1
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Löbbert A, Lorz N, Matthees ESF, Rößler P, Hoffmann C, Gossert AD. GPCR kinases phosphorylate GPCR C-terminal peptides in a hierarchical manner. Commun Biol 2025; 8:899. [PMID: 40490497 DOI: 10.1038/s42003-025-08301-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2025] [Accepted: 05/27/2025] [Indexed: 06/11/2025] Open
Abstract
Responses from G protein-coupled receptors (GPCRs) are downregulated in a precisely orchestrated process called desensitization. This process consists of two major steps: phosphorylation of the receptor by GPCR kinases (GRKs), predominantly on its C-terminus, and recruitment of arrestin, resulting in different signaling outcomes. Yet, it remains unclear how the phosphorylation pattern on the receptor is determined. We carried out an NMR-based study of the phosphorylation patterns generated by GRK1 and GRK2 on C-terminal peptides of selected receptors (rhodopsin for GRK1, and β1- and β2-adrenergic receptors (ARs) for GRK2). Our data reveal that the kinases are promiscuous with respect to the substrate peptide, but produce clearly defined phosphorylation patterns on each substrate. We found pronounced differences in the rates at which certain residues are phosphorylated, in particular in the PXPP motifs in rhodopsin and β1AR. These results show that GRKs produce well-defined phosphorylation patterns in absence of further modulators like the full receptor or Gβγ, and that the time profile of the phosphorylation barcode seems to be largely encoded in the minimal pair of C-terminal peptide and GRK. The data further suggest that arrestin might encounter different phosphorylation barcodes over time, hinting at the possibility of time-dependent arrestin responses.
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Affiliation(s)
- Arnelle Löbbert
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Nils Lorz
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Edda S F Matthees
- Institute of Molecular Cell Biology, University Hospital Jena, Friedrich Schiller University, Jena, Germany
| | - Philip Rößler
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Carsten Hoffmann
- Institute of Molecular Cell Biology, University Hospital Jena, Friedrich Schiller University, Jena, Germany.
| | - Alvar D Gossert
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zürich, Switzerland.
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2
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Fan L, Wang S. Biased GPCR Signaling: Possible Mechanisms and Therapeutic Applications. Biochemistry 2025; 64:1180-1192. [PMID: 40016120 DOI: 10.1021/acs.biochem.4c00827] [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] [Indexed: 03/01/2025]
Abstract
Biased signaling refers to the phenomenon where a ligand selectively activates specific downstream pathways of G protein-coupled receptors (GPCRs), such as the G protein-mediated pathway or the β-arrestin-mediated pathway. This mechanism can be influenced by receptor bias, ligand bias, system bias and spatial bias, all of which are shaped by the receptor's conformational distinctions and kinetics. Since GPCRs are the largest class of drug targets, signaling bias garnered significant attention for its potential to enhance therapeutic efficacy while minimizing side effects. Despite intensive investigation, a major challenge lies in translating in vitro ligand efficacy into in vivo biological responses due to the dynamic and multifaceted nature of the in vivo environment. This review delves into the current understanding of GPCR-biased signaling, examining the role of structural bias at the molecular level, the impact of kinetic context on system and observational bias, and the challenges of applying these insights in drug development. It further explores future directions for advancing biased signaling applications, offering valuable perspectives on how to bridge the gap between in vitro studies and in vivo therapeutic design, ultimately accelerating the development of viable, biased therapeutics.
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Affiliation(s)
- Luyu Fan
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Sheng Wang
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
- Key Laboratory of Multi-Cell Systems, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai 200031, China
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3
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Chung J, Hahn H, Flores-Espinoza E, Thomsen ARB. Artificial Intelligence: A New Tool for Structure-Based G Protein-Coupled Receptor Drug Discovery. Biomolecules 2025; 15:423. [PMID: 40149959 PMCID: PMC11940138 DOI: 10.3390/biom15030423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2025] [Revised: 03/10/2025] [Accepted: 03/11/2025] [Indexed: 03/29/2025] Open
Abstract
Understanding protein structures can facilitate the development of therapeutic drugs. Traditionally, protein structures have been determined through experimental approaches such as X-ray crystallography, NMR spectroscopy, and cryo-electron microscopy. While these methods are effective and are considered the gold standard, they are very resource-intensive and time-consuming, ultimately limiting their scalability. However, with recent developments in computational biology and artificial intelligence (AI), the field of protein prediction has been revolutionized. Innovations like AlphaFold and RoseTTAFold enable protein structure predictions to be made directly from amino acid sequences with remarkable speed and accuracy. Despite the enormous enthusiasm associated with these newly developed AI-approaches, their true potential in structure-based drug discovery remains uncertain. In fact, although these algorithms generally predict overall protein structures well, essential details for computational ligand docking, such as the exact location of amino acid side chains within the binding pocket, are not predicted with the necessary accuracy. Additionally, docking methodologies are considered more as a hypothesis generator rather than a precise predictor of ligand-target interactions, and thus, usually identify many false-positive hits among only a few correctly predicted interactions. In this paper, we are reviewing the latest development in this cutting-edge field with emphasis on the GPCR target class to assess the potential role of AI approaches in structure-based drug discovery.
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Affiliation(s)
- Jason Chung
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY 10010, USA; (J.C.); (H.H.); (E.F.-E.)
- NYU Pain Research Center, New York University College of Dentistry, New York, NY 10010, USA
| | - Hyunggu Hahn
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY 10010, USA; (J.C.); (H.H.); (E.F.-E.)
- NYU Pain Research Center, New York University College of Dentistry, New York, NY 10010, USA
| | - Emmanuel Flores-Espinoza
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY 10010, USA; (J.C.); (H.H.); (E.F.-E.)
- NYU Pain Research Center, New York University College of Dentistry, New York, NY 10010, USA
| | - Alex R. B. Thomsen
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY 10010, USA; (J.C.); (H.H.); (E.F.-E.)
- NYU Pain Research Center, New York University College of Dentistry, New York, NY 10010, USA
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4
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Jiang Q, Che T. How Ligands Achieve Biased Signaling toward Arrestins. Biochemistry 2025; 64:967-977. [PMID: 39943784 PMCID: PMC11936672 DOI: 10.1021/acs.biochem.4c00843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2025]
Abstract
G protein-coupled receptors (GPCRs) mediate the effects of various endogenous and extracellular stimuli through multiple transducers, including heterotrimeric G proteins, GPCR kinases (GRKs), and arrestins. Biased signaling, which preferentially activates certain G protein or GRK/arrestin signaling pathways, provides great opportunities for developing drugs with enhanced therapeutic efficacy and minimized side effects. In this Review, we review studies addressing the structural dynamics of GPCRs bound to balanced and biased ligands and current consensus on how ligand-receptor interactions determine signaling outcomes. We also examine the conformational changes in GPCRs when in complex with G proteins, arrestins, and GRKs, highlighting a more profound impact of signal transducers on receptor rearrangements compared with biased ligands. This evidence supports the idea that biased signaling can be achieved through the promotion of multiple conformational states by biased agonists and the stabilization of specific active conformations by individual signal transducers.
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Affiliation(s)
- Qianru Jiang
- Center for Clinical Pharmacology, Department of Anesthesiology, Washington University Medical School, Saint Louis, Missouri 63110, United States
| | - Tao Che
- Center for Clinical Pharmacology, Department of Anesthesiology, Washington University Medical School, Saint Louis, Missouri 63110, United States
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5
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Thompson MD, Chidiac P, Jose PA, Hauser AS, Gorvin CM. Genetic variants of accessory proteins and G proteins in human genetic disease. Crit Rev Clin Lab Sci 2025; 62:113-134. [PMID: 39743506 PMCID: PMC11854058 DOI: 10.1080/10408363.2024.2431853] [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: 10/16/2023] [Revised: 01/14/2024] [Accepted: 11/16/2024] [Indexed: 01/04/2025]
Abstract
We present a series of three articles on the genetics and pharmacogenetics of G protein- coupled receptors (GPCR). In the first article, we discuss genetic variants of the G protein subunits and accessory proteins that are associated with human phenotypes; in the second article, we build upon this to discuss "G protein-coupled receptor (GPCR) gene variants and human genetic disease" and in the third article, we survey "G protein-coupled receptor pharmacogenomics". In the present article, we review the processes of ligand binding, GPCR activation, inactivation, and receptor trafficking to the membrane in the context of human genetic disease resulting from pathogenic variants of accessory proteins and G proteins. Pathogenic variants of the genes encoding G protein α and β subunits are examined in diverse phenotypes. Variants in the genes encoding accessory proteins that modify or organize G protein coupling have been associated with disease; these include the contribution of variants of the regulator of G protein signaling (RGS) to hypertension; the role of variants of activator of G protein signaling type III in phenotypes such as hypoxia; the contribution of variation at the RGS10 gene to short stature and immunological compromise; and the involvement of variants of G protein-coupled receptor kinases (GRKs), such as GRK4, in hypertension. Variation in genes that encode proteins involved in GPCR signaling are outlined in the context of the changes in structure and function that may be associated with human phenotypes.
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Affiliation(s)
- Miles D. Thompson
- Krembil Brain Institute, Toronto Western Hospital, Toronto, Ontario, Canada
| | - Peter Chidiac
- Department of Physiology and Pharmacology, University of Western Ontario, London, Ontario, Canada
| | - Pedro A. Jose
- Division of Renal Diseases & Hypertension, Departments of Medicine and Pharmacology/Physiology, The George Washington University School of Medicine and Health Sciences, Washington, District of Columbia, USA
| | - Alexander S. Hauser
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Caroline M. Gorvin
- Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Birmingham, West Midlands, UK
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Schafer CT, Pauszek RF, Gustavsson M, Handel TM, Millar DP. Distinct Activation Mechanisms of CXCR4 and ACKR3 Revealed by Single-Molecule Analysis of their Conformational Landscapes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2023.10.31.564925. [PMID: 37961571 PMCID: PMC10635023 DOI: 10.1101/2023.10.31.564925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
The canonical chemokine receptor CXCR4 and atypical receptor ACKR3 both respond to CXCL12 but induce different effector responses to regulate cell migration. While CXCR4 couples to G proteins and directly promotes cell migration, ACKR3 is G protein-independent and scavenges CXCL12 to regulate extracellular chemokine levels and maintain CXCR4 responsiveness, thereby indirectly influencing migration. The receptors also have distinct activation requirements. CXCR4 only responds to wild-type CXCL12 and is sensitive to mutation of the chemokine. By contrast, ACKR3 recruits GPCR kinases (GRKs) and β-arrestins and promiscuously responds to CXCL12, CXCL12 variants, other peptides and proteins, and is relatively insensitive to mutation. To investigate the role of conformational dynamics in the distinct pharmacological behaviors of CXCR4 and ACKR3, we employed single-molecule FRET to track discrete conformational states of the receptors in real-time. The data revealed that apo-CXCR4 preferentially populates a high-FRET inactive state, while apo-ACKR3 shows little conformational preference and high transition probabilities among multiple inactive, intermediate and active conformations, consistent with its propensity for activation. Multiple active-like ACKR3 conformations are populated in response to agonists, compared to the single CXCR4 active-state. This and the markedly different conformational landscapes of the receptors suggest that activation of ACKR3 may be achieved by a broader distribution of conformational states than CXCR4. Much of the conformational heterogeneity of ACKR3 is linked to a single residue that differs between ACKR3 and CXCR4. The dynamic properties of ACKR3 may underly its inability to form productive interactions with G proteins that would drive canonical GPCR signaling.
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Affiliation(s)
- Christopher T. Schafer
- Skaggs School of Pharmacy and Pharmaceutical Sciences, Department of Pharmacology, University of California San Diego, La Jolla, CA 92037
| | - Raymond F. Pauszek
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037
| | - Martin Gustavsson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, Department of Pharmacology, University of California San Diego, La Jolla, CA 92037
| | - Tracy M. Handel
- Skaggs School of Pharmacy and Pharmaceutical Sciences, Department of Pharmacology, University of California San Diego, La Jolla, CA 92037
| | - David P. Millar
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037
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7
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Vishnivetskiy SA, Paul T, Gurevich EV, Gurevich VV. The Role of Individual Residues in the N-Terminus of Arrestin-1 in Rhodopsin Binding. Int J Mol Sci 2025; 26:715. [PMID: 39859432 PMCID: PMC11765510 DOI: 10.3390/ijms26020715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2024] [Revised: 01/06/2025] [Accepted: 01/08/2025] [Indexed: 01/27/2025] Open
Abstract
Sequences and three-dimensional structures of the four vertebrate arrestins are very similar, yet in sharp contrast to other subtypes, arrestin-1 demonstrates exquisite selectivity for the active phosphorylated form of its cognate receptor, rhodopsin. The N-terminus participates in receptor binding and serves as the anchor of the C-terminus, the release of which facilitates arrestin transition into a receptor-binding state. We tested the effects of substitutions of fourteen residues in the N-terminus of arrestin-1 on the binding to phosphorylated and unphosphorylated light-activated rhodopsin of wild-type protein and its enhanced mutant with C-terminal deletion that demonstrates higher binding to both functional forms of rhodopsin. Profound effects of mutations identified lysine-15 as the main phosphate sensor and phenylalanine-13 as the key anchor of the C-terminus. These residues are conserved in all arrestin subtypes. Substitutions of five other residues reduced arrestin-1 selectivity for phosphorylated rhodopsin, indicating that wild-type residues participate in fine-tuning of arrestin-1 binding. Differential effects of numerous substitutions in wild-type and an enhanced mutant arrestin-1 suggest that these two proteins bind rhodopsin differently.
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Affiliation(s)
- Sergey A. Vishnivetskiy
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA; (S.A.V.); (E.V.G.)
| | - Trishita Paul
- Department of Biomedical Engineering, Tulane University, New Orleans, LA 70118, USA;
| | - Eugenia V. Gurevich
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA; (S.A.V.); (E.V.G.)
| | - Vsevolod V. Gurevich
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA; (S.A.V.); (E.V.G.)
