Seungil Han
- Discovery Sciences, Medicine Design, Pfizer Inc., Groton, CT, USA.
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7
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Wu A, Salom D, Hong JD, Tworak A, Watanabe K, Pardon E, Steyaert J, Kandori H, Katayama K, Kiser PD, Palczewski K. Structural basis for the allosteric modulation of rhodopsin by nanobody binding to its extracellular domain. Nat Commun 2023; 14:5209. [PMID: 37626045 PMCID: PMC10457330 DOI: 10.1038/s41467-023-40911-9] [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: 01/03/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
Rhodopsin is a prototypical G protein-coupled receptor (GPCR) critical for vertebrate vision. Research on GPCR signaling states has been facilitated using llama-derived nanobodies (Nbs), some of which bind to the intracellular surface to allosterically modulate the receptor. Extracellularly binding allosteric nanobodies have also been investigated, but the structural basis for their activity has not been resolved to date. Here, we report a library of Nbs that bind to the extracellular surface of rhodopsin and allosterically modulate the thermodynamics of its activation process. Crystal structures of Nb2 in complex with native rhodopsin reveal a mechanism of allosteric modulation involving extracellular loop 2 and native glycans. Nb2 binding suppresses Schiff base deprotonation and hydrolysis and prevents intracellular outward movement of helices five and six - a universal activation event for GPCRs. Nb2 also mitigates protein misfolding in a disease-associated mutant rhodopsin. Our data show the power of nanobodies to modulate the photoactivation of rhodopsin and potentially serve as therapeutic agents for disease-associated rhodopsin misfolding.
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Affiliation(s)
- Arum Wu
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, CA, 92697, USA
| | - David Salom
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, CA, 92697, USA
| | - John D Hong
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, CA, 92697, USA
- Department of Chemistry, University of California, Irvine, CA, 92697, USA
| | - Aleksander Tworak
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, CA, 92697, USA
| | - Kohei Watanabe
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, 466- 8555, Japan
- PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
| | - Els Pardon
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
- VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - Jan Steyaert
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
- VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, 466- 8555, Japan
- OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya, 466-8555, Japan
| | - Kota Katayama
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, 466- 8555, Japan.
- PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan.
- OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya, 466-8555, Japan.
| | - Philip D Kiser
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, CA, 92697, USA.
- Department of Physiology & Biophysics, University of California, Irvine, CA, USA.
- Department of Clinical Pharmacy Practice, University of California, Irvine, CA, USA.
- Research Service, VA Long Beach Healthcare System, Long Beach, CA, USA.
| | - Krzysztof Palczewski
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, CA, 92697, USA.
- Department of Chemistry, University of California, Irvine, CA, 92697, USA.
- Department of Physiology & Biophysics, University of California, Irvine, CA, USA.
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, 92697, USA.
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8
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van Aalst EJ, Jang J, Halligan TC, Wylie BJ. Strategies for acquisition of resonance assignment spectra of highly dynamic membrane proteins: a GPCR case study. JOURNAL OF BIOMOLECULAR NMR 2023; 77:191-202. [PMID: 37493866 PMCID: PMC10838152 DOI: 10.1007/s10858-023-00421-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 07/11/2023] [Indexed: 07/27/2023]
Abstract
In protein nuclear magnetic resonance (NMR), chemical shift assignment provides a wealth of information. However, acquisition of high-quality solid-state NMR spectra depends on protein-specific dynamics. For membrane proteins, bilayer heterogeneity further complicates this observation. Since the efficiency of cross-polarization transfer is strongly entwined with protein dynamics, optimal temperatures for spectral sensitivity and resolution will depend not only on inherent protein dynamics, but temperature-dependent phase properties of the bilayer environment. We acquired 1-, 2-, and 3D homo- and heteronuclear experiments of the chemokine receptor CCR3 in a 7:3 phosphatidylcholine:cholesterol lipid environment. 1D direct polarization, cross polarization (CP), and T2' experiments indicate sample temperatures below - 25 °C facilitate higher CP enhancement and longer-lived transverse relaxation times. T1rho experiments indicate intermediate timescales are minimized below a sample temperature of - 20 °C. 2D DCP NCA experiments indicated optimal CP efficiency and resolution at a sample temperature of - 30 °C, corroborated by linewidth analysis in 3D NCACX at - 30 °C compared to - 5 °C. This optimal temperature is concluded to be directly related the lipid phase transition, measured to be between - 20 and 15 °C based on rINEPT signal of all-trans and trans-gauche lipid acyl conformations. Our results have critical implications in acquisition of SSNMR membrane protein assignment spectra, as we hypothesize that different lipid compositions with different phase transition properties influence protein dynamics and therefore the optimal acquisition temperature.
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Affiliation(s)
- Evan J van Aalst
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79415, USA
| | - Jun Jang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79415, USA
| | - Ty C Halligan
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79415, USA
| | - Benjamin J Wylie
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79415, USA.
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9
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van Aalst EJ, McDonald CJ, Wylie BJ. Cholesterol Biases the Conformational Landscape of the Chemokine Receptor CCR3: A MAS SSNMR-Filtered Molecular Dynamics Study. J Chem Inf Model 2023; 63:3068-3085. [PMID: 37127541 PMCID: PMC10208230 DOI: 10.1021/acs.jcim.2c01546] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Indexed: 05/03/2023]
Abstract
Cholesterol directs the pathway of ligand-induced G protein-coupled receptor (GPCR) signal transduction. The GPCR C-C motif chemokine receptor 3 (CCR3) is the principal chemotactic receptor for eosinophils, with roles in cancer metastasis and autoinflammatory conditions. Recently, we discovered a direct correlation between bilayer cholesterol and increased agonist-triggered CCR3 signal transduction. However, the allosteric molecular mechanism escalating ligand affinity and G protein coupling is unknown. To study cholesterol-guided CCR3 conformational selection, we implement comparative, objective measurement of protein architectures by scoring shifts (COMPASS) to grade model structures from molecular dynamics simulations. In this workflow, we scored predicted chemical shifts against 2-dimensional solid-state NMR 13C-13C correlation spectra of U-15N,13C-CCR3 samples prepared with and without cholesterol. Our analysis of trajectory model structures uncovers that cholesterol induces site-specific conformational restraint of extracellular loop (ECL) 2 and conserved motion in transmembrane helices and ECL3 not observed in simulations of bilayers with only phosphatidylcholine lipids. PyLipID analysis implicates direct cholesterol agency in CCR3 conformational selection and dynamics. Residue-residue contact scoring shows that cholesterol biases the conformational selection of the orthosteric pocket involving Y411.39, Y1133.32, and E2877.39. Lastly, we observe contact remodeling in activation pathway residues centered on the initial transmission switch, Na+ pocket, and R3.50 in the DRY motif. Our observations have unique implications for understanding of CCR3 ligand recognition and specificity and provide mechanistic insight into how cholesterol functions as an allosteric regulator of CCR3 signal transduction.
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Affiliation(s)
- Evan J. van Aalst
- Department of Chemistry and
Biochemistry, Texas Tech University, Lubbock, Texas 79415, United States
| | - Corey J. McDonald
- Department of Chemistry and
Biochemistry, Texas Tech University, Lubbock, Texas 79415, United States
| | - Benjamin J. Wylie
- Department of Chemistry and
Biochemistry, Texas Tech University, Lubbock, Texas 79415, United States
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10
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Abstract
Rhodopsin is the photoreceptor in human rod cells responsible for dim-light vision. The visual receptors are part of the large superfamily of G protein-coupled receptors (GPCRs) that mediate signal transduction in response to diverse diffusible ligands. The high level of sequence conservation within the transmembrane helices of the visual receptors and the family A GPCRs has long been considered evidence for a common pathway for signal transduction. I review recent studies that reveal a comprehensive mechanism for how light absorption by the retinylidene chromophore drives rhodopsin activation and highlight those features of the mechanism that are conserved across the ligand-activated GPCRs.
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Affiliation(s)
- Steven O Smith
- Department of Biochemistry and Cell Biology, Center for Structural Biology, Stony Brook University, Stony Brook, New York, USA;
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11
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Interdisciplinary biophysical studies of membrane proteins bacteriorhodopsin and rhodopsin. Biophys Rev 2023; 15:111-125. [PMID: 36909961 PMCID: PMC9995646 DOI: 10.1007/s12551-022-01003-y] [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: 05/12/2022] [Accepted: 09/28/2022] [Indexed: 10/10/2022] Open
Abstract
The centenary of the birth of H. Gobind Khorana provides an auspicious opportunity to review the origins and evolution of parallel advances in biophysical methodology and molecular genetics technology used to study membrane proteins. Interdisciplinary work in the Khorana laboratory in the late 1970s and for the next three decades led to productive collaborations and fostered three subsequent scientific generations whose biophysical work on membrane proteins has led to detailed elucidation of the molecular mechanisms of energy transduction by the light-driven proton pump bacteriorhodopsin (bR) and signal transduction by the G protein-coupled receptor (GPCR) rhodopsin. This review will highlight the origins and advances of biophysical studies of membrane proteins made possible by the application of molecular genetics approaches to engineer site-specific alterations of membrane protein structures.
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12
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Chandler B, Todd L, Smith SO. Magic angle spinning NMR of G protein-coupled receptors. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2022; 128:25-43. [PMID: 35282868 PMCID: PMC10718405 DOI: 10.1016/j.pnmrs.2021.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 06/14/2023]
Abstract
G protein-coupled receptors (GPCRs) have a simple seven transmembrane helix architecture which has evolved to recognize a diverse number of chemical signals. The more than 800 GPCRs encoded in the human genome function as receptors for vision, smell and taste, and mediate key physiological processes. Consequently, these receptors are a major target for pharmaceuticals. Protein crystallography and electron cryo-microscopy have provided high resolution structures of many GPCRs in both active and inactive conformations. However, these structures have not sparked a surge in rational drug design, in part because GPCRs are inherently dynamic and the structural changes induced by ligand or drug binding to stabilize inactive or active conformations are often subtle rearrangements in packing or hydrogen-bonding interactions. NMR spectroscopy provides a sensitive probe of local structure and dynamics at specific sites within these receptors as well as global changes in receptor structure and dynamics. These methods can also capture intermediate states and conformations with low populations that provide insights into the activation pathways. We review the use of solid-state magic angle spinning NMR to address the structure and activation mechanisms of GPCRs. The focus is on the large and diverse class A family of receptors. We highlight three specific class A GPCRs in order to illustrate how solid-state, as well as solution-state, NMR spectroscopy can answer questions in the field involving how different GPCR classes and subfamilies are activated by their associated ligands, and how small molecule drugs can modulate GPCR activation.
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Affiliation(s)
- Bianca Chandler
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, United States.
| | - Lauren Todd
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, United States.
| | - Steven O Smith
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, United States.