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8
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Azam M, Jastrzebska B. Mechanisms of Rhodopsin-Related Inherited Retinal Degeneration and Pharmacological Treatment Strategies. Cells 2025; 14:49. [PMID: 39791750 PMCID: PMC11720364 DOI: 10.3390/cells14010049] [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: 11/25/2024] [Revised: 12/18/2024] [Accepted: 12/21/2024] [Indexed: 01/12/2025] Open
Abstract
Retinitis pigmentosa (RP) is a hereditary disease characterized by progressive vision loss ultimately leading to blindness. This condition is initiated by mutations in genes expressed in retinal cells, resulting in the degeneration of rod photoreceptors, which is subsequently followed by the loss of cone photoreceptors. Mutations in various genes expressed in the retina are associated with RP. Among them, mutations in the rhodopsin gene (RHO) are the most common cause of this condition. Due to the involvement of numerous genes and multiple mutations in a single gene, RP is a highly heterogeneous disease making the development of effective treatments particularly challenging. The progression of this disease involves complex cellular responses to restore cellular homeostasis, including the unfolded protein response (UPR) signaling, autophagy, and various cell death pathways. These mechanisms, however, often fail to prevent photoreceptor cell degradation and instead contribute to cell death under certain conditions. Current research focuses on the pharmacological modulation of the components of these pathways and the direct stabilization of mutated receptors as potential treatment strategies. Despite these efforts, the intricate interplay between these mechanisms and the diverse causative mutations involved has hindered the development of effective treatments. Advancing our understanding of the interactions between photoreceptor cell death mechanisms and the specific genetic mutations driving RP is critical to accelerate the discovery and development of therapeutic strategies for this currently incurable disease.
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Affiliation(s)
- Maria Azam
- Department of Pharmacology, School of Medicine, Case Western Reserve University, 10900 Euclid Ave., Cleveland, OH 44106, USA
| | - Beata Jastrzebska
- Department of Pharmacology, School of Medicine, Case Western Reserve University, 10900 Euclid Ave., Cleveland, OH 44106, USA
- Cleveland Center for Membrane and Structural Biology, Case Western Reserve University, 10900 Euclid Ave., Cleveland, OH 44106, USA
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9
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Xie P, Li Y, Lamon G, Kuang H, Wang DN, Traaseth NJ. A fiducial-assisted strategy compatible with resolving small MFS transporter structures in multiple conformations using cryo-EM. Nat Commun 2025; 16:7. [PMID: 39746942 PMCID: PMC11695964 DOI: 10.1038/s41467-024-54986-5] [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: 04/26/2024] [Accepted: 11/24/2024] [Indexed: 01/04/2025] Open
Abstract
Advancements in cryo-EM have stimulated a revolution in structural biology. Yet, for membrane proteins near the cryo-EM size threshold of approximately 40 kDa, including transporters and G-protein coupled receptors, the absence of distinguishable structural features makes image alignment and structure determination a significant challenge. Furthermore, resolving more than one protein conformation within a sample, a major advantage of cryo-EM, represents an even greater degree of difficulty. Here, we describe a strategy for introducing a rigid fiducial marker (BRIL domain) at the C-terminus of membrane transporters from the Major Facilitator Superfamily (MFS) with AlphaFold2. This approach involves fusion of the last transmembrane domain helix of the target protein with the first helix of BRIL through a short poly-alanine linker to promote helicity. Combining this strategy with a BRIL-specific Fab, we elucidated four cryo-EM structures of the 42 kDa Staphylococcus aureus transporter NorA, three of which were derived from a single sample corresponding to inward-open, inward-occluded, and occluded conformations. Hence, this fusion construct facilitated experiments to characterize the conformational landscape of NorA and validated our design to position the BRIL/antibody pair in an orientation that avoids steric clash with the transporter. The latter was enabled through AlphaFold2 predictions, which minimized guesswork and reduced the need for screening several constructs. We further validated the suitability of the method to three additional MFS transporters (GlpT, Bmr, and Blt), results that supported a rigid linker between the transporter and BRIL. The successful application to four MFS proteins, the largest family of secondary transporters in nature, and analysis of predicted structures for the family indicates this strategy will be a valuable tool for studying other MFS members using cryo-EM.
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Affiliation(s)
- Pujun Xie
- Department of Chemistry, New York University, New York, NY, USA
| | - Yan Li
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA
| | - Gaëlle Lamon
- Department of Chemistry, New York University, New York, NY, USA
| | - Huihui Kuang
- Cryo-EM Core Laboratory, New York University School of Medicine, New York, NY, USA
| | - Da-Neng Wang
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA.
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10
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Li J, Inoue A, Manglik A, von Zastrow M. Role of the G protein-coupled receptor kinase 2/3 N terminus in discriminating the endocytic effects of opioid agonist drugs. Mol Pharmacol 2025; 107:100003. [PMID: 39919161 DOI: 10.1124/molpharm.124.000951] [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: 05/13/2024] [Revised: 10/23/2024] [Accepted: 10/28/2024] [Indexed: 11/08/2024] Open
Abstract
Endocytosis of the μ-type opioid receptor (MOR) is a fundamentally important cellular regulatory process that is characteristically driven less effectively by partial relative to full agonist ligands. Such agonist-selective endocytic discrimination depends on how strongly drugs promote MOR binding to β-arrestins, and this, in turn, depends on how strongly they stimulate phosphorylation of the MOR cytoplasmic tail by G protein-coupled receptor kinases (GRKs) from the GRK2/3 subfamily. While these relatively "downstream" steps in the agonist selective endocytic pathway are now well defined, it remains unclear how agonist-bound receptors are distinguished "upstream" by GRKs. Focusing on GRK2 as a prototype, we show that this single GRK subtype can distinguish the endocytic activities of different MOR agonists in cells lacking other GRKs and that agonist selectivity is introduced at the most upstream step of GRK2 binding to MOR. This interaction requires prior membrane recruitment of GRK2 by its conserved Pleckstrin homology domain and is enhanced by phosphorylation of the MOR tail, but neither reaction can explain the high degree of agonist selectivity in the observed interaction of GRK2 with MOR. We identify the N-terminal domain (NTD) of GRK2, which is identical in GRK3, as a discrete element required for the full agonist selectivity of MOR-GRK2 interaction and show that the NTD is also required for GRK2 to promote MOR endocytosis after it is bound. We propose a simple cellular mechanism of upstream agonist discrimination that is organized as a series of biochemical checkpoints and uses the NTD as an agonist-selective sensor. SIGNIFICANCE STATEMENT: This study investigates how G protein-coupled receptor kinases (GRKs) distinguish the effects of opioid agonist drugs on regulated endocytosis of the μ-type opioid receptor (MOR). It shows that a single GRK subtype is sufficient to determine the agonist selectivity of MOR internalization, agonists are distinguished by how strongly they promote GRK2 recruitment by MOR, and the GRK2/3 N terminus is a key determinant of agonist discrimination.
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Affiliation(s)
- Joy Li
- Tetrad Graduate Program, Department of Biochemistry and Biophysics, University of California San Francisco School of Medicine, San Francisco, California, USA; Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California, USA; Department of Psychiatry and Behavioral Sciences, University of California San Francisco, San Francisco, California, USA; Quantitative Biology Institute, University of California San Francisco, San Francisco, California, USA
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, Aoba-ku, Sendai, Miyagi, Japan; Graduate School of Pharmaceutical Sciences, Kyoto University, Yoshida-Shimo-Adachi-cho, Sakyo-ku, Kyoto, Japan
| | - Aashish Manglik
- Quantitative Biology Institute, University of California San Francisco, San Francisco, California, USA; Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA; Department of Anesthesia and Perioperative Care, University of California San Francisco, San Francisco, California, USA
| | - Mark von Zastrow
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California, USA; Department of Psychiatry and Behavioral Sciences, University of California San Francisco, San Francisco, California, USA; Quantitative Biology Institute, University of California San Francisco, San Francisco, California, USA.
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11
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Petrovic I, Grzesiek S, Isaikina P. Advances in the molecular understanding of GPCR-arrestin complexes. Biochem Soc Trans 2024; 52:2333-2342. [PMID: 39508463 DOI: 10.1042/bst20240170] [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: 07/16/2024] [Revised: 09/17/2024] [Accepted: 10/07/2024] [Indexed: 11/15/2024]
Abstract
Arrestins are essential proteins for the regulation of G protein-coupled receptors (GPCRs). They mediate GPCR desensitization after the activated receptor has been phosphorylated by G protein receptor kinases (GRKs). In addition, GPCR-arrestin interactions may trigger signaling pathways that are distinct and independent from G proteins. The non-visual GPCRs encompass hundreds of receptors with varying phosphorylation patterns and amino acid sequences, which are regulated by only two human non-visual arrestin isoforms. This review describes recent findings on GPCR-arrestin complexes, obtained by structural techniques, biophysical, biochemical, and cellular assays. The solved structures of complete GPCR-arrestin complexes are of limited resolution ranging from 3.2 to 4.7 Å and reveal a high variability in the relative receptor-arrestin orientation. In contrast, biophysical and functional data indicate that arrestin recruitment, activation and GPCR-arrestin complex stability depend on the receptor phosphosite sequence patterns and density. At present, there is still a manifest lack of high-resolution structural and dynamical information on the interactions of native GPCRs with both GRKs and arrestins, which could provide a detailed molecular understanding of the genesis of receptor phosphorylation patterns and the specificity GPCR-arrestin interactions. Such insights seem crucial for progress in the rational design of advanced, arrestin-specific therapeutics.
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Affiliation(s)
- Ivana Petrovic
- Biozentrum, University of Basel, CH-4056 Basel, Switzerland
| | | | - Polina Isaikina
- Center for Life Sciences, Paul Scherrer Institut, CH-5232 Villigen, Switzerland
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12
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Fouillen A, Couvineau P, Gaibelet G, Riché S, Orcel H, Mendre C, Kanso A, Lanotte R, Nguyen J, Dimon J, Urbach S, Sounier R, Granier S, Bonnet D, Cong X, Mouillac B, Déméné H. Biased activation of the vasopressin V2 receptor probed by molecular dynamics simulations, NMR and pharmacological studies. Comput Struct Biotechnol J 2024; 23:3784-3799. [PMID: 39525085 PMCID: PMC11550766 DOI: 10.1016/j.csbj.2024.10.039] [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: 07/15/2024] [Revised: 10/22/2024] [Accepted: 10/22/2024] [Indexed: 11/16/2024] Open
Abstract
G protein-coupled receptors (GPCRs) control critical cell signaling. Their response to extracellular stimuli involves conformational changes to convey signals to intracellular effectors, among which the most important are G proteins and β-arrestins (βArrs). Biased activation of one pathway is a field of intense research in GPCR pharmacology. Combining NMR, site-directed mutagenesis, molecular pharmacology, and molecular dynamics (MD) simulations, we studied the conformational diversity of the vasopressin V2 receptor (V2R) bound to different types of ligands: the antagonist Tolvaptan, the endogenous unbiased agonist arginine-vasopressin, and MCF14, a partial Gs protein-biased agonist. A double-labeling NMR scheme was developed to study the receptor conformational changes and ligand binding: V2R was subjected to lysine 13CH3 methylation for complementary NMR studies, whereas the agonists were tagged with a paramagnetic probe. Paramagnetic relaxation enhancements and site-directed mutagenesis validated the ligand binding modes in the MD simulations. We found that the bias for the Gs protein over the βArr pathway involves interactions between the conserved NPxxY motif in the transmembrane helix 7 (TM7) and TM3, compacting helix 8 (H8) toward TM1 and likely inhibiting βArr signaling. A similar mechanism was elicited for the pathogenic mutation I130N, which constitutively activates the Gs proteins without concomitant βArr recruitment. The findings suggest common patterns of biased signaling in class A GPCRs, as well as a rationale for the design of G protein-biased V2R agonists.
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Affiliation(s)
- Aurélien Fouillen
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, 34094 Montpellier, France
| | - Pierre Couvineau
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, 34094 Montpellier, France
| | - Gérald Gaibelet
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, 34094 Montpellier, France
| | - Stéphanie Riché
- Laboratoire d’Innovation Thérapeutique, UMR7200 CNRS, Université de Strasbourg, Institut du Médicament de Strasbourg, 67412 Illkirch-Graffenstaden, France
| | - Hélène Orcel
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, 34094 Montpellier, France
| | - Christiane Mendre
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, 34094 Montpellier, France
| | - Ali Kanso
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, 34094 Montpellier, France
| | - Romain Lanotte
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, 34094 Montpellier, France
| | - Julie Nguyen
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, 34094 Montpellier, France
| | - Juliette Dimon
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, 34094 Montpellier, France
| | - Serge Urbach
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, 34094 Montpellier, France
| | - Rémy Sounier
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, 34094 Montpellier, France
| | - Sébastien Granier
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, 34094 Montpellier, France
| | - Dominique Bonnet
- Laboratoire d’Innovation Thérapeutique, UMR7200 CNRS, Université de Strasbourg, Institut du Médicament de Strasbourg, 67412 Illkirch-Graffenstaden, France
| | - Xiaojing Cong
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, 34094 Montpellier, France
| | - Bernard Mouillac
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, 34094 Montpellier, France
| | - Hélène Déméné
- Centre de Biologie Structurale (CBS), Univ Montpellier, INSERM, CNRS, 34090, Montpellier, France
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13
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Steiner WP, Iverson N, Venkatakrishnan V, Wu J, Stepniewski TM, Michaelson Z, Bröckel JW, Zhu JF, Bruystens J, Lee A, Nelson I, Bertinetti D, Arveseth CD, Tan G, Spaltenstein P, Xu J, Hüttenhain R, Kay M, Herberg FW, Selent J, Anand GS, Dunbrack RL, Taylor SS, Myers BR. A Structural Mechanism for Noncanonical GPCR Signal Transduction in the Hedgehog Pathway. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.31.621410. [PMID: 39554190 PMCID: PMC11565934 DOI: 10.1101/2024.10.31.621410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/19/2024]
Abstract
The Hedgehog (Hh) signaling pathway is fundamental to embryogenesis, tissue homeostasis, and cancer. Hh signals are transduced via an unusual mechanism: upon agonist-induced phosphorylation, the noncanonical G protein-coupled receptor SMOOTHENED (SMO) binds the catalytic subunit of protein kinase A (PKA-C) and physically blocks its enzymatic activity. By combining computational structural approaches with biochemical and functional studies, we show that SMO mimics strategies prevalent in canonical GPCR and PKA signaling complexes, despite little sequence or secondary structural homology. An intrinsically disordered region of SMO binds the PKA-C active site, resembling the PKA regulatory subunit (PKA-R) / PKA-C holoenzyme, while the SMO transmembrane domain binds a conserved PKA-C interaction hub, similar to other GPCR-effector complexes. In contrast with prevailing GPCR signal transduction models, phosphorylation of SMO promotes intramolecular electrostatic interactions that stabilize key structural elements within the SMO cytoplasmic domain, thereby remodeling it into a PKA-inhibiting conformation. Our work provides a structural mechanism for a central step in the Hh cascade and defines a paradigm for disordered GPCR domains to transmit signals intracellularly.
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Affiliation(s)
- William P. Steiner
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
- Department of Bioengineering, University of Utah, Salt Lake City, UT, USA
| | - Nathan Iverson
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
- Department of Bioengineering, University of Utah, Salt Lake City, UT, USA
| | | | - Jian Wu
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Tomasz Maciej Stepniewski
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM) – Pompeu Fabra University (UPF), Dr Aiguader 88, Barcelona, Spain
- InterAx Biotech AG, Villigen, Switzerland
| | - Zachary Michaelson
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
- Department of Bioengineering, University of Utah, Salt Lake City, UT, USA
| | - Jan W. Bröckel
- Institute for Biology, Department of Biochemistry, University of Kassel, Kassel, Germany
| | - Ju-Fen Zhu
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
- Department of Bioengineering, University of Utah, Salt Lake City, UT, USA
| | - Jessica Bruystens
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Annabel Lee
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
- Department of Bioengineering, University of Utah, Salt Lake City, UT, USA
| | - Isaac Nelson
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
- Department of Bioengineering, University of Utah, Salt Lake City, UT, USA
| | - Daniela Bertinetti
- Institute for Biology, Department of Biochemistry, University of Kassel, Kassel, Germany
| | - Corvin D. Arveseth
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
- Department of Bioengineering, University of Utah, Salt Lake City, UT, USA
| | - Gerald Tan
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
| | - Paul Spaltenstein
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Jiewei Xu
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
| | - Ruth Hüttenhain
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael Kay
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Friedrich W. Herberg
- Institute for Biology, Department of Biochemistry, University of Kassel, Kassel, Germany
| | - Jana Selent
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM) – Pompeu Fabra University (UPF), Dr Aiguader 88, Barcelona, Spain
| | - Ganesh S. Anand
- Department of Chemistry, Pennsylvania State University, University Park, PA, USA
- The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Roland L. Dunbrack
- Institute for Cancer Research. Fox Chase Cancer Center. Philadelphia PA, USA
| | - Susan S. Taylor
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Benjamin R. Myers
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
- Department of Bioengineering, University of Utah, Salt Lake City, UT, USA
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14
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Navarro G, Gómez-Autet M, Morales P, Rebassa JB, Llinas Del Torrent C, Jagerovic N, Pardo L, Franco R. Homodimerization of CB 2 cannabinoid receptor triggered by a bivalent ligand enhances cellular signaling. Pharmacol Res 2024; 208:107363. [PMID: 39179054 DOI: 10.1016/j.phrs.2024.107363] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Revised: 08/17/2024] [Accepted: 08/18/2024] [Indexed: 08/26/2024]
Abstract
G protein-coupled receptors (GPCRs) exist within a landscape of interconvertible conformational states and in dynamic equilibrium between monomers and higher-order oligomers, both influenced by ligand binding. Here, we show that a homobivalent ligand formed by equal chromenopyrazole moieties as pharmacophores, connected by 14 methylene units, can modulate the dynamics of the cannabinoid CB2 receptor (CB2R) homodimerization by simultaneously binding both protomers of the CB2R-CB2R homodimer. Computational and pharmacological experiments showed that one of the ligand pharmacophores binds to the orthosteric site of one protomer, and the other pharmacophore to a membrane-oriented pocket between transmembranes 1 and 7 of the partner protomer. This results in unique pharmacological properties, including increased potency in Gi-mediated signaling and enhanced recruitment of β-arrestin. Thus, by modulating dimerization dynamics, it may be possible to fine-tune CB2R activity, potentially leading to improved therapeutic outcomes.
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Affiliation(s)
- Gemma Navarro
- Department of Biochemistry and Physiology. Faculty of Pharmacy and Food Sciences. Universitat de Barcelona, Barcelona 08028, Spain; Institute of Neuroscience, University of Barcelona (NeuroUB), Barcelona 08035, Spain; Centro de Investigación en Red, Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid 28031, Spain
| | - Marc Gómez-Autet
- Laboratory of Computational Medicine, Biostatistics Unit, Faculty of Medicine, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Paula Morales
- Medicinal Chemistry Institute, Spanish National Research Council, CSIC, Madrid 28006, Spain
| | - Joan Biel Rebassa
- Department of Biochemistry and Physiology. Faculty of Pharmacy and Food Sciences. Universitat de Barcelona, Barcelona 08028, Spain; Institute of Neuroscience, University of Barcelona (NeuroUB), Barcelona 08035, Spain
| | - Claudia Llinas Del Torrent
- Laboratory of Computational Medicine, Biostatistics Unit, Faculty of Medicine, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Nadine Jagerovic
- Medicinal Chemistry Institute, Spanish National Research Council, CSIC, Madrid 28006, Spain.
| | - Leonardo Pardo
- Laboratory of Computational Medicine, Biostatistics Unit, Faculty of Medicine, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain.
| | - Rafael Franco
- Centro de Investigación en Red, Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid 28031, Spain; Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, Barcelona 08028, Spain.
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15
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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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16
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Saha S, Khanppnavar B, Maharana J, Kim H, Carino CMC, Daly C, Houston S, Sharma S, Zaidi N, Dalal A, Mishra S, Ganguly M, Tiwari D, Kumari P, Jhingan GD, Yadav PN, Plouffe B, Inoue A, Chung KY, Banerjee R, Korkhov VM, Shukla AK. Molecular mechanism of distinct chemokine engagement and functional divergence of the human Duffy antigen receptor. Cell 2024; 187:4751-4769.e25. [PMID: 39089252 PMCID: PMC11349380 DOI: 10.1016/j.cell.2024.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 04/13/2024] [Accepted: 07/03/2024] [Indexed: 08/03/2024]
Abstract
The Duffy antigen receptor is a seven-transmembrane (7TM) protein expressed primarily at the surface of red blood cells and displays strikingly promiscuous binding to multiple inflammatory and homeostatic chemokines. It serves as the basis of the Duffy blood group system in humans and also acts as the primary attachment site for malarial parasite Plasmodium vivax and pore-forming toxins secreted by Staphylococcus aureus. Here, we comprehensively profile transducer coupling of this receptor, discover potential non-canonical signaling pathways, and determine the cryoelectron microscopy (cryo-EM) structure in complex with the chemokine CCL7. The structure reveals a distinct binding mode of chemokines, as reflected by relatively superficial binding and a partially formed orthosteric binding pocket. We also observe a dramatic shortening of TM5 and 6 on the intracellular side, which precludes the formation of the docking site for canonical signal transducers, thereby providing a possible explanation for the distinct pharmacological and functional phenotype of this receptor.
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Affiliation(s)
- Shirsha Saha
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Basavraj Khanppnavar
- Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, Switzerland; Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Jagannath Maharana
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Heeryung Kim
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Carlo Marion C Carino
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Carole Daly
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, UK
| | - Shane Houston
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, UK
| | - Saloni Sharma
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Nashrah Zaidi
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Annu Dalal
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Sudha Mishra
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Manisankar Ganguly
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Divyanshu Tiwari
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Poonam Kumari
- Division of Neuroscience and Ageing Biology, CSIR-Central Drug Research Institute, Lucknow, India
| | | | - Prem N Yadav
- Division of Neuroscience and Ageing Biology, CSIR-Central Drug Research Institute, Lucknow, India
| | - Bianca Plouffe
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, UK
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Ka Young Chung
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Ramanuj Banerjee
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016, India.
| | - Volodymyr M Korkhov
- Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, Switzerland; Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland.
| | - Arun K Shukla
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016, India.
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17
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Underwood O, Fritzwanker S, Glenn J, Blum NK, Batista-Gondin A, Drube J, Hoffmann C, Briddon SJ, Schulz S, Canals M. Key phosphorylation sites for robust β-arrestin2 binding at the MOR revisited. Commun Biol 2024; 7:933. [PMID: 39095612 PMCID: PMC11297201 DOI: 10.1038/s42003-024-06571-1] [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: 01/09/2024] [Accepted: 07/09/2024] [Indexed: 08/04/2024] Open
Abstract
Desensitisation of the mu-opioid receptor (MOR) is proposed to underlie the initiation of opioid analgesic tolerance and previous work has shown that agonist-induced phosphorylation of the MOR C-tail contributes to this desensitisation. Moreover, phosphorylation is important for β-arrestin recruitment to the receptor, and ligands of different efficacies induce distinct phosphorylation barcodes. The C-tail 370TREHPSTANT379 motif harbours Ser/Thr residues important for these regulatory functions. 375Ser is the primary phosphorylation site of a ligand-dependent, hierarchical, and sequential process, whereby flanking 370Thr, 376Thr and 379Thr get subsequently and rapidly phosphorylated. Here we used GRK KO cells, phosphosite specific antibodies and site-directed mutagenesis to evaluate the contribution of the different GRK subfamilies to ligand-induced phosphorylation barcodes and β-arrestin2 recruitment. We show that both GRK2/3 and GRK5/6 subfamilies promote phosphorylation of 370Thr and 375Ser. Importantly, only GRK2/3 induce phosphorylation of 376Thr and 379Thr, and we identify these residues as key sites to promote robust β-arrestin recruitment to the MOR. These data provide insight into the mechanisms of MOR regulation and suggest that the cellular complement of GRK subfamilies plays an important role in determining the tissue responses of opioid agonists.
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Affiliation(s)
- Owen Underwood
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, UK
- Centre of Membrane Proteins and Receptors (COMPARE), Universities of Nottingham and Birmingham, Birmingham, Midlands, UK
| | - Sebastian Fritzwanker
- Institut für Pharmakologie und Toxikologie, Universitätsklinikum Jena, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - Jaqueline Glenn
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, UK
- Centre of Membrane Proteins and Receptors (COMPARE), Universities of Nottingham and Birmingham, Birmingham, Midlands, UK
| | - Nina Kathleen Blum
- Institut für Pharmakologie und Toxikologie, Universitätsklinikum Jena, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - Arisbel Batista-Gondin
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Victoria, Australia
| | - Julia Drube
- Institut fur Molekulare Zellbiologie, CMB - Center for Molecular Biomedicine, Universitätsklinikum Jena, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - Carsten Hoffmann
- Institut fur Molekulare Zellbiologie, CMB - Center for Molecular Biomedicine, Universitätsklinikum Jena, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - Stephen J Briddon
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, UK
- Centre of Membrane Proteins and Receptors (COMPARE), Universities of Nottingham and Birmingham, Birmingham, Midlands, UK
| | - Stefan Schulz
- Institut für Pharmakologie und Toxikologie, Universitätsklinikum Jena, Friedrich-Schiller-Universität Jena, Jena, Germany
- 7TM Antibodies GmbH, Hans-Knöll-Straße 6, D-07745, Jena, Germany
| | - Meritxell Canals
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, UK.
- Centre of Membrane Proteins and Receptors (COMPARE), Universities of Nottingham and Birmingham, Birmingham, Midlands, UK.
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18
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Walker MF, Zhang J, Steiner W, Ku PI, Zhu JF, Michaelson Z, Yen YC, Lee A, Long AB, Casey MJ, Poddar A, Nelson IB, Arveseth CD, Nagel F, Clough R, LaPotin S, Kwan KM, Schulz S, Stewart RA, Tesmer JJG, Caspary T, Subramanian R, Ge X, Myers BR. GRK2 kinases in the primary cilium initiate SMOOTHENED-PKA signaling in the Hedgehog cascade. PLoS Biol 2024; 22:e3002685. [PMID: 39138140 PMCID: PMC11322411 DOI: 10.1371/journal.pbio.3002685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 05/21/2024] [Indexed: 08/15/2024] Open
Abstract
During Hedgehog (Hh) signal transduction in development and disease, the atypical G protein-coupled receptor (GPCR) SMOOTHENED (SMO) communicates with GLI transcription factors by binding the protein kinase A catalytic subunit (PKA-C) and physically blocking its enzymatic activity. Here, we show that GPCR kinase 2 (GRK2) orchestrates this process during endogenous mouse and zebrafish Hh pathway activation in the primary cilium. Upon SMO activation, GRK2 rapidly relocalizes from the ciliary base to the shaft, triggering SMO phosphorylation and PKA-C interaction. Reconstitution studies reveal that GRK2 phosphorylation enables active SMO to bind PKA-C directly. Lastly, the SMO-GRK2-PKA pathway underlies Hh signal transduction in a range of cellular and in vivo models. Thus, GRK2 phosphorylation of ciliary SMO and the ensuing PKA-C binding and inactivation are critical initiating events for the intracellular steps in Hh signaling. More broadly, our study suggests an expanded role for GRKs in enabling direct GPCR interactions with diverse intracellular effectors.