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13
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Ippolito M, De Pascali F, Inoue A, Benovic JL. Phenylalanine 193 in Extracellular Loop 2 of the β 2-Adrenergic Receptor Coordinates β-Arrestin Interaction. Mol Pharmacol 2022; 101:87-94. [PMID: 34853152 PMCID: PMC8969133 DOI: 10.1124/molpharm.121.000332] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 11/21/2021] [Indexed: 02/03/2023] Open
Abstract
G protein-coupled receptors (GPCRs) transduce a diverse variety of extracellular stimuli into intracellular signaling. These receptors are the most clinically productive drug targets at present. Despite decades of research on the signaling consequences of molecule-receptor interactions, conformational components of receptor-effector interactions remain incompletely described. The β 2-adrenergic receptor (β 2AR) is a prototypical and extensively studied GPCR that can provide insight into this aspect of GPCR signaling thanks to robust structural data and rich pharmacopeia. Using bioluminescence resonance energy transfer -based biosensors, second messenger assays, and biochemical techniques, we characterize the properties of β 2AR-F193A. This single point mutation in extracellular loop 2 of the β 2AR is sufficient to intrinsically bias the β 2AR away from β-arrestin interaction and demonstrates altered regulatory outcomes downstream of this functional selectivity. This study highlights the importance of extracellular control of intracellular response to stimuli and suggests a previously undescribed role for the extracellular loops of the receptor and the extracellular pocket formed by transmembrane domains 2, 3, and 7 in GPCR regulation that may contribute to biased signaling at GPCRs. SIGNIFICANCE STATEMENT: The role of extracellular G protein-coupled receptor (GPCR) domains in mediating intracellular interactions is poorly understood. We characterized the effects of extracellular loop mutations on agonist-promoted interactions of GPCRs with G protein and β-arrestin. Our studies reveal that F193 in extracellular loop 2 in the β2-adrenergic receptor mediates interactions with G protein and β-arrestin with a biased loss of β-arrestin binding. These results provide new insights on the role of the extracellular domain in differentially modulating intracellular interactions with GPCRs.
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Affiliation(s)
- Michael Ippolito
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, (M.I., F.D.P., J.L.B.); and Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan (A.I.)
| | - Francesco De Pascali
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, (M.I., F.D.P., J.L.B.); and Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan (A.I.)
| | - Asuka Inoue
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, (M.I., F.D.P., J.L.B.); and Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan (A.I.)
| | - Jeffrey L Benovic
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, (M.I., F.D.P., J.L.B.); and Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan (A.I.)
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14
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Ji S, Yang W, Yu W. Understanding the role of the CB1 toggle switch in interaction networks using molecular dynamics simulation. Sci Rep 2021; 11:22369. [PMID: 34785728 PMCID: PMC8595625 DOI: 10.1038/s41598-021-01767-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 10/26/2021] [Indexed: 11/09/2022] Open
Abstract
The cannabinoid receptor 1 (CB1) is a class A G-protein coupled receptor (GPCR) that can exert various effects on the human body through the endocannabinoid system. Understanding CB1 activation has many benefits for the medical use of cannabinoids. A previous study reported that CB1 has two notable residues referred to as the toggle switch, F3.36 and W6.48, which are important for its activation mechanism. We performed a molecular dynamics simulation with a mutation in the toggle switch to examine its role in active and inactive states. We also examined structural changes, the residue-residue interaction network, and the interaction network among helices and loops of wildtype and mutant CB1 for both activation states. As a result, we found that the energetic changes in the hydrogen-bond network of the Na+ pocket, extracellular N-terminus-TM2-ECL1-TM3 interface including D2.63-K3.28 salt-bridge, and extracellular ECL2-TM5-ECL3-TM6 interface directly linked to the toggle switch contribute to the stability of CB1 by the broken aromatic interaction of the toggle switch. It makes the conformation of inactive CB1 receptor to be unstable. Our study explained the role of the toggle switch regarding the energetic interactions related to the Na+ pocket and extracellular loop interfaces, which could contribute to a better understanding of the activation mechanism of CB1.
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Affiliation(s)
- Sangho Ji
- Department of Brain and Cognitive Sciences, DGIST, 333 Techno jungang-daero, Daegu, 42988, Republic of Korea
| | - Wonjin Yang
- Department of Brain and Cognitive Sciences, DGIST, 333 Techno jungang-daero, Daegu, 42988, Republic of Korea
| | - Wookyung Yu
- Department of Brain and Cognitive Sciences, DGIST, 333 Techno jungang-daero, Daegu, 42988, Republic of Korea. .,Core Protein Resources Center, DGIST, 333 Techno jungang-daero, 42988, Daegu, Republic of Korea.
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15
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Hegron A, Huh E, Deupi X, Sokrat B, Gao W, Le Gouill C, Canouil M, Boissel M, Charpentier G, Roussel R, Balkau B, Froguel P, Plouffe B, Bonnefond A, Lichtarge O, Jockers R, Bouvier M. Identification of Key Regions Mediating Human Melatonin Type 1 Receptor Functional Selectivity Revealed by Natural Variants. ACS Pharmacol Transl Sci 2021; 4:1614-1627. [PMID: 34661078 PMCID: PMC8507577 DOI: 10.1021/acsptsci.1c00157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Indexed: 11/30/2022]
Abstract
Melatonin is a hormone mainly produced by the pineal gland and MT1 is one of the two G protein-coupled receptors (GPCRs) mediating its action. Despite an increasing number of available GPCR crystal structures, the molecular mechanism of activation of a large number of receptors, including MT1, remains poorly understood. The purpose of this study is to elucidate the structural elements involved in the process of MT1's activation using naturally occurring variants affecting its function. Thirty-six nonsynonymous variants, including 34 rare ones, were identified in MTNR1A (encoding MT1) from a cohort of 8687 individuals and their signaling profiles were characterized using Bioluminescence Resonance Energy Transfer-based sensors probing 11 different signaling pathways. Computational analysis of the experimental data allowed us to group the variants in clusters according to their signaling profiles and to analyze the position of each variant in the context of the three-dimensional structure of MT1 to link functional selectivity to structure. MT1 variant signaling profiles revealed three clusters characterized by (1) wild-type-like variants, (2) variants with selective defect of βarrestin-2 recruitment, and (3) severely defective variants on all pathways. Our structural analysis allows us to identify important regions for βarrestin-2 recruitment as well as for Gα12 and Gα15 activation. In addition to identifying MT1 domains differentially controlling the activation of the various signaling effectors, this study illustrates how natural variants can be used as tools to study the molecular mechanisms of receptor activation.
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Affiliation(s)
- Alan Hegron
- Université
de Paris, Institut Cochin, CNRS, INSERM, F-75014 Paris, France
- Department
of Biochemistry and Molecular Medicine, University de Montréal, Montreal, Quebec, H3T 1J4 Canada
- Institute
for Research in Immunology and Cancer, University
of Montreal, Montreal, Quebec, H3T 1J4 Canada
| | - Eunna Huh
- Department
of Pharmacology and Chemical Biology, Baylor
College of Medicine, Houston, Texas 77030, United States of America
| | - Xavier Deupi
- Laboratory
of Biomolecular Research, Paul Scherrer
Institute (PSI), 5232 Villigen, Switzerland
- Condensed
Matter Theory group, Paul Scherrer Institute
(PSI), 5232 Villigen, Switzerland
| | - Badr Sokrat
- Department
of Biochemistry and Molecular Medicine, University de Montréal, Montreal, Quebec, H3T 1J4 Canada
- Institute
for Research in Immunology and Cancer, University
of Montreal, Montreal, Quebec, H3T 1J4 Canada
| | - Wenwen Gao
- Université
de Paris, Institut Cochin, CNRS, INSERM, F-75014 Paris, France
| | - Christian Le Gouill
- Institute
for Research in Immunology and Cancer, University
of Montreal, Montreal, Quebec, H3T 1J4 Canada
| | - Mickaël Canouil
- Inserm
UMR1283, CNRS UMR8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, Lille, 59000, France
- University
of Lille, Lille University
Hospital, Lille, 59000, France
| | - Mathilde Boissel
- Inserm
UMR1283, CNRS UMR8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, Lille, 59000, France
- University
of Lille, Lille University
Hospital, Lille, 59000, France
| | - Guillaume Charpentier
- Centre d’Étude et de Recherche pour l’Intensification
du Traitement du Diabète, 91000, Evry, France
| | - Ronan Roussel
- Department
of Diabetology Endocrinology Nutrition, Hôpital Bichat, DHU FIRE, Assistance Publique Hôpitaux
de Paris, 75004 Paris, France
- Inserm U1138, Centre de Recherche des Cordeliers, 75006 Paris, France
- UFR de Médecine, University Paris
Diderot, Sorbonne Paris Cité, 75006 Paris, France
| | - Beverley Balkau
- Inserm U1018, Center for Research in Epidemiology and Population
Health, 94805 Villejuif, France
- University
Paris-Saclay, University Paris-Sud, 94270 Villejuif, France
| | - Philippe Froguel
- Inserm
UMR1283, CNRS UMR8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, Lille, 59000, France
- University
of Lille, Lille University
Hospital, Lille, 59000, France
- Department
of Metabolism, Imperial College London, London, W12 0NN, United Kingdom
| | - Bianca Plouffe
- Department
of Biochemistry and Molecular Medicine, University de Montréal, Montreal, Quebec, H3T 1J4 Canada
- Institute
for Research in Immunology and Cancer, University
of Montreal, Montreal, Quebec, H3T 1J4 Canada
| | - Amélie Bonnefond
- Inserm
UMR1283, CNRS UMR8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, Lille, 59000, France
- University
of Lille, Lille University
Hospital, Lille, 59000, France
- Department
of Metabolism, Imperial College London, London, W12 0NN, United Kingdom
| | - Olivier Lichtarge
- Department
of Pharmacology and Chemical Biology, Baylor
College of Medicine, Houston, Texas 77030, United States of America
- Department
of Molecular and Human Genetics, Baylor
College of Medicine, Houston, Texas 77030, United States
| | - Ralf Jockers
- Université
de Paris, Institut Cochin, CNRS, INSERM, F-75014 Paris, France
| | - Michel Bouvier
- Department
of Biochemistry and Molecular Medicine, University de Montréal, Montreal, Quebec, H3T 1J4 Canada
- Institute
for Research in Immunology and Cancer, University
of Montreal, Montreal, Quebec, H3T 1J4 Canada
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16
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Pitch SG, Yao W, Szundi I, Fay J, Chen E, Shumate A, Kliger DS, Farrens DL. Functional integrity of membrane protein rhodopsin solubilized by styrene-maleic acid copolymer. Biophys J 2021; 120:3508-3515. [PMID: 34022241 DOI: 10.1016/j.bpj.2021.05.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 04/18/2021] [Accepted: 05/13/2021] [Indexed: 11/25/2022] Open
Abstract
Membrane proteins often require solubilization to study their structure or define the mechanisms underlying their function. In this study, the functional properties of the membrane protein rhodopsin in its native lipid environment were investigated after being solubilized with styrene-maleic acid (SMA) copolymer. The static absorption spectra of rhodopsin before and after the addition of SMA were recorded at room temperature to quantify the amount of membrane protein solubilized. The samples were then photobleached to analyze the functionality of rhodopsin upon solubilization. Samples with low or high SMA/rhodopsin ratios were compared to find a threshold in which the maximal amount of active rhodopsin was solubilized from membrane suspensions. Interestingly, whereas the highest SMA/rhodopsin ratios yielded the most solubilized rhodopsin, the rhodopsin produced under these conditions could not reach the active (Meta II) state upon photoactivation. The results confirm that SMA is a useful tool for membrane protein research, but SMA added in excess can interfere with the dynamics of protein activation.
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Affiliation(s)
- Stephanie G Pitch
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, California
| | - Weekie Yao
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, Oregon
| | - Istvan Szundi
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, California
| | - Jonathan Fay
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, Oregon
| | - Eefei Chen
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, California
| | - Anthony Shumate
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, Oregon
| | - David S Kliger
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, California
| | - David L Farrens
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, Oregon.
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17
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Pacull EM, Sendker F, Bernhard F, Scheidt HA, Schmidt P, Huster D, Krug U. Integration of Cell-Free Expression and Solid-State NMR to Investigate the Dynamic Properties of Different Sites of the Growth Hormone Secretagogue Receptor. Front Pharmacol 2020; 11:562113. [PMID: 33324203 PMCID: PMC7723455 DOI: 10.3389/fphar.2020.562113] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 09/21/2020] [Indexed: 01/09/2023] Open
Abstract
Cell-free expression represents an attractive method to produce large quantities of selectively labeled protein for NMR applications. Here, cell-free expression was used to label specific regions of the growth hormone secretagogue receptor (GHSR) with NMR-active isotopes. The GHSR is a member of the class A family of G protein-coupled receptors. A cell-free expression system was established to produce the GHSR in the precipitated form. The solubilized receptor was refolded in vitro and reconstituted into DMPC lipid membranes. Methionines, arginines, and histidines were chosen for 13C-labeling as they are representative for the transmembrane domains, the loops and flanking regions of the transmembrane α-helices, and the C-terminus of the receptor, respectively. The dynamics of the isotopically labeled residues was characterized by solid-state NMR measuring motionally averaged 1H-13C dipolar couplings, which were converted into molecular order parameters. Separated local field DIPSHIFT experiments under magic-angle spinning conditions using either varying cross polarization contact times or direct excitation provided order parameters for these residues showing that the C-terminus was the segment with the highest motional amplitude. The loop regions and helix ends as well as the transmembrane regions of the GHSR represent relatively rigid segments in the overall very flexible receptor molecule. Although no site resolution could be achieved in the experiments, the previously reported highly dynamic character of the receptor concluded from uniformly 13C labeled receptor samples could be further specified by this segmental labeling approach, leading to a more diversified understanding of the receptor dynamics under equilibrium conditions.
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Affiliation(s)
- Emelyne M Pacull
- Institute for Medical Physics and Biophysics, University of Leipzig, Leipzig, Germany
| | - Franziska Sendker
- Institute for Medical Physics and Biophysics, University of Leipzig, Leipzig, Germany
| | - Frank Bernhard
- Institute of Biophysical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany.,Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Holger A Scheidt
- Institute for Medical Physics and Biophysics, University of Leipzig, Leipzig, Germany
| | - Peter Schmidt
- Institute for Medical Physics and Biophysics, University of Leipzig, Leipzig, Germany
| | - Daniel Huster
- Institute for Medical Physics and Biophysics, University of Leipzig, Leipzig, Germany
| | - Ulrike Krug
- Institute for Medical Physics and Biophysics, University of Leipzig, Leipzig, Germany
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18
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Riedmayr LM, Böhm S, Biel M, Becirovic E. Enigmatic rhodopsin mutation creates an exceptionally strong splice acceptor site. Hum Mol Genet 2020; 29:295-304. [PMID: 31816042 DOI: 10.1093/hmg/ddz291] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 11/28/2019] [Accepted: 12/02/2019] [Indexed: 01/16/2023] Open
Abstract
The c.620 T > G mutation in rhodopsin found in the first mapped autosomal dominant retinitis pigmentosa (adRP) locus is associated with severe, early-onset RP. Intriguingly, another mutation affecting the same nucleotide (c.620 T > A) is related to a mild, late-onset RP. Assuming that both mutations are missense mutations (Met207Arg and Met207Lys) hampering the ligand-binding pocket, previous work addressed how they might differentially impair rhodopsin function. Here, we investigated the impact of both mutations at the mRNA and protein level in HEK293 cells and in the mouse retina. We show that, in contrast to c.620 T > A, c.620 T > G is a splicing mutation, which generates an exceptionally strong splice acceptor site (SAS) resulting in a 90 bp in-frame deletion and protein mislocalization in vitro and in vivo. Moreover, we identified the core element underlying the c.620 T > G SAS strength. Finally, we demonstrate that the c.620 T > G SAS is very flexible in branch point choice, which might explain its remarkable performance. Based on these results, we suggest that (i) point mutations should be routinely tested for mRNA splicing to avoid dispensable analysis of mutations on protein level, which do not naturally exist. (ii) Puzzling disease courses of mutations in other genes might also correlate with their effects on mRNA splicing. (iii) Flexibility in branch point choice might be another factor influencing the SAS strength. (iv) The core splice element identified in this study could be useful for biotechnological applications requiring effective SAS.
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Affiliation(s)
- Lisa M Riedmayr
- Center for Integrated Protein Science Munich (CIPSM), 81377 Munich, Germany.,Department of Pharmacy-Center for Drug Research, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Sybille Böhm
- Center for Integrated Protein Science Munich (CIPSM), 81377 Munich, Germany.,Department of Pharmacy-Center for Drug Research, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Martin Biel
- Center for Integrated Protein Science Munich (CIPSM), 81377 Munich, Germany.,Department of Pharmacy-Center for Drug Research, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Elvir Becirovic
- Center for Integrated Protein Science Munich (CIPSM), 81377 Munich, Germany.,Department of Pharmacy-Center for Drug Research, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
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19
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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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20
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Structural Complexity and Plasticity of Signaling Regulation at the Melanocortin-4 Receptor. Int J Mol Sci 2020; 21:ijms21165728. [PMID: 32785054 PMCID: PMC7460885 DOI: 10.3390/ijms21165728] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 08/03/2020] [Accepted: 08/06/2020] [Indexed: 02/06/2023] Open
Abstract
The melanocortin-4 receptor (MC4R) is a class A G protein-coupled receptor (GPCR), essential for regulation of appetite and metabolism. Pathogenic inactivating MC4R mutations are the most frequent cause of monogenic obesity, a growing medical and socioeconomic problem worldwide. The MC4R mediates either ligand-independent or ligand-dependent signaling. Agonists such as α-melanocyte-stimulating hormone (α-MSH) induce anorexigenic effects, in contrast to the endogenous inverse agonist agouti-related peptide (AgRP), which causes orexigenic effects by suppressing high basal signaling activity. Agonist action triggers the binding of different subtypes of G proteins and arrestins, leading to concomitant induction of diverse intracellular signaling cascades. An increasing number of experimental studies have unraveled molecular properties and mechanisms of MC4R signal transduction related to physiological and pathophysiological aspects. In addition, the MC4R crystal structure was recently determined at 2.75 Å resolution in an inactive state bound with a peptide antagonist. Underpinned by structural homology models of MC4R complexes simulating a presumably active-state conformation compared to the structure of the inactive state, we here briefly summarize the current understanding and key players involved in the MC4R switching process between different activity states. Finally, these perspectives highlight the complexity and plasticity in MC4R signaling regulation and identify gaps in our current knowledge.
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21
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Characterization of cancer-related somatic mutations in the adenosine A2B receptor. Eur J Pharmacol 2020; 880:173126. [DOI: 10.1016/j.ejphar.2020.173126] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 04/16/2020] [Accepted: 04/20/2020] [Indexed: 01/10/2023]
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22
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Li W. Residue-Residue Mutual Work Analysis of Retinal-Opsin Interaction in Rhodopsin: Implications for Protein-Ligand Binding. J Chem Theory Comput 2020; 16:1834-1842. [PMID: 31972074 DOI: 10.1021/acs.jctc.9b01035] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Energetic contributions at the single-residue level for retinal-opsin interactions in rhodopsin were studied by combining molecular dynamics simulations, transition path sampling, and a newly developed energy decomposition approach. The virtual work at an infinitesimal time interval was decomposed into the work components on one residue due to its interaction with another residue, which were then averaged over the transition path ensemble along a proposed reaction coordinate. Such residue-residue mutual work analysis on 62 residues within the active center of rhodopsin resulted in a very sparse interaction matrix, which is generally not symmetric but antisymmetric to some extent. Fourteen residues were identified to be major players in retinal relaxation along a plausible pathway from bathorhodopsin to the blue-shifted intermediate, which is in good agreement with an existing NMR study. Based on the matrix of mutual work, a comprehensive network was constructed to provide detailed insights into the chromophore-protein interaction from a viewpoint of energy flow.
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Affiliation(s)
- Wenjin Li
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
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23
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Ferraro M, Decherchi S, De Simone A, Recanatini M, Cavalli A, Bottegoni G. Multi-target dopamine D3 receptor modulators: Actionable knowledge for drug design from molecular dynamics and machine learning. Eur J Med Chem 2019; 188:111975. [PMID: 31940507 DOI: 10.1016/j.ejmech.2019.111975] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 12/02/2019] [Accepted: 12/16/2019] [Indexed: 10/25/2022]
Abstract
Local changes in the structure of G-protein coupled receptors (GPCR) binders largely affect their pharmacological profile. While the sought efficacy can be empirically obtained by introducing local modifications, the underlining structural explanation can remain elusive. Here, molecular dynamics (MD) simulations of the eticlopride-bound inactive state of the Dopamine D3 Receptor (D3DR) have been clustered using a machine learning-based approach in the attempt to rationalize the efficacy change in four congeneric modulators. Accumulating extended MD trajectories of receptor-ligand complexes, we observed how the increase in ligand flexibility progressively destabilized the crystal structure of the inactivated receptor. To prospectively validate this model, a partial agonist was rationally designed based on structural insights and computational modeling, and eventually synthesized and tested. Results turned out to be in line with the predictions. This case study suggests that the investigation of ligand flexibility in the framework of extended MD simulations can assist and inform drug design strategies, highlighting its potential role as a powerful in silico counterpart to functional assays.