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Affiliation(s)
- Madison F. Walker
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
- Department of Bioengineering, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Jingyi Zhang
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California, Merced, California, United States of America
| | - William Steiner
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
- Department of Bioengineering, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Pei-I Ku
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Ju-Fen Zhu
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
- Department of Bioengineering, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Zachary Michaelson
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
- Department of Bioengineering, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Yu-Chen Yen
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America
| | - Annabel Lee
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
- Department of Bioengineering, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Alyssa B. Long
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Mattie J. Casey
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Abhishek Poddar
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Isaac B. Nelson
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
- Department of Bioengineering, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Corvin D. Arveseth
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
- Department of Bioengineering, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | | | - Ryan Clough
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Sarah LaPotin
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Kristen M. Kwan
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Stefan Schulz
- 7TM Antibodies GmbH, Jena, Germany
- Institute of Pharmacology and Toxicology, University Hospital Jena, Jena, Germany
| | - Rodney A. Stewart
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - John J. G. Tesmer
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana, United States of America
| | - Tamara Caspary
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Radhika Subramanian
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Xuecai Ge
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California, Merced, California, United States of America
| | - Benjamin R. Myers
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
- Department of Bioengineering, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
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19
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Trogdon M, Abbott K, Arang N, Lande K, Kaur N, Tong M, Bakhoum M, Gutkind JS, Stites EC. Systems modeling of oncogenic G-protein and GPCR signaling reveals unexpected differences in downstream pathway activation. NPJ Syst Biol Appl 2024; 10:75. [PMID: 39013872 PMCID: PMC11252164 DOI: 10.1038/s41540-024-00400-1] [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: 07/12/2023] [Accepted: 06/27/2024] [Indexed: 07/18/2024] Open
Abstract
Mathematical models of biochemical reaction networks are an important and emerging tool for the study of cell signaling networks involved in disease processes. One promising potential application of such mathematical models is the study of how disease-causing mutations promote the signaling phenotype that contributes to the disease. It is commonly assumed that one must have a thorough characterization of the network readily available for mathematical modeling to be useful, but we hypothesized that mathematical modeling could be useful when there is incomplete knowledge and that it could be a tool for discovery that opens new areas for further exploration. In the present study, we first develop a mechanistic mathematical model of a G-protein coupled receptor signaling network that is mutated in almost all cases of uveal melanoma and use model-driven explorations to uncover and explore multiple new areas for investigating this disease. Modeling the two major, mutually-exclusive, oncogenic mutations (Gαq/11 and CysLT2R) revealed the potential for previously unknown qualitative differences between seemingly interchangeable disease-promoting mutations, and our experiments confirmed oncogenic CysLT2R was impaired at activating the FAK/YAP/TAZ pathway relative to Gαq/11. This led us to hypothesize that CYSLTR2 mutations in UM must co-occur with other mutations to activate FAK/YAP/TAZ signaling, and our bioinformatic analysis uncovers a role for co-occurring mutations involving the plexin/semaphorin pathway, which has been shown capable of activating this pathway. Overall, this work highlights the power of mechanism-based computational systems biology as a discovery tool that can leverage available information to open new research areas.
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Affiliation(s)
- Michael Trogdon
- Integrative Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
- Pfizer, La Jolla, CA, 92037, USA
| | - Kodye Abbott
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Nadia Arang
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, 92093, USA
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Kathryn Lande
- Razavi Newman Integrative Genomics and Bioinformatics Core, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Navneet Kaur
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Melinda Tong
- Integrative Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Mathieu Bakhoum
- Department of Ophthalmology and Visual Science, Yale School of Medicine, New Haven, CT, 06520, USA
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, 06520, USA
| | - J Silvio Gutkind
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Edward C Stites
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, 06520, USA.
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, 06520, USA.
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20
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Gurevich VV. Arrestins: A Small Family of Multi-Functional Proteins. Int J Mol Sci 2024; 25:6284. [PMID: 38892473 PMCID: PMC11173308 DOI: 10.3390/ijms25116284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 05/24/2024] [Accepted: 05/31/2024] [Indexed: 06/21/2024] Open
Abstract
The first member of the arrestin family, visual arrestin-1, was discovered in the late 1970s. Later, the other three mammalian subtypes were identified and cloned. The first described function was regulation of G protein-coupled receptor (GPCR) signaling: arrestins bind active phosphorylated GPCRs, blocking their coupling to G proteins. It was later discovered that receptor-bound and free arrestins interact with numerous proteins, regulating GPCR trafficking and various signaling pathways, including those that determine cell fate. Arrestins have no enzymatic activity; they function by organizing multi-protein complexes and localizing their interaction partners to particular cellular compartments. Today we understand the molecular mechanism of arrestin interactions with GPCRs better than the mechanisms underlying other functions. However, even limited knowledge enabled the construction of signaling-biased arrestin mutants and extraction of biologically active monofunctional peptides from these multifunctional proteins. Manipulation of cellular signaling with arrestin-based tools has research and likely therapeutic potential: re-engineered proteins and their parts can produce effects that conventional small-molecule drugs cannot.
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21
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Verma S, Singh V, Nagampalli V, Ponsky LE, Li CSR, Chao H, Gupta S. Ligand-gated ion channels as potential biomarkers for ADT-mediated cognitive decline in prostate cancer patients. Mol Carcinog 2024; 63:1051-1063. [PMID: 38482990 PMCID: PMC11096008 DOI: 10.1002/mc.23708] [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: 11/27/2023] [Revised: 02/01/2024] [Accepted: 02/13/2024] [Indexed: 05/16/2024]
Abstract
Men with prostate cancer are at increased risk of developing cognitive decline by the use of second-generation androgen signaling inhibitors. To date, reliable and sensitive biomarkers that could distinguish men at high risk of cognitive dysfunction under androgen deprivation therapy (ADT) have not been characterized. We used high-throughput transcriptional profiling utilizing human prostate cancer cell culture models mimicking ADT, biomarker selection using minimal common oncology data elements-cytoscape, and bioinformatic analyses employing Advaita® iPathwayGuide and DisGeNET for identification of disease-related gene associations. Validation analysis of genes was performed on brain neuronal and glial cells by quantitative real-time polymerase chain reaction assay. Our systematic analysis of androgen deprivation-associated genes involved multiple biological processes, including neuroactive ligand-receptor interaction, axon guidance, cytokine-cytokine receptor interaction, and metabolic and cancer signaling pathways. Genes associated with neuroreceptor ligand interaction, including gamma-aminobutyric acid (GABA) A and B receptors and nuclear core proteins, were identified as top upstream regulators. Functional enrichment and protein-protein interaction network analysis highlighted the role of ligand-gated ion channels (LGICs) and their receptors in cognitive dysfunction. Gene-disease association assigned forgetfulness, intellectual disability, visuospatial deficit, bipolar disorder, and other neurocognitive impairment with upregulation of type-1 angiotensin II receptor, brain-derived neurotrophic factor, GABA type B receptor subunit 2 (GABBR2), GABRA3, GABRA5, GABRB1, glycine receptor beta, glutamate ionotropic receptor N-methyl-D-aspartate receptor (NMDA) type subunit 1, glutamate ionotropic receptor NMDA type subunit 2D, 5-hydroxytryptamine receptor 1D, interferon beta 1, and nuclear receptor subfamily 3 group C member 1 as top differentially expressed genes. Validation studies of brain glial cells, neurons, and patients on ADT demonstrated the association of these genes with cognitive decline. Our findings highlight LGICs as potential biomarkers for ADT-mediated cognitive decline. Further validation of these biomarkers may lead to future practical clinical use.
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Affiliation(s)
- Shiv Verma
- Department of Urology, Case Western Reserve University, School of Medicine, Cleveland, OH 44106, USA
- The Urology Institute, University Hospitals Cleveland Medical Center, Cleveland, OH 44106 USA
| | - Vaibhav Singh
- Department of Pathology, Case Western Reserve University, School of Medicine, Cleveland, OH 44106, USA
| | | | - Lee E Ponsky
- Department of Urology, Case Western Reserve University, School of Medicine, Cleveland, OH 44106, USA
- The Urology Institute, University Hospitals Cleveland Medical Center, Cleveland, OH 44106 USA
| | - Chiang-Shan R Li
- Department of Psychiatry and of Neuroscience, Yale University School of Medicine, New Haven, CT 06519
| | - Herta Chao
- Department of Medicine & Yale Comprehensive Cancer Center, Yale University, New Haven, CT 06510, USA
| | - Sanjay Gupta
- Department of Urology, Case Western Reserve University, School of Medicine, Cleveland, OH 44106, USA
- The Urology Institute, University Hospitals Cleveland Medical Center, Cleveland, OH 44106 USA
- Department of Pathology, Case Western Reserve University, School of Medicine, Cleveland, OH 44106, USA
- Department of Pharmacology, Case Western Reserve University, School of Medicine, Cleveland, OH 44106, USA
- Department of Nutrition, Case Western Reserve University, School of Medicine, Cleveland, OH 44106, USA
- Division of General Medical Sciences, Case Comprehensive Cancer Center, Cleveland, OH 44106 USA
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22
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Duan J, He XH, Li SJ, Xu HE. Cryo-electron microscopy for GPCR research and drug discovery in endocrinology and metabolism. Nat Rev Endocrinol 2024; 20:349-365. [PMID: 38424377 DOI: 10.1038/s41574-024-00957-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/29/2024] [Indexed: 03/02/2024]
Abstract
G protein-coupled receptors (GPCRs) are the largest family of cell surface receptors, with many GPCRs having crucial roles in endocrinology and metabolism. Cryogenic electron microscopy (cryo-EM) has revolutionized the field of structural biology, particularly regarding GPCRs, over the past decade. Since the first pair of GPCR structures resolved by cryo-EM were published in 2017, the number of GPCR structures resolved by cryo-EM has surpassed the number resolved by X-ray crystallography by 30%, reaching >650, and the number has doubled every ~0.63 years for the past 6 years. At this pace, it is predicted that the structure of 90% of all human GPCRs will be completed within the next 5-7 years. This Review highlights the general structural features and principles that guide GPCR ligand recognition, receptor activation, G protein coupling, arrestin recruitment and regulation by GPCR kinases. The Review also highlights the diversity of GPCR allosteric binding sites and how allosteric ligands could dictate biased signalling that is selective for a G protein pathway or an arrestin pathway. Finally, the authors use the examples of glycoprotein hormone receptors and glucagon-like peptide 1 receptor to illustrate the effect of cryo-EM on understanding GPCR biology in endocrinology and metabolism, as well as on GPCR-related endocrine diseases and drug discovery.
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Affiliation(s)
- Jia Duan
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, China.
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Xin-Heng He
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shu-Jie Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- Department of Traditional Chinese Medicine, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
| | - H Eric Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
- University of Chinese Academy of Sciences, Beijing, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
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23
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Vlasova AD, Bukhalovich SM, Bagaeva DF, Polyakova AP, Ilyinsky NS, Nesterov SV, Tsybrov FM, Bogorodskiy AO, Zinovev EV, Mikhailov AE, Vlasov AV, Kuklin AI, Borshchevskiy VI, Bamberg E, Uversky VN, Gordeliy VI. Intracellular microbial rhodopsin-based optogenetics to control metabolism and cell signaling. Chem Soc Rev 2024; 53:3327-3349. [PMID: 38391026 DOI: 10.1039/d3cs00699a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
Microbial rhodopsin (MRs) ion channels and pumps have become invaluable optogenetic tools for neuroscience as well as biomedical applications. Recently, MR-optogenetics expanded towards subcellular organelles opening principally new opportunities in optogenetic control of intracellular metabolism and signaling via precise manipulations of organelle ion gradients using light. This new optogenetic field expands the opportunities for basic and medical studies of cancer, cardiovascular, and metabolic disorders, providing more detailed and accurate control of cell physiology. This review summarizes recent advances in studies of the cellular metabolic processes and signaling mediated by optogenetic tools targeting mitochondria, endoplasmic reticulum (ER), lysosomes, and synaptic vesicles. Finally, we discuss perspectives of such an optogenetic approach in both fundamental and applied research.
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Affiliation(s)
- Anastasiia D Vlasova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Siarhei M Bukhalovich
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Diana F Bagaeva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Aleksandra P Polyakova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Nikolay S Ilyinsky
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Semen V Nesterov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Fedor M Tsybrov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Andrey O Bogorodskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Egor V Zinovev
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Anatolii E Mikhailov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Alexey V Vlasov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna, Russia
| | - Alexander I Kuklin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna, Russia
| | - Valentin I Borshchevskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna, Russia
| | - Ernst Bamberg
- Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Vladimir N Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.
| | - Valentin I Gordeliy
- Institut de Biologie Structurale Jean-Pierre Ebel, Université Grenoble Alpes-Commissariat à l'Energie Atomique et aux Energies Alternatives-CNRS, 38027 Grenoble, France.
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24
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Wu S, Hao J, Guo D, Ma Z, Wu Q, Zhang M, Bi H. Characterization of lncRNA and mRNA profiles in ciliary body in experimental myopia. Exp Eye Res 2024; 241:109849. [PMID: 38430983 DOI: 10.1016/j.exer.2024.109849] [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: 10/06/2023] [Revised: 02/20/2024] [Accepted: 02/26/2024] [Indexed: 03/05/2024]
Abstract
Currently, researchers have mainly focused on the role of the tissues of the posterior segment of the eyes in the development of myopia. However, the ciliary body, an anterior ocular tissue that contracts to initiate the process of accommodation, may also play an important role in the progression of myopia due to the increased demand for near work. In the present study, we established a lens-induced myopia (LIM) animal model in guinea pigs and investigated the molecular changes in the ciliary body associated with the development of myopia based on RNA sequencing. As a result, 871 differentially expressed (DE) mRNAs and 19 DE lncRNAs were identified in the ciliary body between the LIM group and the normal control group. In addition, the lncRNA-mRNA co-expression analysis was performed to explore the target genes of lncRNAs, which were mainly enriched in the Rap1 signaling pathway, cytokine-cytokine receptor interaction, and complement and coagulation cascades pathways based on the functional enrichment analysis. Among the target genes of lncRNAs, three hub genes, including Ctnnb1, Pik3r1, and Itgb1, were found to be involved in the Rap1 signaling pathway. Interestingly, two crucial genes, Grk1 and Pde6a, which are mainly expressed in retinal photoreceptors, were enriched in visual perception in the ciliary body in functional analysis and were verified to be expressed in the ciliary body. These findings indicate the molecular pathogenetic role of the ciliary body in myopia and provide new insights into the underlying mechanism of myopia development. Further studies are needed to explore the specific contributions of these identified lncRNAs and mRNAs to the development of myopia.
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Affiliation(s)
- Shanshan Wu
- Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, 610041, China; Shandong University of Traditional Chinese Medicine, Jinan, 250002, China
| | - Jiawen Hao
- Shandong University of Traditional Chinese Medicine, Jinan, 250002, China
| | - Dadong Guo
- Shandong Academy of Eye Disease Prevention and Therapy, Medical College of Optometry and Ophthalmology, Shandong University of Traditional Chinese Medicine, Jinan, 250002, China.
| | - Zhongyu Ma
- Shandong University of Traditional Chinese Medicine, Jinan, 250002, China
| | - Qiuxin Wu
- Affiliated Eye Hospital of Shandong University of Traditional Chinese Medicine, Jinan, 250002, China
| | - Ming Zhang
- Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Hongsheng Bi
- Shandong Provincial Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Therapy of Ocular Diseases, Shandong Academy of Eye Disease Prevention and Therapy, Shandong Provincial Clinical Research Center of Ophthalmology and Children Visual Impairment Prevention and Control, Shandong Engineering Technology Research Center of Visual Intelligence, Shandong Academy of Health and Myopia Prevention and Control of Children and Adolescents, Jinan, 250002, China.
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25
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Hoppe N, Harrison S, Hwang SH, Chen Z, Karelina M, Deshpande I, Suomivuori CM, Palicharla VR, Berry SP, Tschaikner P, Regele D, Covey DF, Stefan E, Marks DS, Reiter JF, Dror RO, Evers AS, Mukhopadhyay S, Manglik A. GPR161 structure uncovers the redundant role of sterol-regulated ciliary cAMP signaling in the Hedgehog pathway. Nat Struct Mol Biol 2024; 31:667-677. [PMID: 38326651 PMCID: PMC11221913 DOI: 10.1038/s41594-024-01223-8] [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: 05/10/2023] [Accepted: 01/08/2024] [Indexed: 02/09/2024]
Abstract
The orphan G protein-coupled receptor (GPCR) GPR161 plays a central role in development by suppressing Hedgehog signaling. The fundamental basis of how GPR161 is activated remains unclear. Here, we determined a cryogenic-electron microscopy structure of active human GPR161 bound to heterotrimeric Gs. This structure revealed an extracellular loop 2 that occupies the canonical GPCR orthosteric ligand pocket. Furthermore, a sterol that binds adjacent to transmembrane helices 6 and 7 stabilizes a GPR161 conformation required for Gs coupling. Mutations that prevent sterol binding to GPR161 suppress Gs-mediated signaling. These mutants retain the ability to suppress GLI2 transcription factor accumulation in primary cilia, a key function of ciliary GPR161. By contrast, a protein kinase A-binding site in the GPR161 C terminus is critical in suppressing GLI2 ciliary accumulation. Our work highlights how structural features of GPR161 interface with the Hedgehog pathway and sets a foundation to understand the role of GPR161 function in other signaling pathways.
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Affiliation(s)
- Nicholas Hoppe
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
- Biophysics Graduate Program, University of California, San Francisco, CA, USA
| | - Simone Harrison
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
- Biophysics Graduate Program, University of California, San Francisco, CA, USA
| | - Sun-Hee Hwang
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ziwei Chen
- Department of Anesthesiology, Washington University School of Medicine, St Louis, MO, USA
- Taylor Institute for Innovative Psychiatric Research, St Louis, MO, USA
| | - Masha Karelina
- Biophysics Program, Stanford University, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA
| | - Ishan Deshpande
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
| | - Carl-Mikael Suomivuori
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA
| | - Vivek R Palicharla
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Samuel P Berry
- Department of Systems Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Philipp Tschaikner
- Institute of Molecular Biology and Center for Molecular Biosciences, University of Innsbruck, Innsbruck, Austria
- Tyrolean Cancer Research Institute (TKFI), Innsbruck, Austria
| | - Dominik Regele
- Institute of Molecular Biology and Center for Molecular Biosciences, University of Innsbruck, Innsbruck, Austria
| | - Douglas F Covey
- Department of Anesthesiology, Washington University School of Medicine, St Louis, MO, USA
- Taylor Institute for Innovative Psychiatric Research, St Louis, MO, USA
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
- Department of Developmental Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Eduard Stefan
- Institute of Molecular Biology and Center for Molecular Biosciences, University of Innsbruck, Innsbruck, Austria
- Tyrolean Cancer Research Institute (TKFI), Innsbruck, Austria
| | - Debora S Marks
- Department of Systems Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Jeremy F Reiter
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of California, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Ron O Dror
- Biophysics Program, Stanford University, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA
| | - Alex S Evers
- Department of Anesthesiology, Washington University School of Medicine, St Louis, MO, USA
- Taylor Institute for Innovative Psychiatric Research, St Louis, MO, USA
- Department of Developmental Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Saikat Mukhopadhyay
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Aashish Manglik
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
- Department of Anesthesia and Perioperative Care, University of California, San Francisco, CA, USA.
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26
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Khorn PA, Luginina AP, Pospelov VA, Dashevsky DE, Khnykin AN, Moiseeva OV, Safronova NA, Belousov AS, Mishin AV, Borshchevsky VI. Rational Design of Drugs Targeting G-Protein-Coupled Receptors: A Structural Biology Perspective. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:747-764. [PMID: 38831510 DOI: 10.1134/s0006297924040138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 02/22/2024] [Accepted: 02/29/2024] [Indexed: 06/05/2024]
Abstract
G protein-coupled receptors (GPCRs) play a key role in the transduction of extracellular signals to cells and regulation of many biological processes, which makes these membrane proteins one of the most important targets for pharmacological agents. A significant increase in the number of resolved atomic structures of GPCRs has opened the possibility of developing pharmaceuticals targeting these receptors via structure-based drug design (SBDD). SBDD employs information on the structure of receptor-ligand complexes to search for selective ligands without the need for an extensive high-throughput experimental ligand screening and can significantly expand the chemical space for ligand search. In this review, we describe the process of deciphering GPCR structures using X-ray diffraction analysis and cryoelectron microscopy as an important stage in the rational design of drugs targeting this receptor class. Our main goal was to present modern developments and key features of experimental methods used in SBDD of GPCR-targeting agents to a wide range of specialists.
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Affiliation(s)
- Polina A Khorn
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Aleksandra P Luginina
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Vladimir A Pospelov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Dmitrii E Dashevsky
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Andrey N Khnykin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Olga V Moiseeva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
- Scryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Nadezhda A Safronova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Anatolii S Belousov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Alexey V Mishin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia.
| | - Valentin I Borshchevsky
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia.
- Joint Institute for Nuclear Research, Frank Laboratory of Neutron Physics, Dubna, Moscow Region, 141980, Russia
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Gardner J, Eiger DS, Hicks C, Choi I, Pham U, Chundi A, Namjoshi O, Rajagopal S. GPCR kinases differentially modulate biased signaling downstream of CXCR3 depending on their subcellular localization. Sci Signal 2024; 17:eadd9139. [PMID: 38349966 PMCID: PMC10927030 DOI: 10.1126/scisignal.add9139] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 01/22/2024] [Indexed: 02/15/2024]
Abstract
Some G protein-coupled receptors (GPCRs) demonstrate biased signaling such that ligands of the same receptor exclusively or preferentially activate certain downstream signaling pathways over others. This phenomenon may result from ligand-specific receptor phosphorylation by GPCR kinases (GRKs). GPCR signaling can also exhibit location bias because GPCRs traffic to and signal from subcellular compartments in addition to the plasma membrane. Here, we investigated whether GRKs contributed to location bias in GPCR signaling. GRKs translocated to endosomes after stimulation of the chemokine receptor CXCR3 or other GPCRs in cultured cells. GRK2, GRK3, GRK5, and GRK6 showed distinct patterns of recruitment to the plasma membrane and to endosomes depending on the identity of the biased ligand used to activate CXCR3. Analysis of engineered forms of GRKs that localized to either the plasma membrane or endosomes demonstrated that biased CXCR3 ligands elicited different signaling profiles that depended on the subcellular location of the GRK. Each GRK exerted a distinct effect on the regulation of CXCR3 engagement of β-arrestin, internalization, and activation of the downstream effector kinase ERK. Our work highlights a role for GRKs in location-biased GPCR signaling and demonstrates the complex interactions between ligands, GRKs, and cellular location that contribute to biased signaling.
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Affiliation(s)
- Julia Gardner
- Trinity College, Duke University, Durham, NC, 27710, USA
| | | | - Chloe Hicks
- Trinity College, Duke University, Durham, NC, 27710, USA
| | - Issac Choi
- Department of Medicine, Duke University, Durham, NC, 27710, USA
| | - Uyen Pham
- Department of Biochemistry, Duke University, Durham, NC, 27710, USA
| | - Anand Chundi
- Pratt School of Engineering, Duke University, Durham, NC, 27710, USA
| | - Ojas Namjoshi
- Center for Drug Discovery RTI International, Research Triangle Park, NC, 27709, USA
- Present address: Engine Biosciences, 733 Industrial Rd., San Carlos, CA, 94070, USA
| | - Sudarshan Rajagopal
- Department of Biochemistry, Duke University, Durham, NC, 27710, USA
- Department of Medicine, Duke University, Durham, NC, 27710, USA
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28
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Varney MJ, Benovic JL. The Role of G Protein-Coupled Receptors and Receptor Kinases in Pancreatic β-Cell Function and Diabetes. Pharmacol Rev 2024; 76:267-299. [PMID: 38351071 PMCID: PMC10877731 DOI: 10.1124/pharmrev.123.001015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 12/01/2023] [Accepted: 12/07/2023] [Indexed: 02/16/2024] Open
Abstract
Type 2 diabetes (T2D) mellitus has emerged as a major global health concern that has accelerated in recent years due to poor diet and lifestyle. Afflicted individuals have high blood glucose levels that stem from the inability of the pancreas to make enough insulin to meet demand. Although medication can help to maintain normal blood glucose levels in individuals with chronic disease, many of these medicines are outdated, have severe side effects, and often become less efficacious over time, necessitating the need for insulin therapy. G protein-coupled receptors (GPCRs) regulate many physiologic processes, including blood glucose levels. In pancreatic β cells, GPCRs regulate β-cell growth, apoptosis, and insulin secretion, which are all critical in maintaining sufficient β-cell mass and insulin output to ensure euglycemia. In recent years, new insights into the signaling of incretin receptors and other GPCRs have underscored the potential of these receptors as desirable targets in the treatment of diabetes. The signaling of these receptors is modulated by GPCR kinases (GRKs) that phosphorylate agonist-activated GPCRs, marking the receptor for arrestin binding and internalization. Interestingly, genome-wide association studies using diabetic patient cohorts link the GRKs and arrestins with T2D. Moreover, recent reports show that GRKs and arrestins expressed in the β cell serve a critical role in the regulation of β-cell function, including β-cell growth and insulin secretion in both GPCR-dependent and -independent pathways. In this review, we describe recent insights into GPCR signaling and the importance of GRK function in modulating β-cell physiology. SIGNIFICANCE STATEMENT: Pancreatic β cells contain a diverse array of G protein-coupled receptors (GPCRs) that have been shown to improve β-cell function and survival, yet only a handful have been successfully targeted in the treatment of diabetes. This review discusses recent advances in our understanding of β-cell GPCR pharmacology and regulation by GPCR kinases while also highlighting the necessity of investigating islet-enriched GPCRs that have largely been unexplored to unveil novel treatment strategies.
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Affiliation(s)
- Matthew J Varney
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Jeffrey L Benovic
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania
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29
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Madhu MK, Shewani K, Murarka RK. Biased Signaling in Mutated Variants of β 2-Adrenergic Receptor: Insights from Molecular Dynamics Simulations. J Chem Inf Model 2024; 64:449-469. [PMID: 38194225 DOI: 10.1021/acs.jcim.3c01481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
The molecular basis of receptor bias in G protein-coupled receptors (GPCRs) caused by mutations that preferentially activate specific intracellular transducers over others remains poorly understood. Two experimentally identified biased variants of β2-adrenergic receptors (β2AR), a prototypical GPCR, are a triple mutant (T68F, Y132A, and Y219A) and a single mutant (Y219A); the former bias the receptor toward the β-arrestin pathway by disfavoring G protein engagement, while the latter induces G protein signaling explicitly due to selection against GPCR kinases (GRKs) that phosphorylate the receptor as a prerequisite of β-arrestin binding. Though rigorous characterizations have revealed functional implications of these mutations, the atomistic origin of the observed transducer selectivity is not clear. In this study, we investigated the allosteric mechanism of receptor bias in β2AR using microseconds of all-atom Gaussian accelerated molecular dynamics (GaMD) simulations. Our observations reveal distinct rearrangements in transmembrane helices, intracellular loop 3, and critical residues R1313.50 and Y3267.53 in the conserved motifs D(E)RY and NPxxY for the mutant receptors, leading to their specific transducer interactions. Moreover, partial dissociation of G protein from the receptor core is observed in the simulations of the triple mutant in contrast to the single mutant and wild-type receptor. The reorganization of allosteric communications from the extracellular agonist BI-167107 to the intracellular receptor-transducer interfaces drives the conformational rearrangements responsible for receptor bias in the single and triple mutants. The molecular insights into receptor bias of β2AR presented here could improve the understanding of biased signaling in GPCRs, potentially opening new avenues for designing novel therapeutics with fewer side-effects and superior efficacy.
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Affiliation(s)
- Midhun K Madhu
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal, Madhya Pradesh 462066, India
| | - Kunal Shewani
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal, Madhya Pradesh 462066, India
| | - Rajesh K Murarka
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal, Madhya Pradesh 462066, India
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30
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Margo TE, Chen FS, Chen YJ, Chen CK. Grk1 Missense Mutations in Type II Oguchi Disease: A Literature Review. ANNALS OF BIOMEDICAL RESEARCH 2024; 5:1-7. [PMID: 39906762 PMCID: PMC11793915 DOI: 10.61545/abr-5-128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2025]
Abstract
Oguchi disease is a rare form of congenital stationary night blindness resulting from arrestin-1 (SAG) or rhodopsin kinase (GRK1) loss-of-function mutations. Unlike other congenital nyctalopias, patients with Oguchi disease can reach the dark-adapted state, albeit only after several hours of sustained darkness exposure. The mechanism underlying rhodopsin kinase dysfunction in Oguchi disease remains understudied. Previous research utilized the Grk1 knockout mice to reveal its role in phototransduction, the process that transduces light into neuronal signals in rod and cone photoreceptors. By studying Grk1 missense mutations via a knock-in approach, a more complete picture of the Oguchi disease mechanism involving GRK1 may be readily harvested. We summarize here the current knowledge on the Type II Oguchi disease with Grk1 missense mutations by focusing on the interaction of GRK1 with other proteins, and how these interactions influence dark adaptation. We call for more detailed analyses of GRK1 missense mutations in animal models, particularly V380D and L157P, to reveal novel disease mechanisms to gain further insight onto GRK1's action and function.