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Affiliation(s)
- Mariarosaria Ferraro
- Istituto di Chimica Del Riconoscimento Molecolare, Consiglio Nazionale Delle Ricerche (ICRM-CNR), Via Mario Bianco 9, 20131, Milan, Italy.
| | - Sergio Decherchi
- Computational & Chemical Biology, Italian Institute of Technology, Via Morego 30, 16163, Genoa, Italy.
| | - Alessio De Simone
- Sygnature Discovery Ltd, Bio City, Pennyfoot St, Nottingham NG1 1GR, United Kingdom.
| | - Maurizio Recanatini
- Dept. of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, 40126, Bologna, Italy.
| | - Andrea Cavalli
- Computational & Chemical Biology, Italian Institute of Technology, Via Morego 30, 16163, Genoa, Italy; Dept. of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, 40126, Bologna, Italy.
| | - Giovanni Bottegoni
- School of Pharmacy, University of Birmingham, Sir Robert Aitken Institute for Clinical Research, Edgbaston, B15 2TT, United Kingdom.
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24
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Allosteric Modulation of Cannabinoid Receptor 1-Current Challenges and Future Opportunities. Int J Mol Sci 2019; 20:ijms20235874. [PMID: 31771126 PMCID: PMC6928801 DOI: 10.3390/ijms20235874] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 11/19/2019] [Accepted: 11/20/2019] [Indexed: 02/07/2023] Open
Abstract
The cannabinoid receptor type 1 (CB1R), a G protein-coupled receptor (GPCR), plays an essential role in the control of many physiological processes such as hunger, memory loss, gastrointestinal activity, catalepsy, fear, depression, and chronic pain. Therefore, it is an attractive target for drug discovery to manage pain, neurodegenerative disorders, obesity, and substance abuse. However, the psychoactive adverse effects, generated by CB1R activation in the brain, limit the use of the orthosteric CB1R ligands as drugs. The discovery of CB1R allosteric modulators during the last decade provided new tools to target the CB1R. Moreover, application of the site-directed mutagenesis in combination with advanced physical methods, especially X-ray crystallography and computational modeling, has opened new horizons for understanding the complexity of the structure, function, and activity of cannabinoid receptors. In this paper, we present the latest advances in research on the CB1R, its allosteric modulation and allosteric ligands, and their translational potential. We focused on structural essentials of the cannabinoid 1 receptor- ligand (drug) interactions, as well as modes of CB1R signaling regulation.
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25
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Zhang Y, Chen HF. Allosteric mechanism of an oximino-piperidino-piperidine antagonist for the CCR5 chemokine receptor. Chem Biol Drug Des 2019; 95:113-123. [PMID: 31571405 DOI: 10.1111/cbdd.13627] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 08/29/2019] [Accepted: 09/04/2019] [Indexed: 11/30/2022]
Abstract
The first step for the HIV-1 virus infecting host cell is bound with the CCR5 chemokine receptor. A set of allosteric inhibitors of oximino-piperidino-piperidine antagonists for CCR5 chemokine receptor was discovered. However, the allosteric mechanism of these inhibitors is still unsolved. Therefore, residue-level dynamics correlation network combining with on molecular dynamics simulation was used to investigate the allosteric mechanism. The dynamics correlation network of bound CCR5 is significantly different from that of free CCR5. The community of the most active complex suggests that the allosteric information can freely transfer from the allosteric site to the effector site of the second extracellular loop, while the information transfers bottleneck for the less active one. Here, a hypothesis was proposed that "binding-induced allosteric mechanism" was used to reveal the allosteric regulation of antagonists and the network perturbation confirmed it. Finally, the shortest path algorithm was used to identify the possible allosteric pathway with Gly173-Lys171-Thr177-Tyr89-LIG which was evaluated by the network perturbation of key residue. Furthermore, the efficiency of allostery for the most active system is the highest among these antagonist complexes. The strategy targeting the allosteric pathway can be used to design novel inhibitors of HIV-1 virus.
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Affiliation(s)
- Yangpeng Zhang
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, College of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Hai-Feng Chen
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, College of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Center for Bioinformation Technology, Shanghai, China
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26
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Ryazantsev MN, Nikolaev DM, Struts AV, Brown MF. Quantum Mechanical and Molecular Mechanics Modeling of Membrane-Embedded Rhodopsins. J Membr Biol 2019; 252:425-449. [PMID: 31570961 DOI: 10.1007/s00232-019-00095-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 09/10/2019] [Indexed: 12/20/2022]
Abstract
Computational chemistry provides versatile methods for studying the properties and functioning of biological systems at different levels of precision and at different time scales. The aim of this article is to review the computational methodologies that are applicable to rhodopsins as archetypes for photoactive membrane proteins that are of great importance both in nature and in modern technologies. For each class of computational techniques, from methods that use quantum mechanics for simulating rhodopsin photophysics to less-accurate coarse-grained methodologies used for long-scale protein dynamics, we consider possible applications and the main directions for improvement.
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Affiliation(s)
- Mikhail N Ryazantsev
- Institute of Chemistry, Saint Petersburg State University, 26 Universitetskii pr, Saint Petersburg, Russia, 198504
| | - Dmitrii M Nikolaev
- Saint-Petersburg Academic University - Nanotechnology Research and Education Centre RAS, Saint Petersburg, Russia, 194021
| | - Andrey V Struts
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, USA.,Laboratory of Biomolecular NMR, Saint Petersburg State University, Saint Petersburg, Russia, 199034
| | - Michael F Brown
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, USA. .,Department of Physics, University of Arizona, Tucson, AZ, 85721, USA.
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27
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Munro RA, de Vlugt J, Ward ME, Kim SY, Lee KA, Jung KH, Ladizhansky V, Brown LS. Biosynthetic production of fully carbon-13 labeled retinal in E. coli for structural and functional studies of rhodopsins. JOURNAL OF BIOMOLECULAR NMR 2019; 73:49-58. [PMID: 30719609 DOI: 10.1007/s10858-019-00225-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 01/16/2019] [Indexed: 06/09/2023]
Abstract
The isomerization of a covalently bound retinal is an integral part of both microbial and animal rhodopsin function. As such, detailed structure and conformational changes in the retinal binding pocket are of significant interest and are studied in various NMR, FTIR, and Raman spectroscopy experiments, which commonly require isotopic labeling of retinal. Unfortunately, the de novo organic synthesis of an isotopically-labeled retinal is complex and often cost-prohibitive, especially for large scale expression required for solid-state NMR. We present the novel protocol for biosynthetic production of an isotopically labeled retinal ligand concurrently with an apoprotein in E. coli as a cost-effective alternative to the de novo organic synthesis. Previously, the biosynthesis of a retinal precursor, β-carotene, has been introduced into many different organisms. We extended this system to the prototrophic E. coli expression strain BL21 in conjunction with the inducible expression of a β-dioxygenase and proteo-opsin. To demonstrate the applicability of this system, we were able to assign several new carbon resonances for proteorhodopsin-bound retinal by using fully 13C-labeled glucose as the sole carbon source. Furthermore, we demonstrated that this biosynthetically produced retinal can be extracted from E. coli cells by applying a hydrophobic solvent layer to the growth medium and reconstituted into an externally produced opsin of any desired labeling pattern.
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Affiliation(s)
- Rachel A Munro
- Departments of Physics, and Biophysics Interdepartmental Group, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
| | - Jeffrey de Vlugt
- Departments of Physics, and Biophysics Interdepartmental Group, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
| | - Meaghan E Ward
- Departments of Physics, and Biophysics Interdepartmental Group, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
| | - So Young Kim
- Deptartment of Life Science, Institute of Biological Interfaces, Sogang University, Shinsu-Dong 1, Mapo-Gu, Seoul, 121-742, Republic of Korea
- Division of Biotechnology, College of Environmental & Bioresource Sciences, Chonbuk National University, Jeonju, Republic of Korea
| | - Keon Ah Lee
- Deptartment of Life Science, Institute of Biological Interfaces, Sogang University, Shinsu-Dong 1, Mapo-Gu, Seoul, 121-742, Republic of Korea
| | - Kwang-Hwan Jung
- Deptartment of Life Science, Institute of Biological Interfaces, Sogang University, Shinsu-Dong 1, Mapo-Gu, Seoul, 121-742, Republic of Korea
| | - Vladimir Ladizhansky
- Departments of Physics, and Biophysics Interdepartmental Group, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
| | - Leonid S Brown
- Departments of Physics, and Biophysics Interdepartmental Group, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada.
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28
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Brinkmann A, Sternberg U, Bovee-Geurts PHM, Fernández Fernández I, Lugtenburg J, Kentgens APM, DeGrip WJ. Insight into the chromophore of rhodopsin and its Meta-II photointermediate by 19F solid-state NMR and chemical shift tensor calculations. Phys Chem Chem Phys 2018; 20:30174-30188. [PMID: 30484791 DOI: 10.1039/c8cp05886e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
19F nuclei are useful labels in solid-state NMR studies, since their chemical shift and tensor elements are very sensitive to the electrostatic and space-filling properties of their local environment. In this study we have exploited a fluorine substituent, strategically placed at the C-12-position of 11-cis retinal, the chromophore of visual rhodopsins. This label was used to explore the local environment of the chromophore in the ground state of bovine rhodopsin and its active photo-intermediate Meta II. In addition, the chemical shift and tensor elements of the chromophore in the free state in a membrane environment and the bound state in the protein were determined. Upon binding of the chromophore into rhodopsin and Meta II, the isotropic chemical shift changes in the opposite direction by +9.7 and -8.4 ppm, respectively. An unusually large isotropic shift difference of 35.9 ppm was observed between rhodopsin and Meta II. This partly originates in the light-triggered 11-cis to all-trans isomerization of the chromophore. The other part reflects the local conformational rearrangements in the chromophore and the binding pocket. These NMR data were correlated with the available X-ray structures of rhodopsin and Meta II using bond polarization theory. For this purpose hydrogen atoms have to be inserted and hereto a family of structures were derived that best correlated with the well-established 13C chemical shifts. Based upon these structures, a 12-F derivative was obtained that best corresponded with the experimentally determined 19F chemical shifts and tensor elements. The combined data indicate strong changes in the local environment of the C-12 position and a substantially different interaction pattern with the protein in Meta II as compared to rhodopsin.
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Affiliation(s)
- Andreas Brinkmann
- Metrology, National Research Council Canada, 1200 Montreal Road, Ottawa, Ontario K1A 0R6, Canada.