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Affiliation(s)
- Theodore Edward Margo
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Frank Sungping Chen
- Division of Otolaryngology, PeaceHealth Medical Group, Eugene, Oregan, OR 97401, USA
| | - Yu-Jiun Chen
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Ching-Kang Chen
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
- Department of Ophthalmology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
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31
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Cheng L, Xia F, Li Z, Shen C, Yang Z, Hou H, Sun S, Feng Y, Yong X, Tian X, Qin H, Yan W, Shao Z. Structure, function and drug discovery of GPCR signaling. MOLECULAR BIOMEDICINE 2023; 4:46. [PMID: 38047990 PMCID: PMC10695916 DOI: 10.1186/s43556-023-00156-w] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 11/06/2023] [Indexed: 12/05/2023] Open
Abstract
G protein-coupled receptors (GPCRs) are versatile and vital proteins involved in a wide array of physiological processes and responses, such as sensory perception (e.g., vision, taste, and smell), immune response, hormone regulation, and neurotransmission. Their diverse and essential roles in the body make them a significant focus for pharmaceutical research and drug development. Currently, approximately 35% of marketed drugs directly target GPCRs, underscoring their prominence as therapeutic targets. Recent advances in structural biology have substantially deepened our understanding of GPCR activation mechanisms and interactions with G-protein and arrestin signaling pathways. This review offers an in-depth exploration of both traditional and recent methods in GPCR structure analysis. It presents structure-based insights into ligand recognition and receptor activation mechanisms and delves deeper into the mechanisms of canonical and noncanonical signaling pathways downstream of GPCRs. Furthermore, it highlights recent advancements in GPCR-related drug discovery and development. Particular emphasis is placed on GPCR selective drugs, allosteric and biased signaling, polyphamarcology, and antibody drugs. Our goal is to provide researchers with a thorough and updated understanding of GPCR structure determination, signaling pathway investigation, and drug development. This foundation aims to propel forward-thinking therapeutic approaches that target GPCRs, drawing upon the latest insights into GPCR ligand selectivity, activation, and biased signaling mechanisms.
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Affiliation(s)
- Lin Cheng
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
- Department of Otolaryngology Head and Neck Surgery, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610000, China
| | - Fan Xia
- Department of Neurosurgery, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Ziyan Li
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Chenglong Shen
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Zhiqian Yang
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Hanlin Hou
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Suyue Sun
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Yuying Feng
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Xihao Yong
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Xiaowen Tian
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Hongxi Qin
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Wei Yan
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
| | - Zhenhua Shao
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
- Tianfu Jincheng Laboratory, Frontiers Medical Center, Chengdu, 610212, China.
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32
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Che T, Roth BL. Molecular basis of opioid receptor signaling. Cell 2023; 186:5203-5219. [PMID: 37995655 PMCID: PMC10710086 DOI: 10.1016/j.cell.2023.10.029] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 10/13/2023] [Accepted: 10/27/2023] [Indexed: 11/25/2023]
Abstract
Opioids are used for pain management despite the side effects that contribute to the opioid crisis. The pursuit of non-addictive opioid analgesics remains unattained due to the unresolved intricacies of opioid actions, receptor signaling cascades, and neuronal plasticity. Advancements in structural, molecular, and computational tools illuminate the dynamic interplay between opioids and opioid receptors, as well as the molecular determinants of signaling pathways, which are potentially interlinked with pharmacological responses. Here, we review the molecular basis of opioid receptor signaling with a focus on the structures of opioid receptors bound to endogenous peptides or pharmacological agents. These insights unveil specific interactions that dictate ligand selectivity and likely their distinctive pharmacological profiles. Biochemical analysis further unveils molecular features governing opioid receptor signaling. Simultaneously, the synergy between computational biology and medicinal chemistry continues to expedite the discovery of novel chemotypes with the promise of yielding more efficacious and safer opioid compounds.
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Affiliation(s)
- Tao Che
- Department of Anesthesiology, Washington University School of Medicine, Saint Louis, MO 63110, USA; Center for Clinical Pharmacology, University of Health Sciences & Pharmacy and Washington University School of Medicine, Saint Louis, MO 63110, USA.
| | - Bryan L Roth
- Department of Pharmacology, University of North Carolina Chapel Hill School of Medicine, Chapel Hill 27599, NC, USA.
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33
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Jin L, Zhang Z, Pan P, Zhao Y, Zhou M, Liu L, Zhai Y, Wang H, Xu L, Mei D, Zhang H, Yang Y, Hua J, Zhang X, Zhang L. Low-dose ethanol consumption inhibits neutrophil extracellular traps formation to alleviate rheumatoid arthritis. Commun Biol 2023; 6:1088. [PMID: 37884797 PMCID: PMC10603044 DOI: 10.1038/s42003-023-05473-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 10/17/2023] [Indexed: 10/28/2023] Open
Abstract
Rheumatoid arthritis (RA) is a chronic systemic autoimmune disease. Ethanol consumption has been reported to reduce morbidity in RA patients, but the mechanism behind it remains unclear. Our results showed that Muribaculaceae was predominant in the gut microbiota of mice after ethanol treatment, and the levels of microbiota metabolite acetate were increased. Acetate reduced arthritis severity in collagen-induced arthritis (CIA) mice, which was associated with a decrease in the articular neutrophils and the myeloperoxidase-deoxyribonucleic acid complex in serum. Meanwhile, in vitro experiments confirmed that acetate affected neutrophil activity by acting on G-protein-coupled receptor 43, which reduced endoplasmic reticulum stress in neutrophils and inhibited neutrophil extracellular traps formation. Furthermore, exogenous acetate reversed CIA mice with exacerbated gut microbial disruption, further confirming that the effect of gut microbial metabolite acetate on neutrophils in vivo is crucial for the immune regulation. Our findings illuminate the metabolic and cellular mechanisms of the gut-joint axis in the regulation of autoimmune arthritis, and may offer alternative avenues to replicate or induce the joint-protective benefits of ethanol without associated detrimental effects.
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Affiliation(s)
- Lin Jin
- Institute of Clinical Pharmacology, Anhui Medical University, Hefei, 230032, Anhui, China
- Key Laboratory of Anti-inflammatory and Immune Medicine, Ministry of Education, Hefei, 230032, Anhui, China
- Anti-inflammatory Immune Drugs Collaborative Innovation Center, Hefei, 230032, Anhui, China
| | - Ziwei Zhang
- Institute of Clinical Pharmacology, Anhui Medical University, Hefei, 230032, Anhui, China
- Key Laboratory of Anti-inflammatory and Immune Medicine, Ministry of Education, Hefei, 230032, Anhui, China
- Anti-inflammatory Immune Drugs Collaborative Innovation Center, Hefei, 230032, Anhui, China
| | - Pin Pan
- Department of orthopedics, The Second People's Hospital of Hefei, Hefei Hospital Affiliated to Anhui Medical University, Hefei, 230011, Anhui, China
| | - Yuchen Zhao
- Institute of Clinical Pharmacology, Anhui Medical University, Hefei, 230032, Anhui, China
- Key Laboratory of Anti-inflammatory and Immune Medicine, Ministry of Education, Hefei, 230032, Anhui, China
- Anti-inflammatory Immune Drugs Collaborative Innovation Center, Hefei, 230032, Anhui, China
| | - Mengqi Zhou
- Institute of Clinical Pharmacology, Anhui Medical University, Hefei, 230032, Anhui, China
- Key Laboratory of Anti-inflammatory and Immune Medicine, Ministry of Education, Hefei, 230032, Anhui, China
- Anti-inflammatory Immune Drugs Collaborative Innovation Center, Hefei, 230032, Anhui, China
| | - Lianghu Liu
- Institute of Clinical Pharmacology, Anhui Medical University, Hefei, 230032, Anhui, China
- Key Laboratory of Anti-inflammatory and Immune Medicine, Ministry of Education, Hefei, 230032, Anhui, China
- Anti-inflammatory Immune Drugs Collaborative Innovation Center, Hefei, 230032, Anhui, China
| | - Yuanfang Zhai
- Institute of Clinical Pharmacology, Anhui Medical University, Hefei, 230032, Anhui, China
- Key Laboratory of Anti-inflammatory and Immune Medicine, Ministry of Education, Hefei, 230032, Anhui, China
- Anti-inflammatory Immune Drugs Collaborative Innovation Center, Hefei, 230032, Anhui, China
| | - Han Wang
- Institute of Clinical Pharmacology, Anhui Medical University, Hefei, 230032, Anhui, China
- Key Laboratory of Anti-inflammatory and Immune Medicine, Ministry of Education, Hefei, 230032, Anhui, China
- Anti-inflammatory Immune Drugs Collaborative Innovation Center, Hefei, 230032, Anhui, China
| | - Li Xu
- Institute of Clinical Pharmacology, Anhui Medical University, Hefei, 230032, Anhui, China
- Key Laboratory of Anti-inflammatory and Immune Medicine, Ministry of Education, Hefei, 230032, Anhui, China
- Anti-inflammatory Immune Drugs Collaborative Innovation Center, Hefei, 230032, Anhui, China
| | - Dan Mei
- Institute of Clinical Pharmacology, Anhui Medical University, Hefei, 230032, Anhui, China
- Key Laboratory of Anti-inflammatory and Immune Medicine, Ministry of Education, Hefei, 230032, Anhui, China
- Anti-inflammatory Immune Drugs Collaborative Innovation Center, Hefei, 230032, Anhui, China
| | - Han Zhang
- Institute of Clinical Pharmacology, Anhui Medical University, Hefei, 230032, Anhui, China
- Key Laboratory of Anti-inflammatory and Immune Medicine, Ministry of Education, Hefei, 230032, Anhui, China
- Anti-inflammatory Immune Drugs Collaborative Innovation Center, Hefei, 230032, Anhui, China
| | - Yining Yang
- Institute of Clinical Pharmacology, Anhui Medical University, Hefei, 230032, Anhui, China
- Key Laboratory of Anti-inflammatory and Immune Medicine, Ministry of Education, Hefei, 230032, Anhui, China
- Anti-inflammatory Immune Drugs Collaborative Innovation Center, Hefei, 230032, Anhui, China
| | - Jinghan Hua
- Institute of Clinical Pharmacology, Anhui Medical University, Hefei, 230032, Anhui, China
- Key Laboratory of Anti-inflammatory and Immune Medicine, Ministry of Education, Hefei, 230032, Anhui, China
- Anti-inflammatory Immune Drugs Collaborative Innovation Center, Hefei, 230032, Anhui, China
| | - Xianzheng Zhang
- Institute of Clinical Pharmacology, Anhui Medical University, Hefei, 230032, Anhui, China.
- Key Laboratory of Anti-inflammatory and Immune Medicine, Ministry of Education, Hefei, 230032, Anhui, China.
- Anti-inflammatory Immune Drugs Collaborative Innovation Center, Hefei, 230032, Anhui, China.
| | - Lingling Zhang
- Institute of Clinical Pharmacology, Anhui Medical University, Hefei, 230032, Anhui, China.
- Key Laboratory of Anti-inflammatory and Immune Medicine, Ministry of Education, Hefei, 230032, Anhui, China.
- Anti-inflammatory Immune Drugs Collaborative Innovation Center, Hefei, 230032, Anhui, China.
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34
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Maggio R, Fasciani I, Petragnano F, Coppolino MF, Scarselli M, Rossi M. Unraveling the Functional Significance of Unstructured Regions in G Protein-Coupled Receptors. Biomolecules 2023; 13:1431. [PMID: 37892113 PMCID: PMC10604838 DOI: 10.3390/biom13101431] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 10/29/2023] Open
Abstract
Unstructured regions in functional proteins have gained attention in recent years due to advancements in informatics tools and biophysical methods. G protein-coupled receptors (GPCRs), a large family of cell surface receptors, contain unstructured regions in the form of the i3 loop and C-terminus. This review provides an overview of the functional significance of these regions in GPCRs. GPCRs transmit signals from the extracellular environment to the cell interior, regulating various physiological processes. The i3 loop, located between the fifth and sixth transmembrane helices, and the C-terminus, connected to the seventh transmembrane helix, are determinant of interactions with G proteins and with other intracellular partners such as arrestins. Recent studies demonstrate that the i3 loop and C-terminus play critical roles in allosterically regulating GPCR activation. They can act as autoregulators, adopting conformations that, by restricting G protein access, modulate receptor coupling specificity. The length and unstructured nature of the i3 loop and C-terminus provide unique advantages in GPCR interactions with intracellular protein partners. They act as "fishing lines", expanding the radius of interaction and enabling GPCRs to tether scaffolding proteins, thus facilitating receptor stability during cell membrane movements. Additionally, the i3 loop may be involved in domain swapping between GPCRs, generating novel receptor dimers with distinct binding and coupling characteristics. Overall, the i3 loop and C-terminus are now widely recognized as crucial elements in GPCR function and regulation. Understanding their functional roles enhances our comprehension of GPCR structure and signaling complexity and holds promise for advancements in receptor pharmacology and drug development.
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Affiliation(s)
- Roberto Maggio
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, 67100 L’Aquila, Italy; (I.F.); (F.P.); (M.R.)
| | - Irene Fasciani
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, 67100 L’Aquila, Italy; (I.F.); (F.P.); (M.R.)
| | - Francesco Petragnano
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, 67100 L’Aquila, Italy; (I.F.); (F.P.); (M.R.)
| | - Maria Francesca Coppolino
- Department of Life, Health and Environmental Sciences, University of L’Aquila, 67100 L’Aquila, Italy;
| | - Marco Scarselli
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, 56126 Pisa, Italy;
| | - Mario Rossi
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, 67100 L’Aquila, Italy; (I.F.); (F.P.); (M.R.)