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29
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Clement N, Renault N, Guillaume J, Cecon E, Journé A, Laurent X, Tadagaki K, Cogé F, Gohier A, Delagrange P, Chavatte P, Jockers R. Importance of the second extracellular loop for melatonin MT 1 receptor function and absence of melatonin binding in GPR50. Br J Pharmacol 2018; 175:3281-3297. [PMID: 28898928 PMCID: PMC6057912 DOI: 10.1111/bph.14029] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 08/09/2017] [Accepted: 09/03/2017] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND AND PURPOSE Recent crystal structures of GPCRs have emphasized the previously unappreciated role of the second extracellular (E2) loop in ligand binding and gating and receptor activation. Here, we have assessed the role of the E2 loop in the activation of the melatonin MT1 receptor and in the inactivation of the closely related orphan receptor GPR50. EXPERIMENTAL APPROACH Chimeric MT1 -GPR50 receptors were generated and functionally analysed in terms of 2-[125 I]iodomelatonin binding, Gi /cAMP signalling and β-arrestin2 recruitment. We also used computational molecular dynamics (MD) simulations. KEY RESULTS MD simulations of 300 ns revealed (i) the tight hairpin structure of the E2 loop of the MT1 receptor (ii) the most suitable features for melatonin binding in MT1 receptors and (iii) major predicted rearrangements upon MT1 receptor activation, stabilizing interaction networks between Phe179 or Gln181 in the E2 loop and transmembrane helixes 5 and 6. Functional assays confirmed these predictions, because reciprocal replacement of MT1 and GPR50 residues/domains led to the predicted loss- and gain-of-melatonin action of MT1 receptors and GPR50 respectively. CONCLUSIONS AND IMPLICATIONS Our work demonstrated the crucial role of the E2 loop for MT1 receptor and GPR50 function by proposing a model in which the E2 loop is important in stabilizing active MT1 receptor conformations and by showing how evolutionary processes appear to have selected for modifications in the E2 loop in order to make GPR50 unresponsive to melatonin. LINKED ARTICLES This article is part of a themed section on Recent Developments in Research of Melatonin and its Potential Therapeutic Applications. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v175.16/issuetoc.
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Affiliation(s)
- Nathalie Clement
- Inserm, U1016, Institut CochinParisFrance
- CNRS UMR 8104ParisFrance
- Univ. Paris Descartes, Sorbonne Paris CitéParisFrance
| | - Nicolas Renault
- Univ. Lille, Inserm, CHU Lille, U995 – LIRIC – Lille Inflammation Research International CenterLilleFrance
| | - Jean‐Luc Guillaume
- Inserm, U1016, Institut CochinParisFrance
- CNRS UMR 8104ParisFrance
- Univ. Paris Descartes, Sorbonne Paris CitéParisFrance
| | - Erika Cecon
- Inserm, U1016, Institut CochinParisFrance
- CNRS UMR 8104ParisFrance
- Univ. Paris Descartes, Sorbonne Paris CitéParisFrance
| | - Anne‐Sophie Journé
- Inserm, U1016, Institut CochinParisFrance
- CNRS UMR 8104ParisFrance
- Univ. Paris Descartes, Sorbonne Paris CitéParisFrance
| | - Xavier Laurent
- Univ. Lille, Inserm, CHU Lille, U995 – LIRIC – Lille Inflammation Research International CenterLilleFrance
| | - Kenjiro Tadagaki
- Inserm, U1016, Institut CochinParisFrance
- CNRS UMR 8104ParisFrance
- Univ. Paris Descartes, Sorbonne Paris CitéParisFrance
| | - Francis Cogé
- Pôle d'Innovation Thérapeutique NeuropsychiatrieInstitut de Recherches SERVIERCroissy/SeineFrance
| | - Arnaud Gohier
- Pôle d'Innovation Thérapeutique NeuropsychiatrieInstitut de Recherches SERVIERCroissy/SeineFrance
| | - Philippe Delagrange
- Pôle d'Innovation Thérapeutique NeuropsychiatrieInstitut de Recherches SERVIERCroissy/SeineFrance
| | - Philippe Chavatte
- Univ. Lille, Inserm, CHU Lille, U995 – LIRIC – Lille Inflammation Research International CenterLilleFrance
| | - Ralf Jockers
- Inserm, U1016, Institut CochinParisFrance
- CNRS UMR 8104ParisFrance
- Univ. Paris Descartes, Sorbonne Paris CitéParisFrance
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30
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Clark L, Dikiy I, Rosenbaum DM, Gardner KH. On the use of Pichia pastoris for isotopic labeling of human GPCRs for NMR studies. JOURNAL OF BIOMOLECULAR NMR 2018; 71:203-211. [PMID: 30121871 PMCID: PMC7282444 DOI: 10.1007/s10858-018-0204-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 08/09/2018] [Indexed: 05/21/2023]
Abstract
NMR studies of human integral membrane proteins provide unique opportunities to probe structure and dynamics at specific locations and on multiple timescales, often with significant implications for disease mechanism and drug development. Since membrane proteins such as G protein-coupled receptors (GPCRs) are highly dynamic and regulated by ligands or other perturbations, NMR methods are potentially well suited to answer basic functional questions (such as addressing the biophysical basis of ligand efficacy) as well as guiding applications (such as novel ligand design). However, such studies on eukaryotic membrane proteins have often been limited by the inability to incorporate optimal isotopic labels for NMR methods developed for large protein/lipid complexes, including methyl TROSY. We review the different expression systems for production of isotopically labeled membrane proteins and highlight the use of the yeast Pichia pastoris to achieve perdeuteration and 13C methyl probe incorporation within isoleucine sidechains. We further illustrate the use of this method for labeling of several biomedically significant GPCRs.
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Affiliation(s)
- Lindsay Clark
- Department of Biophysics, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, 75390-8816, USA
- Molecular Biophysics Graduate Program, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Igor Dikiy
- Structural Biology Initiative, CUNY Advanced Science Research Center, 85 St. Nicholas Terrace, New York, NY, 10031, USA
| | - Daniel M Rosenbaum
- Department of Biophysics, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, 75390-8816, USA.
- Molecular Biophysics Graduate Program, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
| | - Kevin H Gardner
- Structural Biology Initiative, CUNY Advanced Science Research Center, 85 St. Nicholas Terrace, New York, NY, 10031, USA.
- Department of Chemistry and Biochemistry, City College of New York, New York, NY, 10031, USA.
- Biochemistry, Chemistry and Biology Ph.D. Programs, Graduate Center, City University of New York, New York, NY, 10016, USA.
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31
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Athanasiou D, Aguila M, Bellingham J, Li W, McCulley C, Reeves PJ, Cheetham ME. The molecular and cellular basis of rhodopsin retinitis pigmentosa reveals potential strategies for therapy. Prog Retin Eye Res 2018; 62:1-23. [PMID: 29042326 PMCID: PMC5779616 DOI: 10.1016/j.preteyeres.2017.10.002] [Citation(s) in RCA: 217] [Impact Index Per Article: 36.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 10/03/2017] [Accepted: 10/13/2017] [Indexed: 12/12/2022]
Abstract
Inherited mutations in the rod visual pigment, rhodopsin, cause the degenerative blinding condition, retinitis pigmentosa (RP). Over 150 different mutations in rhodopsin have been identified and, collectively, they are the most common cause of autosomal dominant RP (adRP). Mutations in rhodopsin are also associated with dominant congenital stationary night blindness (adCSNB) and, less frequently, recessive RP (arRP). Recessive RP is usually associated with loss of rhodopsin function, whereas the dominant conditions are a consequence of gain of function and/or dominant negative activity. The in-depth characterisation of many rhodopsin mutations has revealed that there are distinct consequences on the protein structure and function associated with different mutations. Here we categorise rhodopsin mutations into seven discrete classes; with defects ranging from misfolding and disruption of proteostasis, through mislocalisation and disrupted intracellular traffic to instability and altered function. Rhodopsin adRP offers a unique paradigm to understand how disturbances in photoreceptor homeostasis can lead to neuronal cell death. Furthermore, a wide range of therapies have been tested in rhodopsin RP, from gene therapy and gene editing to pharmacological interventions. The understanding of the disease mechanisms associated with rhodopsin RP and the development of targeted therapies offer the potential of treatment for this currently untreatable neurodegeneration.
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Affiliation(s)
| | - Monica Aguila
- UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK
| | - James Bellingham
- UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK
| | - Wenwen Li
- UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK
| | - Caroline McCulley
- UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK
| | - Philip J Reeves
- School of Biological Sciences, University of Essex, Wivenhoe Park, Essex CO4 3SQ, UK.
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32
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Plazinska A, Plazinski W, Luchowski R, Wnorowski A, Grudzinski W, Gruszecki WI. Ligand-induced action of the W286 6.48 rotamer toggle switch in the β 2-adrenergic receptor. Phys Chem Chem Phys 2017; 20:581-594. [PMID: 29226293 DOI: 10.1039/c7cp04808d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Studies focused on GPCRs, particularly on the β2-adrenergic receptor (β2-AR), have demonstrated the relationship between ligand structure, receptor conformational changes and the corresponding pharmacological outcomes. Herein, we studied the molecular details of the rotameric flip of the W2866.48 sidechain, i.e. a presumed action switch that has not been reported in native β2-AR thus far. It is believed that although both the 'active' and 'inactive' conformers of β2-AR exhibit similar conformations of this switch, it may still play a substantial role in the ligand-induced activation of the receptor. By using both experimental methods (time-resolved fluorescence spectroscopy) and molecular modeling techniques (enhanced-sampling molecular dynamics), we characterized the conformational rearrangements of W2866.48 in relation to the type of ligand present in the binding cavity and to the conformation of the receptor ('active' vs. 'inactive' β2-AR). We found that the conformational behaviour of W2866.48 is correlated with the pharmacological character of the ligand present in the binding cavity but not with the instantaneous conformation of the receptor. Namely, agonists promote the W2866.48 conformations that facilitate the increase of the solvation within the inner receptor channel. In contrast, antagonists and inverse agonists act toward the decrease of the solvation in the inner channel. This creates an opportunity for using computational methodologies in determining the pharmacological properties of various ligands. The combination of the time-resolved fluorescence spectroscopy technique with the enhanced-sampling molecular dynamics simulations is shown to be a powerful tool for studying the ligand-induced conformational rearrangements in GPCRs.
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Affiliation(s)
- Anita Plazinska
- Department of Biopharmacy, Faculty of Pharmacy, Medical University of Lublin, W. Chodzki Str., 4a, 20-093 Lublin, Poland.
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33
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Structure-inspired design of β-arrestin-biased ligands for aminergic GPCRs. Nat Chem Biol 2017; 14:126-134. [PMID: 29227473 PMCID: PMC5771956 DOI: 10.1038/nchembio.2527] [Citation(s) in RCA: 120] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 10/20/2017] [Indexed: 01/06/2023]
Abstract
Development of biased ligands targeting G protein-coupled receptors (GPCRs) is a promising approach for current drug discovery. Although structure-based drug design of biased agonists remains challenging even with an abundance of GPCR crystal structures, we present an approach for translating GPCR structural data into β-arrestin-biased ligands for aminergic GPCRs. We identified specific amino acid-ligand contacts at transmembrane helix 5 (TM5) and extracellular loop 2 (EL2) responsible for Gi/o and β-arrestin signaling, respectively, and targeted those residues to develop biased ligands. For these ligands, we found that bias is conserved at other aminergic GPCRs that retain similar residues at TM5 and EL2. Our approach provides a template for generating arrestin-biased ligands by modifying predicted ligand interactions that block TM5 interactions and promote EL2 interactions. This strategy could facilitate the structure-guided design of arrestin-biased ligands at other GPCRs, including polypharmacological biased ligands.
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34
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Flavonoid allosteric modulation of mutated visual rhodopsin associated with retinitis pigmentosa. Sci Rep 2017; 7:11167. [PMID: 28894166 PMCID: PMC5593859 DOI: 10.1038/s41598-017-11391-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 08/22/2017] [Indexed: 11/08/2022] Open
Abstract
Dietary flavonoids exhibit many biologically-relevant functions and can potentially have beneficial effects in the treatment of pathological conditions. In spite of its well known antioxidant properties, scarce structural information is available on the interaction of flavonoids with membrane receptors. Advances in the structural biology of a specific class of membrane receptors, the G protein-coupled receptors, have significantly increased our understanding of drug action and paved the way for developing improved therapeutic approaches. We have analyzed the effect of the flavonoid quercetin on the conformation, stability and function of the G protein-coupled receptor rhodopsin, and the G90V mutant associated with the retinal degenerative disease retinitis pigmentosa. By using a combination of experimental and computational methods, we suggest that quercetin can act as an allosteric modulator of opsin regenerated with 9-cis-retinal and more importantly, that this binding has a positive effect on the stability and conformational properties of the G90V mutant associated with retinitis pigmentosa. These results open new possibilities to use quercetin and other flavonoids, in combination with specific retinoids like 9-cis-retinal, for the treatment of retinal degeneration associated with retinitis pigmentosa. Moreover, the use of flavonoids as allosteric modulators may also be applicable to other members of the G protein-coupled receptors superfamily.
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35
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Sim DW, Lu Z, Won HS, Lee SN, Seo MD, Lee BJ, Kim JH. Application of Solution NMR to Structural Studies on α-Helical Integral Membrane Proteins. Molecules 2017; 22:molecules22081347. [PMID: 28809779 PMCID: PMC6152068 DOI: 10.3390/molecules22081347] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 08/10/2017] [Accepted: 08/12/2017] [Indexed: 02/05/2023] Open
Abstract
A large portion of proteins in living organisms are membrane proteins which play critical roles in the biology of the cell, from maintenance of the biological membrane integrity to communication of cells with their surroundings. To understand their mechanism of action, structural information is essential. Nevertheless, structure determination of transmembrane proteins is still a challenging area, even though recently the number of deposited structures of membrane proteins in the PDB has rapidly increased thanks to the efforts using X-ray crystallography, electron microscopy, and solid and solution nuclear magnetic resonance (NMR) technology. Among these technologies, solution NMR is a powerful tool for studying protein-protein, protein-ligand interactions and protein dynamics at a wide range of time scales as well as structure determination of membrane proteins. This review provides general and useful guideline for membrane protein sample preparation and the choice of membrane-mimetic media, which are the key step for successful structural analysis. Furthermore, this review provides an opportunity to look at recent applications of solution NMR to structural studies on α-helical membrane proteins through some success stories.
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Affiliation(s)
- Dae-Won Sim
- Department of Biotechnology, College of Biomedical and Health Science, Konkuk University, Chungbuk 27478, Korea.
| | - Zhenwei Lu
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37204, USA.
| | - Hyung-Sik Won
- Department of Biotechnology, College of Biomedical and Health Science, Konkuk University, Chungbuk 27478, Korea.
| | - Seu-Na Lee
- Department of Biotechnology, College of Biomedical and Health Science, Konkuk University, Chungbuk 27478, Korea.
| | - Min-Duk Seo
- Department of Molecular Science and Technology & College of Pharmacy, Ajou University, Suwon 16499, Korea.
| | - Bong-Jin Lee
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Gwanak-gu, Seoul 151-742, Korea.
| | - Ji-Hun Kim
- College of Pharmacy, Chungbuk National University, Cheongju 28160, Chungbuk, Korea.
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36
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Applications of solid-state NMR to membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1577-1586. [PMID: 28709996 DOI: 10.1016/j.bbapap.2017.07.004] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 06/30/2017] [Accepted: 07/07/2017] [Indexed: 11/23/2022]
Abstract
Membrane proteins mediate flow of molecules, signals, and energy between cells and intracellular compartments. Understanding membrane protein function requires a detailed understanding of the structural and dynamic properties involved. Lipid bilayers provide a native-like environment for structure-function investigations of membrane proteins. In this review we give a general discourse on the recent progress in the field of solid-state NMR of membrane proteins. Solid-state NMR is a variation of NMR spectroscopy that is applicable to molecular systems with restricted mobility, such as high molecular weight proteins and protein complexes, supramolecular assemblies, or membrane proteins in a phospholipid environment. We highlight recent advances in applications of solid-state NMR to membrane proteins, specifically focusing on the recent developments in the field of Dynamic Nuclear Polarization, proton detection, and solid-state NMR applications in situ (in cell membranes). This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman.
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Hofrnann L, Alexander NS, Sun W, Zhang J, Orban T, Palczewski K. Hydrogen/Deuterium Exchange Mass Spectrometry of Human Green Opsin Reveals a Conserved Pro-Pro Motif in Extracellular Loop 2 of Monostable Visual G Protein-Coupled Receptors. Biochemistry 2017; 56:2338-2348. [PMID: 28402104 PMCID: PMC5501310 DOI: 10.1021/acs.biochem.7b00165] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Opsins comprise the protein component of light sensitive G protein-coupled receptors (GPCRs) in the retina of the eye that are responsible for the transduction of light into a biochemical signal. Here, we used hydrogen/deuterium (H/D) exchange coupled with mass spectrometry to map conformational changes in green cone opsin upon light activation. We then compared these findings with those reported for rhodopsin. The extent of H/D exchange in green cone opsin was greater than in rhodopsin in the dark and bleached states, suggesting a higher structural heterogeneity for green cone opsin. Further analysis revealed that green cone opsin exists as a dimer in both dark (inactive) and bleached (active) states, and that the predicted glycosylation sites at N32 and N34 are indeed glycosylated. Comparison of deuterium uptake between inactive and active states of green cone opsin also disclosed a reduced solvent accessibility of the extracellular N-terminal region and an increased accessibility of the chromophore binding site. Increased H/D exchange at the extracellular side of transmembrane helix four (TM4) combined with an analysis of sequence alignments revealed a conserved Pro-Pro motif in extracellular loop 2 (EL2) of monostable visual GPCRs. These data present new insights into the locus of chromophore release at the extracellular side of TM4 and TM5 and provide a foundation for future functional evaluation.
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Affiliation(s)
- Lukas Hofrnann
- Department of Pharmacology and Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Nathan S. Alexander
- Department of Pharmacology and Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Wenyu Sun
- Department of Pharmacology and Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Jianye Zhang
- Department of Pharmacology and Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Tivadar Orban
- Department of Pharmacology and Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Krzysztof Palczewski
- Department of Pharmacology and Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
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38
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Kamiya M, Hayashi S. Photoactivation Intermediates of a G-Protein Coupled Receptor Rhodopsin Investigated by a Hybrid Molecular Simulation. J Phys Chem B 2017; 121:3842-3852. [PMID: 28240904 DOI: 10.1021/acs.jpcb.6b13050] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Rhodopsin is a G-protein coupled receptor functioning as a photoreceptor for vision through photoactivation of a covalently bound ligand of a retinal protonated Schiff base chromophore. Despite the availability of structural information on the inactivated and activated forms of the receptor, the transition processes initiated by the photoabsorption have not been well understood. Here we theoretically examined the photoactivation processes by means of molecular dynamics (MD) simulations and ab initio quantum mechanical/molecular mechanical (QM/MM) free energy geometry optimizations which enabled accurate geometry determination of the ligand molecule in ample statistical conformational samples of the protein. Structures of the intermediate states of the activation process, blue-shifted intermediate and Lumi, as well as the dark state first generated by MD simulations and then refined by the QM/MM free energy geometry optimizations were characterized by large displacement of the β-ionone ring of retinal along with change in the hydrogen bond of the protonated Schiff base. The ab initio calculations of vibrational and electronic spectroscopic properties of those states well reproduced the experimental observations and successfully identified the molecular origins underlying the spectroscopic features. The structural evolution in the formation of the intermediates provides a molecular insight into the efficient activation processes of the receptor.
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Affiliation(s)
- Motoshi Kamiya
- Department of Chemistry, Graduate School of Science, Kyoto University , Kyoto 606-8502, Japan
| | - Shigehiko Hayashi
- Department of Chemistry, Graduate School of Science, Kyoto University , Kyoto 606-8502, Japan
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39
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Abstract
Conformational equilibria of G-protein-coupled receptors (GPCRs) are intimately involved in intracellular signaling. Here conformational substates of the GPCR rhodopsin are investigated in micelles of dodecyl maltoside (DDM) and in phospholipid nanodiscs by monitoring the spatial positions of transmembrane helices 6 and 7 at the cytoplasmic surface using site-directed spin labeling and double electron-electron resonance spectroscopy. The photoactivated receptor in DDM is dominated by one conformation with weak pH dependence. In nanodiscs, however, an ensemble of pH-dependent conformational substates is observed, even at pH 6.0 where the MIIbH+ form defined by proton uptake and optical spectroscopic methods is reported to be the sole species present in native disk membranes. In nanodiscs, the ensemble of substates in the photoactivated receptor spontaneously decays to that characteristic of the inactive state with a lifetime of ∼16 min at 20 °C. Importantly, transducin binding to the activated receptor selects a subset of the ensemble in which multiple substates are apparently retained. The results indicate that in a native-like lipid environment rhodopsin activation is not analogous to a simple binary switch between two defined conformations, but the activated receptor is in equilibrium between multiple conformers that in principle could recognize different binding partners.