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35
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Duan J, Liu H, Zhao F, Yuan Q, Ji Y, Cai X, He X, Li X, Li J, Wu K, Gao T, Zhu S, Lin S, Wang MW, Cheng X, Yin W, Jiang Y, Yang D, Xu HE. GPCR activation and GRK2 assembly by a biased intracellular agonist. Nature 2023; 620:676-681. [PMID: 37532940 DOI: 10.1038/s41586-023-06395-9] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 07/03/2023] [Indexed: 08/04/2023]
Abstract
Phosphorylation of G-protein-coupled receptors (GPCRs) by GPCR kinases (GRKs) desensitizes G-protein signalling and promotes arrestin signalling, which is also modulated by biased ligands1-6. The molecular assembly of GRKs on GPCRs and the basis of GRK-mediated biased signalling remain largely unknown owing to the weak GPCR-GRK interactions. Here we report the complex structure of neurotensin receptor 1 (NTSR1) bound to GRK2, Gαq and the arrestin-biased ligand SBI-5537. The density map reveals the arrangement of the intact GRK2 with the receptor, with the N-terminal helix of GRK2 docking into the open cytoplasmic pocket formed by the outward movement of the receptor transmembrane helix 6, analogous to the binding of the G protein to the receptor. SBI-553 binds at the interface between GRK2 and NTSR1 to enhance GRK2 binding. The binding mode of SBI-553 is compatible with arrestin binding but clashes with the binding of Gαq protein, thus providing a mechanism for its arrestin-biased signalling capability. In sum, our structure provides a rational model for understanding the details of GPCR-GRK interactions and GRK2-mediated biased signalling.
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Affiliation(s)
- Jia Duan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Heng Liu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Fenghui Zhao
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Qingning Yuan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Yujie Ji
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoqing Cai
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Xinheng He
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xinzhu Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Junrui Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Kai Wu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Tianyu Gao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Shengnan Zhu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Shi Lin
- Research Center for Deepsea Bioresources, Sanya, Hainan, China
| | - Ming-Wei Wang
- Research Center for Deepsea Bioresources, Sanya, Hainan, China
| | - Xi Cheng
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Wanchao Yin
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yi Jiang
- Lingang Laboratory, Shanghai, China
| | - Dehua Yang
- University of Chinese Academy of Sciences, Beijing, China.
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
- Research Center for Deepsea Bioresources, Sanya, Hainan, China.
| | - H Eric Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
- University of Chinese Academy of Sciences, Beijing, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
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Chen Q, Schafer CT, Mukherjee S, Gustavsson M, Agrawal P, Yao XQ, Kossiakoff AA, Handel TM, Tesmer JJG. ACKR3-arrestin2/3 complexes reveal molecular consequences of GRK-dependent barcoding. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.18.549504. [PMID: 37502840 PMCID: PMC10370059 DOI: 10.1101/2023.07.18.549504] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Atypical chemokine receptor 3 (ACKR3, also known as CXCR7) is a scavenger receptor that regulates extracellular levels of the chemokine CXCL12 to maintain responsiveness of its partner, the G protein-coupled receptor (GPCR), CXCR4. ACKR3 is notable because it does not couple to G proteins and instead is completely biased towards arrestins. Our previous studies revealed that GRK2 and GRK5 install distinct distributions of phosphates (or "barcodes") on the ACKR3 carboxy terminal tail, but how these unique barcodes drive different cellular outcomes is not understood. It is also not known if arrestin2 (Arr2) and 3 (Arr3) bind to these barcodes in distinct ways. Here we report cryo-electron microscopy structures of Arr2 and Arr3 in complex with ACKR3 phosphorylated by either GRK2 or GRK5. Unexpectedly, the finger loops of Arr2 and 3 directly insert into the detergent/membrane instead of the transmembrane core of ACKR3, in contrast to previously reported "core" GPCR-arrestin complexes. The distance between the phosphorylation barcode and the receptor transmembrane core regulates the interaction mode of arrestin, alternating between a tighter complex for GRK5 sites and heterogenous primarily "tail only" complexes for GRK2 sites. Arr2 and 3 bind at different angles relative to the core of ACKR3, likely due to differences in membrane/micelle anchoring at their C-edge loops. Our structural investigations were facilitated by Fab7, a novel Fab that binds both Arr2 and 3 in their activated states irrespective of receptor or phosphorylation status, rendering it a potentially useful tool to aid structure determination of any native GPCR-arrestin complex. The structures provide unprecedented insight into how different phosphorylation barcodes and arrestin isoforms can globally affect the configuration of receptor-arrestin complexes. These differences may promote unique downstream intracellular interactions and cellular responses. Our structures also suggest that the 100% bias of ACKR3 for arrestins is driven by the ability of arrestins, but not G proteins, to bind GRK-phosphorylated ACKR3 even when excluded from the receptor cytoplasmic binding pocket.
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Affiliation(s)
- Qiuyan Chen
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Biological Sciences, Purdue University, West Lafayette IN 47907-2054, USA
| | - Christopher T Schafer
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093 USA
- Department of Medicinal Chemistry, Amsterdam Institute for Molecular and Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, Netherlands
| | - Somnath Mukherjee
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL60637, USA
| | - Martin Gustavsson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093 USA
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Parth Agrawal
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL60637, USA
| | - Xin-Qiu Yao
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Anthony A Kossiakoff
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL60637, USA
| | - Tracy M Handel
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093 USA
| | - John J G Tesmer
- Department of Biological Sciences, Purdue University, West Lafayette IN 47907-2054, USA
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Gusach A, García-Nafría J, Tate CG. New insights into GPCR coupling and dimerisation from cryo-EM structures. Curr Opin Struct Biol 2023; 80:102574. [PMID: 36963163 PMCID: PMC10423944 DOI: 10.1016/j.sbi.2023.102574] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 02/01/2023] [Accepted: 02/19/2023] [Indexed: 03/26/2023]
Abstract
Over the past three years (2020-2022) more structures of GPCRs have been determined than in the previous twenty years (2000-2019), primarily of GPCR complexes that are large enough for structure determination by single-particle cryo-EM. This review will present some structural highlights that have advanced our molecular understanding of promiscuous G protein coupling, how a G protein receptor kinase and β-arrestins couple to GPCRs, and GPCR dimerisation. We will also discuss advances in the use of gene fusions, nanobodies, and Fab fragments to facilitate the structure determination of GPCRs in the inactive state that, on their own, are too small for structure determination by single-particle cryo-EM.
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Affiliation(s)
- Anastasiia Gusach
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 2QH, UK. https://twitter.com/GusachAnastasia
| | - Javier García-Nafría
- Institute for Biocomputation and Physics of Complex Systems (BIFI) and Laboratorio de Microscopías Avanzadas (LMA), University of Zaragoza, 50018, Zaragoza, Spain. https://twitter.com/JGarciaNafria
| | - Christopher G Tate
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 2QH, UK.
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38
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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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39
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Eiger DS, Smith JS, Shi T, Stepniewski TM, Tsai CF, Honeycutt C, Boldizsar N, Gardner J, Nicora CD, Moghieb AM, Kawakami K, Choi I, Hicks C, Zheng K, Warman A, Alagesan P, Knape NM, Huang O, Silverman JD, Smith RD, Inoue A, Selent J, Jacobs JM, Rajagopal S. Phosphorylation barcodes direct biased chemokine signaling at CXCR3. Cell Chem Biol 2023; 30:362-382.e8. [PMID: 37030291 PMCID: PMC10147449 DOI: 10.1016/j.chembiol.2023.03.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 02/10/2023] [Accepted: 03/13/2023] [Indexed: 04/10/2023]
Abstract
G protein-coupled receptor (GPCR)-biased agonism, selective activation of certain signaling pathways relative to others, is thought to be directed by differential GPCR phosphorylation "barcodes." At chemokine receptors, endogenous chemokines can act as "biased agonists", which may contribute to the limited success when pharmacologically targeting these receptors. Here, mass spectrometry-based global phosphoproteomics revealed that CXCR3 chemokines generate different phosphorylation barcodes associated with differential transducer activation. Chemokine stimulation resulted in distinct changes throughout the kinome in global phosphoproteomics studies. Mutation of CXCR3 phosphosites altered β-arrestin 2 conformation in cellular assays and was consistent with conformational changes observed in molecular dynamics simulations. T cells expressing phosphorylation-deficient CXCR3 mutants resulted in agonist- and receptor-specific chemotactic profiles. Our results demonstrate that CXCR3 chemokines are non-redundant and act as biased agonists through differential encoding of phosphorylation barcodes, leading to distinct physiological processes.
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Affiliation(s)
- Dylan S Eiger
- Department of Biochemistry, Duke University, Durham, NC 27710, USA
| | - Jeffrey S Smith
- Department of Dermatology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Dermatology, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Dermatology, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA; Dermatology Program, Boston Children's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Tujin Shi
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Tomasz Maciej Stepniewski
- Research Program on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Department of Experimental and Health Sciences of Pompeu Fabra University (UPF), 08003 Barcelona, Spain
| | - Chia-Feng Tsai
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | | | | | - Julia Gardner
- Trinity College, Duke University, Durham, NC 27710, USA
| | - Carrie D Nicora
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | | | - Kouki Kawakami
- Department of Pharmaceutical Sciences, Tohoku University, Sendai 980-8577, Japan
| | - Issac Choi
- Department of Medicine, Duke University, Durham, NC 27710, USA
| | - Chloe Hicks
- Trinity College, Duke University, Durham, NC 27710, USA
| | - Kevin Zheng
- Harvard Medical School, Boston, MA 02115, USA
| | - Anmol Warman
- Trinity College, Duke University, Durham, NC 27710, USA
| | - Priya Alagesan
- Department of Biochemistry, Duke University, Durham, NC 27710, USA
| | - Nicole M Knape
- Department of Biochemistry, Duke University, Durham, NC 27710, USA
| | - Ouwen Huang
- Department of Biomedical Engineering, Duke University, Durham, NC 27710, USA
| | - Justin D Silverman
- College of Information Sciences and Technology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Asuka Inoue
- Department of Pharmaceutical Sciences, Tohoku University, Sendai 980-8577, Japan
| | - Jana Selent
- Research Program on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Department of Experimental and Health Sciences of Pompeu Fabra University (UPF), 08003 Barcelona, Spain
| | - Jon M Jacobs
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Sudarshan Rajagopal
- Department of Biochemistry, Duke University, Durham, NC 27710, USA; Department of Pharmaceutical Sciences, Tohoku University, Sendai 980-8577, Japan.
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Hanai S, Nagata T, Katayama K, Inukai S, Koyanagi M, Inoue K, Terakita A, Kandori H. Difference FTIR Spectroscopy of Jumping Spider Rhodopsin-1 at 77 K. Biochemistry 2023; 62:1347-1359. [PMID: 37001008 DOI: 10.1021/acs.biochem.3c00022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
Abstract
Animal visual rhodopsins can be classified into monostable and bistable rhodopsins, which are typically found in vertebrates and invertebrates, respectively. The former example is bovine rhodopsin (BovRh), whose structures and functions have been extensively studied. On the other hand, those of bistable rhodopsins are less known, despite their importance in optogenetics. Here, low-temperature Fourier-transform infrared (FTIR) spectroscopy was applied to jumping spider rhodopsin-1 (SpiRh1) at 77 K, and the obtained light-induced spectral changes were compared with those of squid rhodopsin (SquRh) and BovRh. Although chromophore distortion of the resting state monitored by HOOP vibrations is not distinctive between invertebrate and vertebrate rhodopsins, distortion of the all-trans chromophore after photoisomerization is unique for BovRh, and the distortion was localized at the center of the chromophore in SpiRh1 and SquRh. Highly conserved aspartate (D83 in BovRh) does not change the hydrogen-bonding environment in invertebrate rhodopsins. Thus, present FTIR analysis provides specific structural changes, leading to activation of invertebrate and vertebrate rhodopsins. On the other hand, the analysis of O-D stretching vibrations in D2O revealed unique features of protein-bound water molecules. Numbers of water bands in SpiRh1 and SquRh were less and more than those in BovRh. The X-ray crystal structure of SpiRh1 observed a bridged water molecule between the protonated Schiff base and its counterion (E194), but strongly hydrogen-bonded water molecules were never detected in SpiRh1, as well as SquRh and BovRh. Thus, absence of strongly hydrogen-bonded water molecules is substantial for animal rhodopsins, which is distinctive from microbial rhodopsins.
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Hofmann KP, Lamb TD. Rhodopsin, light-sensor of vision. Prog Retin Eye Res 2023; 93:101116. [PMID: 36273969 DOI: 10.1016/j.preteyeres.2022.101116] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 08/20/2022] [Accepted: 08/22/2022] [Indexed: 11/06/2022]
Abstract
The light sensor of vertebrate scotopic (low-light) vision, rhodopsin, is a G-protein-coupled receptor comprising a polypeptide chain with bound chromophore, 11-cis-retinal, that exhibits remarkable physicochemical properties. This photopigment is extremely stable in the dark, yet its chromophore isomerises upon photon absorption with 70% efficiency, enabling the activation of its G-protein, transducin, with high efficiency. Rhodopsin's photochemical and biochemical activities occur over very different time-scales: the energy of retinaldehyde's excited state is stored in <1 ps in retinal-protein interactions, but it takes milliseconds for the catalytically active state to form, and many tens of minutes for the resting state to be restored. In this review, we describe the properties of rhodopsin and its role in rod phototransduction. We first introduce rhodopsin's gross structural features, its evolution, and the basic mechanisms of its activation. We then discuss light absorption and spectral sensitivity, photoreceptor electrical responses that result from the activity of individual rhodopsin molecules, and recovery of rhodopsin and the visual system from intense bleaching exposures. We then provide a detailed examination of rhodopsin's molecular structure and function, first in its dark state, and then in the active Meta states that govern its interactions with transducin, rhodopsin kinase and arrestin. While it is clear that rhodopsin's molecular properties are exquisitely honed for phototransduction, from starlight to dawn/dusk intensity levels, our understanding of how its molecular interactions determine the properties of scotopic vision remains incomplete. We describe potential future directions of research, and outline several major problems that remain to be solved.
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Affiliation(s)
- Klaus Peter Hofmann
- Institut für Medizinische Physik und Biophysik (CC2), Charité, and, Zentrum für Biophysik und Bioinformatik, Humboldt-Unversität zu Berlin, Berlin, 10117, Germany.
| | - Trevor D Lamb
- Eccles Institute of Neuroscience, John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2600, Australia.