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40
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Ziarek JJ, Kleist AB, London N, Raveh B, Montpas N, Bonneterre J, St-Onge G, DiCosmo-Ponticello CJ, Koplinski CA, Roy I, Stephens B, Thelen S, Veldkamp CT, Coffman FD, Cohen MC, Dwinell MB, Thelen M, Peterson FC, Heveker N, Volkman BF. Structural basis for chemokine recognition by a G protein-coupled receptor and implications for receptor activation. Sci Signal 2017; 10:10/471/eaah5756. [PMID: 28325822 DOI: 10.1126/scisignal.aah5756] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Chemokines orchestrate cell migration for development, immune surveillance, and disease by binding to cell surface heterotrimeric guanine nucleotide-binding protein (G protein)-coupled receptors (GPCRs). The array of interactions between the nearly 50 chemokines and their 20 GPCR targets generates an extensive signaling network to which promiscuity and biased agonism add further complexity. The receptor CXCR4 recognizes both monomeric and dimeric forms of the chemokine CXCL12, which is a distinct example of ligand bias in the chemokine family. We demonstrated that a constitutively monomeric CXCL12 variant reproduced the G protein-dependent and β-arrestin-dependent responses that are associated with normal CXCR4 signaling and lead to cell migration. In addition, monomeric CXCL12 made specific contacts with CXCR4 that are not present in the structure of the receptor in complex with a dimeric form of CXCL12, a biased agonist that stimulates only G protein-dependent signaling. We produced an experimentally validated model of an agonist-bound chemokine receptor that merged a nuclear magnetic resonance-based structure of monomeric CXCL12 bound to the amino terminus of CXCR4 with a crystal structure of the transmembrane domains of CXCR4. The large CXCL12:CXCR4 protein-protein interface revealed by this structure identified previously uncharacterized functional interactions that fall outside of the classical "two-site model" for chemokine-receptor recognition. Our model suggests a mechanistic hypothesis for how interactions on the extracellular face of the receptor may stimulate the conformational changes required for chemokine receptor-mediated signal transduction.
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Affiliation(s)
- Joshua J Ziarek
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Andrew B Kleist
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Nir London
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Barak Raveh
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Nicolas Montpas
- Centre de Recherche, Centre Hospitalier Universitaire Sainte-Justine, Montréal, Quebec H3T 1C5, Canada.,Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Quebec H3T 1J4, Canada
| | - Julien Bonneterre
- Centre de Recherche, Centre Hospitalier Universitaire Sainte-Justine, Montréal, Quebec H3T 1C5, Canada.,Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Quebec H3T 1J4, Canada
| | - Geneviève St-Onge
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Quebec H3T 1J4, Canada
| | | | - Chad A Koplinski
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Ishan Roy
- Department of Microbiology and Molecular Genetics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Bryan Stephens
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 93093, USA
| | - Sylvia Thelen
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Via Vela 6, Bellinzona CH-6500, Switzerland
| | | | - Frederick D Coffman
- Department of Pathology and Laboratory Medicine and Center for Biophysical Pathology, Rutgers New Jersey Medical School, Newark, NJ 07103, USA
| | - Marion C Cohen
- Rutgers Graduate School of Biomedical Sciences, Newark, NJ 07101, USA
| | - Michael B Dwinell
- Department of Microbiology and Molecular Genetics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Marcus Thelen
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Via Vela 6, Bellinzona CH-6500, Switzerland
| | - Francis C Peterson
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Nikolaus Heveker
- Centre de Recherche, Centre Hospitalier Universitaire Sainte-Justine, Montréal, Quebec H3T 1C5, Canada.,Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Quebec H3T 1J4, Canada
| | - Brian F Volkman
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
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41
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Shigeta A, Ito S, Inoue K, Okitsu T, Wada A, Kandori H, Kawamura I. Solid-State Nuclear Magnetic Resonance Structural Study of the Retinal-Binding Pocket in Sodium Ion Pump Rhodopsin. Biochemistry 2017; 56:543-550. [PMID: 28040890 DOI: 10.1021/acs.biochem.6b00999] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The recently identified Krokinobacter rhodopsin 2 (KR2) functions as a light-driven sodium ion pump. The structure of the retinal-binding pocket of KR2 offers important insights into the mechanisms of KR2, which has motif of Asn112, Asp116, and Gln123 (NDQ) that is common among sodium ion pump rhodopsins but is unique among other microbial rhodopsins. Here we present solid-state nuclear magnetic resonance (NMR) characterization of retinal and functionally important residues in the vicinity of retinal in the ground state. We assigned chemical shifts of retinal C14 and C20 atoms, and Tyr218Cζ, Lys255Cε, and the protonated Schiff base of KR2 in lipid environments at acidic and neutral pH. 15N NMR signals of the protonated Schiff base showed a twist around the N-Cε bond under neutral conditions, compared with other microbial rhodopsins. These data indicated that the location of the counterion Asp116 is one helical pitch toward the cytoplasmic side. In acidic environments, the 15N Schiff base signal was shifted to a lower field, indicating that protonation of Asp116 induces reorientation during interactions between the Schiff base and Asp116. In addition, the Tyr218 residue in the vicinity of retinal formed a weak hydrogen bond with Asp251, a temporary Na+-binding site during the photocycle. These features may indicate unique mechanisms of sodium ion pumps.
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Affiliation(s)
- Arisu Shigeta
- Graduate School of Engineering, Yokohama National University , Hodogaya-ku, Yokohama 240-8501, Japan
| | - Shota Ito
- Department of Frontier Materials, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan
| | - Keiichi Inoue
- Department of Frontier Materials, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan.,OptoBioTechnology Research Center, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan.,PRESTO, Japan Science and Technology Agency (JST) , 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
| | - Takashi Okitsu
- Department of Organic Chemistry for Life Science, Kobe Pharmaceutical University , Higashinada-ku, Kobe 658-8558, Japan
| | - Akimori Wada
- Department of Organic Chemistry for Life Science, Kobe Pharmaceutical University , Higashinada-ku, Kobe 658-8558, Japan
| | - Hideki Kandori
- Department of Frontier Materials, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan.,OptoBioTechnology Research Center, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan
| | - Izuru Kawamura
- Graduate School of Engineering, Yokohama National University , Hodogaya-ku, Yokohama 240-8501, Japan
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42
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Fokas AS, Cole DJ, Ahnert SE, Chin AW. Residue Geometry Networks: A Rigidity-Based Approach to the Amino Acid Network and Evolutionary Rate Analysis. Sci Rep 2016; 6:33213. [PMID: 27623708 PMCID: PMC5021933 DOI: 10.1038/srep33213] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 08/12/2016] [Indexed: 01/23/2023] Open
Abstract
Amino acid networks (AANs) abstract the protein structure by recording the amino acid contacts and can provide insight into protein function. Herein, we describe a novel AAN construction technique that employs the rigidity analysis tool, FIRST, to build the AAN, which we refer to as the residue geometry network (RGN). We show that this new construction can be combined with network theory methods to include the effects of allowed conformal motions and local chemical environments. Importantly, this is done without costly molecular dynamics simulations required by other AAN-related methods, which allows us to analyse large proteins and/or data sets. We have calculated the centrality of the residues belonging to 795 proteins. The results display a strong, negative correlation between residue centrality and the evolutionary rate. Furthermore, among residues with high closeness, those with low degree were particularly strongly conserved. Random walk simulations using the RGN were also successful in identifying allosteric residues in proteins involved in GPCR signalling. The dynamic function of these residues largely remain hidden in the traditional distance-cutoff construction technique. Despite being constructed from only the crystal structure, the results in this paper suggests that the RGN can identify residues that fulfil a dynamical function.
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Affiliation(s)
- Alexander S. Fokas
- Theory of Condensed Matter Group, Cavendish Laboratory, 19 JJ Thomson Avenue, CB3 0HE, Cambridge, U.K
| | - Daniel J. Cole
- Theory of Condensed Matter Group, Cavendish Laboratory, 19 JJ Thomson Avenue, CB3 0HE, Cambridge, U.K
| | - Sebastian E. Ahnert
- Theory of Condensed Matter Group, Cavendish Laboratory, 19 JJ Thomson Avenue, CB3 0HE, Cambridge, U.K
| | - Alex W. Chin
- Theory of Condensed Matter Group, Cavendish Laboratory, 19 JJ Thomson Avenue, CB3 0HE, Cambridge, U.K
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43
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Retinal orientation and interactions in rhodopsin reveal a two-stage trigger mechanism for activation. Nat Commun 2016; 7:12683. [PMID: 27585742 PMCID: PMC5025775 DOI: 10.1038/ncomms12683] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 07/22/2016] [Indexed: 01/28/2023] Open
Abstract
The 11-cis retinal chromophore is tightly packed within the interior of the visual receptor rhodopsin and isomerizes to the all-trans configuration following absorption of light. The mechanism by which this isomerization event drives the outward rotation of transmembrane helix H6, a hallmark of activated G protein-coupled receptors, is not well established. To address this question, we use solid-state NMR and FTIR spectroscopy to define the orientation and interactions of the retinal chromophore in the active metarhodopsin II intermediate. Here we show that isomerization of the 11-cis retinal chromophore generates strong steric interactions between its β-ionone ring and transmembrane helices H5 and H6, while deprotonation of its protonated Schiff's base triggers the rearrangement of the hydrogen-bonding network involving residues on H6 and within the second extracellular loop. We integrate these observations with previous structural and functional studies to propose a two-stage mechanism for rhodopsin activation.
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44
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Kleist AB, Getschman AE, Ziarek JJ, Nevins AM, Gauthier PA, Chevigné A, Szpakowska M, Volkman BF. New paradigms in chemokine receptor signal transduction: Moving beyond the two-site model. Biochem Pharmacol 2016; 114:53-68. [PMID: 27106080 DOI: 10.1016/j.bcp.2016.04.007] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 04/13/2016] [Indexed: 10/21/2022]
Abstract
Chemokine receptor (CKR) signaling forms the basis of essential immune cellular functions, and dysregulated CKR signaling underpins numerous disease processes of the immune system and beyond. CKRs, which belong to the seven transmembrane domain receptor (7TMR) superfamily, initiate signaling upon binding of endogenous, secreted chemokine ligands. Chemokine-CKR interactions are traditionally described by a two-step/two-site mechanism, in which the CKR N-terminus recognizes the chemokine globular core (i.e. site 1 interaction), followed by activation when the unstructured chemokine N-terminus is inserted into the receptor TM bundle (i.e. site 2 interaction). Several recent studies challenge the structural independence of sites 1 and 2 by demonstrating physical and allosteric links between these supposedly separate sites. Others contest the functional independence of these sites, identifying nuanced roles for site 1 and other interactions in CKR activation. These developments emerge within a rapidly changing landscape in which CKR signaling is influenced by receptor PTMs, chemokine and CKR dimerization, and endogenous non-chemokine ligands. Simultaneous advances in the structural and functional characterization of 7TMR biased signaling have altered how we understand promiscuous chemokine-CKR interactions. In this review, we explore new paradigms in CKR signal transduction by considering studies that depict a more intricate architecture governing the consequences of chemokine-CKR interactions.
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Affiliation(s)
- Andrew B Kleist
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
| | - Anthony E Getschman
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
| | - Joshua J Ziarek
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Ave, Boston, MA 02115, USA.
| | - Amanda M Nevins
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
| | - Pierre-Arnaud Gauthier
- Department of Infection and Immunity, Luxembourg Institute of Health, L-4354 Esch-sur-Alzette, Luxembourg.
| | - Andy Chevigné
- Department of Infection and Immunity, Luxembourg Institute of Health, L-4354 Esch-sur-Alzette, Luxembourg.
| | - Martyna Szpakowska
- Department of Infection and Immunity, Luxembourg Institute of Health, L-4354 Esch-sur-Alzette, Luxembourg.
| | - Brian F Volkman
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
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45
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Kimura T, Jennings W, Epand RM. Roles of specific lipid species in the cell and their molecular mechanism. Prog Lipid Res 2016; 62:75-92. [PMID: 26875545 DOI: 10.1016/j.plipres.2016.02.001] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 02/04/2016] [Accepted: 02/10/2016] [Indexed: 12/19/2022]
Abstract
Thousands of different molecular species of lipids are present within a single cell, being involved in modulating the basic processes of life. The vast number of different lipid species can be organized into a number of different lipid classes, which may be defined as a group of lipids with a common chemical structure, such as the headgroup, apart from the nature of the hydrocarbon chains. Each lipid class has unique biological roles. In some cases, a relatively small change in the headgroup chemical structure can result in a drastic change in function. Such phenomena are well documented, and largely understood in terms of specific interactions with proteins. In contrast, there are observations that the entire structural specificity of a lipid molecule, including the hydrocarbon chains, is required for biological activity through specific interactions with membrane proteins. Understanding of these phenomena represents a fundamental change in our thinking of the functions of lipids in biology. There are an increasing number of diverse examples of roles for specific lipids in cellular processes including: Signal transduction; trafficking; morphological changes; cell division. We are gaining knowledge and understanding of the underlying molecular mechanisms. They are of growing importance in both basic and applied sciences.
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Affiliation(s)
- Tomohiro Kimura
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - William Jennings
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Richard M Epand
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada.
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46
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Struts AV, Barmasov AV, Brown MF. CONDENSED-MATTER SPECTROSCOPY SPECTRAL METHODS FOR STUDY OF THE G-PROTEIN-COUPLED RECEPTOR RHODOPSIN. II. MAGNETIC RESONANCE METHODS. OPTICS AND SPECTROSCOPY 2016; 120:286-293. [PMID: 28260816 PMCID: PMC5334789 DOI: 10.1134/s0030400x16010197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
This article continues our review of spectroscopic studies of G-protein-coupled receptors. Magnetic resonance methods including electron paramagnetic resonance (EPR) and nuclear magnetic resonance (NMR) provide specific structural and dynamical data for the protein in conjunction with optical methods (vibrational, electronic spectroscopy) as discussed in the accompanying article. An additional advantage is the opportunity to explore the receptor proteins in the natural membrane lipid environment. Solid-state 2H and 13C NMR methods yield information about the both local structure and dynamics of the cofactor bound to the protein and its light induced changes. Complementary site-directed spin labeling studies monitor the structural alterations over larger distances and correspondingly longer time scales. A multi-scale reaction mechanism describes how local changes of the retinal cofactor unlock the receptor to initiate large-scale conformational changes of rhodopsin. Activation of the G-protein-coupled receptor involves an ensemble of conformational substates within the rhodopsin manifold that characterize the dynamically active receptor.
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Affiliation(s)
- A V Struts
- St. Petersburg State Medical University, 194100 St. Petersburg, Russia; St. Petersburg State University, 199034 St. Petersburg, Russia; University of Arizona, Tucson, AZ 85721 USA
| | - A V Barmasov
- St. Petersburg State Medical University, 194100 St. Petersburg, Russia; St. Petersburg State University, 199034 St. Petersburg, Russia
| | - M F Brown
- St. Petersburg State Medical University, 194100 St. Petersburg, Russia
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47
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Enhanced Functional Activity of the Cannabinoid Type-1 Receptor Mediates Adolescent Behavior. J Neurosci 2016; 35:13975-88. [PMID: 26468198 DOI: 10.1523/jneurosci.1937-15.2015] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
UNLABELLED Adolescence is characterized by drastic behavioral adaptations and comprises a particularly vulnerable period for the emergence of various psychiatric disorders. Growing evidence reveals that the pathophysiology of these disorders might derive from aberrations of normal neurodevelopmental changes in the adolescent brain. Understanding the molecular underpinnings of adolescent behavior is therefore critical for understanding the origin of psychopathology, but the molecular mechanisms that trigger adolescent behavior are unknown. Here, we hypothesize that the cannabinoid type-1 receptor (CB1R) may play a critical role in mediating adolescent behavior because enhanced endocannabinoid (eCB) signaling has been suggested to occur transiently during adolescence. To study enhanced CB1R signaling, we introduced a missense mutation (F238L) into the rat Cnr1 gene that encodes for the CB1R. According to our hypothesis, rats with the F238L mutation (Cnr1(F238L)) should sustain features of adolescent behavior into adulthood. Gain of function of the mutated receptor was demonstrated by in silico modeling and was verified functionally in a series of biochemical and electrophysiological experiments. Mutant rats exhibit an adolescent-like phenotype during adulthood compared with wild-type littermates, with typical high risk/novelty seeking, increased peer interaction, enhanced impulsivity, and augmented reward sensitivity for drug and nondrug reward. Partial inhibition of CB1R activity in Cnr1(F238L) mutant rats normalized behavior and led to a wild-type phenotype. We conclude that the activity state and functionality of the CB1R is critical for mediating adolescent behavior. These findings implicate the eCB system as an important research target for the neuropathology of adolescent-onset mental health disorders. SIGNIFICANCE STATEMENT We present the first rodent model with a gain-of-function mutation in the cannabinoid type-1 receptor (CB1R). Adult mutant rats exhibit an adolescent-like phenotype with typical high risk seeking, impulsivity, and augmented drug and nondrug reward sensitivity. Adolescence is a critical period for suboptimal behavioral choices and the emergence of neuropsychiatric disorders. Understanding the basis of these disorders therefore requires a comprehensive knowledge of how adolescent neurodevelopment triggers behavioral reactions. Our behavioral observations in adult mutant rats, together with reports on enhanced adolescent CB1R signaling, suggest a pivotal role for the CB1R in an adolescent brain as an important molecular mediator of adolescent behavior. These findings implicate the endocannabinoid system as a notable research target for adolescent-onset mental health disorders.
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48
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Culhane KJ, Liu Y, Cai Y, Yan ECY. Transmembrane signal transduction by peptide hormones via family B G protein-coupled receptors. Front Pharmacol 2015; 6:264. [PMID: 26594176 PMCID: PMC4633518 DOI: 10.3389/fphar.2015.00264] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 10/23/2015] [Indexed: 01/28/2023] Open
Abstract
Although family B G protein-coupled receptors (GPCRs) contain only 15 members, they play key roles in transmembrane signal transduction of hormones. Family B GPCRs are drug targets for developing therapeutics for diseases ranging from metabolic to neurological disorders. Despite their importance, the molecular mechanism of activation of family B GPCRs remains largely unexplored due to the challenges in expression and purification of functional receptors to the quantity for biophysical characterization. Currently, there is no crystal structure available of a full-length family B GPCR. However, structures of key domains, including the extracellular ligand binding regions and seven-helical transmembrane regions, have been solved by X-ray crystallography and NMR, providing insights into the mechanisms of ligand recognition and selectivity, and helical arrangements within the cell membrane. Moreover, biophysical and biochemical methods have been used to explore functions, key residues for signaling, and the kinetics and dynamics of signaling processes. This review summarizes the current knowledge of the signal transduction mechanism of family B GPCRs at the molecular level and comments on the challenges and outlook for mechanistic studies of family B GPCRs.
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Affiliation(s)
- Kelly J Culhane
- Department of Molecular Biophysics and Biochemistry, Yale University New Haven, CT, USA
| | - Yuting Liu
- Department of Chemistry, Yale University New Haven, CT, USA
| | - Yingying Cai
- Department of Chemistry, Yale University New Haven, CT, USA
| | - Elsa C Y Yan
- Department of Chemistry, Yale University New Haven, CT, USA
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N-linked glycosylation of protease-activated receptor-1 at extracellular loop 2 regulates G-protein signaling bias. Proc Natl Acad Sci U S A 2015; 112:E3600-8. [PMID: 26100877 DOI: 10.1073/pnas.1508838112] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Protease-activated receptor-1 (PAR1) is a G-protein-coupled receptor (GPCR) for the coagulant protease thrombin. Similar to other GPCRs, PAR1 is promiscuous and couples to multiple heterotrimeric G-protein subtypes in the same cell and promotes diverse cellular responses. The molecular mechanism by which activation of a given GPCR with the same ligand permits coupling to multiple G-protein subtypes is unclear. Here, we report that N-linked glycosylation of PAR1 at extracellular loop 2 (ECL2) controls G12/13 versus Gq coupling specificity in response to thrombin stimulation. A PAR1 mutant deficient in glycosylation at ECL2 was more effective at stimulating Gq-mediated phosphoinositide signaling compared with glycosylated wildtype receptor. In contrast, wildtype PAR1 displayed a greater efficacy at G12/13-dependent RhoA activation compared with mutant receptor lacking glycosylation at ECL2. Endogenous PAR1 rendered deficient in glycosylation using tunicamycin, a glycoprotein synthesis inhibitor, also exhibited increased PI signaling and diminished RhoA activation opposite to native receptor. Remarkably, PAR1 wildtype and glycosylation-deficient mutant were equally effective at coupling to Gi and β-arrestin-1. Consistent with preferential G12/13 coupling, thrombin-stimulated PAR1 wildtype strongly induced RhoA-mediated stress fiber formation compared with mutant receptor. In striking contrast, glycosylation-deficient PAR1 was more effective at increasing cellular proliferation, associated with Gq signaling, than wildtype receptor. These studies suggest that N-linked glycosylation at ECL2 contributes to the stabilization of an active PAR1 state that preferentially couples to G12/13 versus Gq and defines a previously unidentified function for N-linked glycosylation of GPCRs in regulating G-protein signaling bias.
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Brown LS, Ladizhansky V. Membrane proteins in their native habitat as seen by solid-state NMR spectroscopy. Protein Sci 2015; 24:1333-46. [PMID: 25973959 DOI: 10.1002/pro.2700] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 04/07/2015] [Accepted: 04/09/2015] [Indexed: 12/21/2022]
Abstract
Membrane proteins play many critical roles in cells, mediating flow of material and information across cell membranes. They have evolved to perform these functions in the environment of a cell membrane, whose physicochemical properties are often different from those of common cell membrane mimetics used for structure determination. As a result, membrane proteins are difficult to study by traditional methods of structural biology, and they are significantly underrepresented in the protein structure databank. Solid-state Nuclear Magnetic Resonance (SSNMR) has long been considered as an attractive alternative because it allows for studies of membrane proteins in both native-like membranes composed of synthetic lipids and in cell membranes. Over the past decade, SSNMR has been rapidly developing into a major structural method, and a growing number of membrane protein structures obtained by this technique highlights its potential. Here we discuss membrane protein sample requirements, review recent progress in SSNMR methodologies, and describe recent advances in characterizing membrane proteins in the environment of a cellular membrane.
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Affiliation(s)
- Leonid S Brown
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
| | - Vladimir Ladizhansky
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
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