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42
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Kojima K, Sudo Y. Convergent evolution of animal and microbial rhodopsins. RSC Adv 2023; 13:5367-5381. [PMID: 36793294 PMCID: PMC9923458 DOI: 10.1039/d2ra07073a] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 02/05/2023] [Indexed: 02/15/2023] Open
Abstract
Rhodopsins, a family of photoreceptive membrane proteins, contain retinal as a chromophore and were firstly identified as reddish pigments from frog retina in 1876. Since then, rhodopsin-like proteins have been identified mainly from animal eyes. In 1971, a rhodopsin-like pigment was discovered from the archaeon Halobacterium salinarum and named bacteriorhodopsin. While it was believed that rhodopsin- and bacteriorhodopsin-like proteins were expressed only in animal eyes and archaea, respectively, before the 1990s, a variety of rhodopsin-like proteins (called animal rhodopsins or opsins) and bacteriorhodopsin-like proteins (called microbial rhodopsins) have been progressively identified from various tissues of animals and microorganisms, respectively. Here, we comprehensively introduce the research conducted on animal and microbial rhodopsins. Recent analysis has revealed that the two rhodopsin families have common molecular properties, such as the protein structure (i.e., 7-transmembrane structure), retinal structure (i.e., binding ability to cis- and trans-retinal), color sensitivity (i.e., UV- and visible-light sensitivities), and photoreaction (i.e., triggering structural changes by light and heat), more than what was expected at the early stages of rhodopsin research. Contrastingly, their molecular functions are distinctively different (e.g., G protein-coupled receptors and photoisomerases for animal rhodopsins and ion transporters and phototaxis sensors for microbial rhodopsins). Therefore, based on their similarities and dissimilarities, we propose that animal and microbial rhodopsins have convergently evolved from their distinctive origins as multi-colored retinal-binding membrane proteins whose activities are regulated by light and heat but independently evolved for different molecular and physiological functions in the cognate organism.
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Affiliation(s)
- Keiichi Kojima
- Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University Japan
| | - Yuki Sudo
- Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University Japan
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43
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Gulati S, Palczewski K. Structural view of G protein-coupled receptor signaling in the retinal rod outer segment. Trends Biochem Sci 2023; 48:172-186. [PMID: 36163145 PMCID: PMC9868064 DOI: 10.1016/j.tibs.2022.08.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 08/26/2022] [Accepted: 08/29/2022] [Indexed: 01/26/2023]
Abstract
Visual phototransduction is the most extensively studied G protein-coupled receptor (GPCR) signaling pathway because of its quantifiable stimulus, non-redundancy of genes, and immense importance in vision. We summarize recent discoveries that have advanced our understanding of rod outer segment (ROS) morphology and the pathological basis of retinal diseases. We have combined recently published cryo-electron tomography (cryo-ET) data on the ROS with structural knowledge on individual proteins to define the precise spatial limitations under which phototransduction occurs. Although hypothetical, the reconstruction of the rod phototransduction system highlights the potential roles of phosphodiesterase 6 (PDE6) and guanylate cyclases (GCs) in maintaining the spacing between ROS discs, suggesting a plausible mechanism by which intrinsic optical signals are generated in the retina.
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Affiliation(s)
| | - Krzysztof Palczewski
- Gavin Herbert Eye Institute and the Department of Ophthalmology, Center for Translational Vision Research, Department of Physiology and Biophysics, Department of Chemistry, Molecular Biology, and Biochemistry, University of California Irvine, 850 Health Sciences Road, Irvine, CA 92697-4375, USA.
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44
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Google Quantum AI, Acharya R, Aleiner I, Allen R, Andersen TI, Ansmann M, Arute F, Arya K, Asfaw A, Atalaya J, Babbush R, Bacon D, Bardin JC, Basso J, Bengtsson A, Boixo S, Bortoli G, Bourassa A, Bovaird J, Brill L, Broughton M, Buckley BB, Buell DA, Burger T, Burkett B, Bushnell N, Chen Y, Chen Z, Chiaro B, Cogan J, Collins R, Conner P, Courtney W, Crook AL, Curtin B, Debroy DM, Del Toro Barba A, Demura S, Dunsworth A, Eppens D, Erickson C, Faoro L, Farhi E, Fatemi R, Flores Burgos L, Forati E, Fowler AG, Foxen B, Giang W, Gidney C, Gilboa D, Giustina M, Grajales Dau A, Gross JA, Habegger S, Hamilton MC, Harrigan MP, Harrington SD, Higgott O, Hilton J, Hoffmann M, Hong S, Huang T, Huff A, Huggins WJ, Ioffe LB, Isakov SV, Iveland J, Jeffrey E, Jiang Z, Jones C, Juhas P, Kafri D, Kechedzhi K, Kelly J, Khattar T, Khezri M, Kieferová M, Kim S, Kitaev A, Klimov PV, Klots AR, Korotkov AN, Kostritsa F, Kreikebaum JM, Landhuis D, Laptev P, Lau KM, Laws L, Lee J, Lee K, Lester BJ, Lill A, Liu W, Locharla A, Lucero E, Malone FD, Marshall J, Martin O, McClean JR, et alGoogle Quantum AI, Acharya R, Aleiner I, Allen R, Andersen TI, Ansmann M, Arute F, Arya K, Asfaw A, Atalaya J, Babbush R, Bacon D, Bardin JC, Basso J, Bengtsson A, Boixo S, Bortoli G, Bourassa A, Bovaird J, Brill L, Broughton M, Buckley BB, Buell DA, Burger T, Burkett B, Bushnell N, Chen Y, Chen Z, Chiaro B, Cogan J, Collins R, Conner P, Courtney W, Crook AL, Curtin B, Debroy DM, Del Toro Barba A, Demura S, Dunsworth A, Eppens D, Erickson C, Faoro L, Farhi E, Fatemi R, Flores Burgos L, Forati E, Fowler AG, Foxen B, Giang W, Gidney C, Gilboa D, Giustina M, Grajales Dau A, Gross JA, Habegger S, Hamilton MC, Harrigan MP, Harrington SD, Higgott O, Hilton J, Hoffmann M, Hong S, Huang T, Huff A, Huggins WJ, Ioffe LB, Isakov SV, Iveland J, Jeffrey E, Jiang Z, Jones C, Juhas P, Kafri D, Kechedzhi K, Kelly J, Khattar T, Khezri M, Kieferová M, Kim S, Kitaev A, Klimov PV, Klots AR, Korotkov AN, Kostritsa F, Kreikebaum JM, Landhuis D, Laptev P, Lau KM, Laws L, Lee J, Lee K, Lester BJ, Lill A, Liu W, Locharla A, Lucero E, Malone FD, Marshall J, Martin O, McClean JR, McCourt T, McEwen M, Megrant A, Meurer Costa B, Mi X, Miao KC, Mohseni M, Montazeri S, Morvan A, Mount E, Mruczkiewicz W, Naaman O, Neeley M, Neill C, Nersisyan A, Neven H, Newman M, Ng JH, Nguyen A, Nguyen M, Niu MY, O’Brien TE, Opremcak A, Platt J, Petukhov A, Potter R, Pryadko LP, Quintana C, Roushan P, Rubin NC, Saei N, Sank D, Sankaragomathi K, Satzinger KJ, Schurkus HF, Schuster C, Shearn MJ, Shorter A, Shvarts V, Skruzny J, Smelyanskiy V, Smith WC, Sterling G, Strain D, Szalay M, Torres A, Vidal G, Villalonga B, Vollgraff Heidweiller C, White T, Xing C, Yao ZJ, Yeh P, Yoo J, Young G, Zalcman A, Zhang Y, Zhu N. Suppressing quantum errors by scaling a surface code logical qubit. Nature 2023; 614:676-681. [PMID: 36813892 PMCID: PMC9946823 DOI: 10.1038/s41586-022-05434-1] [Show More Authors] [Citation(s) in RCA: 86] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 10/10/2022] [Indexed: 02/24/2023]
Abstract
Practical quantum computing will require error rates well below those achievable with physical qubits. Quantum error correction1,2 offers a path to algorithmically relevant error rates by encoding logical qubits within many physical qubits, for which increasing the number of physical qubits enhances protection against physical errors. However, introducing more qubits also increases the number of error sources, so the density of errors must be sufficiently low for logical performance to improve with increasing code size. Here we report the measurement of logical qubit performance scaling across several code sizes, and demonstrate that our system of superconducting qubits has sufficient performance to overcome the additional errors from increasing qubit number. We find that our distance-5 surface code logical qubit modestly outperforms an ensemble of distance-3 logical qubits on average, in terms of both logical error probability over 25 cycles and logical error per cycle ((2.914 ± 0.016)% compared to (3.028 ± 0.023)%). To investigate damaging, low-probability error sources, we run a distance-25 repetition code and observe a 1.7 × 10-6 logical error per cycle floor set by a single high-energy event (1.6 × 10-7 excluding this event). We accurately model our experiment, extracting error budgets that highlight the biggest challenges for future systems. These results mark an experimental demonstration in which quantum error correction begins to improve performance with increasing qubit number, illuminating the path to reaching the logical error rates required for computation.
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Izsák R, Riplinger C, Blunt NS, de Souza B, Holzmann N, Crawford O, Camps J, Neese F, Schopf P. Quantum computing in pharma: A multilayer embedding approach for near future applications. J Comput Chem 2023; 44:406-421. [PMID: 35789492 DOI: 10.1002/jcc.26958] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 06/09/2022] [Accepted: 06/10/2022] [Indexed: 01/03/2023]
Abstract
Quantum computers are special purpose machines that are expected to be particularly useful in simulating strongly correlated chemical systems. The quantum computer excels at treating a moderate number of orbitals within an active space in a fully quantum mechanical manner. We present a quantum phase estimation calculation on F2 in a (2,2) active space on Rigetti's Aspen-11 QPU. While this is a promising start, it also underlines the need for carefully selecting the orbital spaces treated by the quantum computer. In this work, a scheme for selecting such an active space automatically is described and simulated results obtained using both the quantum phase estimation (QPE) and variational quantum eigensolver (VQE) algorithms are presented and combined with a subtractive method to enable accurate description of the environment. The active occupied space is selected from orbitals localized on the chemically relevant fragment of the molecule, while the corresponding virtual space is chosen based on the magnitude of interactions with the occupied space calculated from perturbation theory. This protocol is then applied to two chemical systems of pharmaceutical relevance: the enzyme [Fe] hydrogenase and the photosenzitizer temoporfin. While the sizes of the active spaces currently amenable to a quantum computational treatment are not enough to demonstrate quantum advantage, the procedure outlined here is applicable to any active space size, including those that are outside the reach of classical computation.
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Affiliation(s)
| | | | | | | | - Nicole Holzmann
- Riverlane Research Ltd, Cambridge, UK.,Astex Pharmaceuticals, Cambridge, UK
| | | | | | - Frank Neese
- Max-Planck Institut für Kohlenforschung, Mülheim an der Ruhr, Germany
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Dmitrieva DA, Kotova TV, Safronova NA, Sadova AA, Dashevskii DE, Mishin AV. Protein Design Strategies for the Structural–Functional Studies of G Protein-Coupled Receptors. BIOCHEMISTRY (MOSCOW) 2023; 88:S192-S226. [PMID: 37069121 DOI: 10.1134/s0006297923140110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
G protein-coupled receptors (GPCRs) are an important family of membrane proteins responsible for many physiological functions in human body. High resolution GPCR structures are required to understand their molecular mechanisms and perform rational drug design, as GPCRs play a crucial role in a variety of diseases. That is difficult to obtain for the wild-type proteins because of their low stability. In this review, we discuss how this problem can be solved by using protein design strategies developed to obtain homogeneous stabilized GPCR samples for crystallization and cryoelectron microscopy.
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Affiliation(s)
- Daria A Dmitrieva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Tatiana V Kotova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Nadezda A Safronova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Alexandra A Sadova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Dmitrii E Dashevskii
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Alexey V Mishin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia.
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Cary BP, Zhang X, Cao J, Johnson RM, Piper SJ, Gerrard EJ, Wootten D, Sexton PM. New insights into the structure and function of class B1 GPCRs. Endocr Rev 2022; 44:492-517. [PMID: 36546772 PMCID: PMC10166269 DOI: 10.1210/endrev/bnac033] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 11/07/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022]
Abstract
G protein-coupled receptors (GPCRs) are the largest family of cell surface receptors. Class B1 GPCRs constitute a subfamily of 15 receptors that characteristically contain large extracellular domains (ECDs) and respond to long polypeptide hormones. Class B1 GPCRs are critical regulators of homeostasis, and as such, many are important drug targets. While most transmembrane proteins, including GPCRs, are recalcitrant to crystallization, recent advances in electron cryo-microscopy (cryo-EM) have facilitated a rapid expansion of the structural understanding of membrane proteins. As a testament to this success, structures for all the class B1 receptors bound to G proteins have been determined by cryo-EM in the past five years. Further advances in cryo-EM have uncovered dynamics of these receptors, ligands, and signalling partners. Here, we examine the recent structural underpinnings of the class B1 GPCRs with an emphasis on structure-function relationships.
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Affiliation(s)
- Brian P Cary
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia.,ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Xin Zhang
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia.,ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Jianjun Cao
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia.,ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Rachel M Johnson
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia.,ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Sarah J Piper
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia.,ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Elliot J Gerrard
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia.,ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Denise Wootten
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia.,ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Patrick M Sexton
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia.,ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
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48
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Xu Q, Seif A, Yan H, Mannucci N, Sane BO, Van Meter R, Cleland AN, Jiang L. Distributed Quantum Error Correction for Chip-Level Catastrophic Errors. PHYSICAL REVIEW LETTERS 2022; 129:240502. [PMID: 36563272 DOI: 10.1103/physrevlett.129.240502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 10/06/2022] [Indexed: 06/17/2023]
Abstract
Quantum error correction holds the key to scaling up quantum computers. Cosmic ray events severely impact the operation of a quantum computer by causing chip-level catastrophic errors, essentially erasing the information encoded in a chip. Here, we present a distributed error correction scheme to combat the devastating effect of such events by introducing an additional layer of quantum erasure error correcting code across separate chips. We show that our scheme is fault tolerant against chip-level catastrophic errors and discuss its experimental implementation using superconducting qubits with microwave links. Our analysis shows that in state-of-the-art experiments, it is possible to suppress the rate of these errors from 1 per 10 s to less than 1 per month.
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Affiliation(s)
- Qian Xu
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois 60637, USA
| | - Alireza Seif
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois 60637, USA
| | - Haoxiong Yan
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois 60637, USA
| | - Nam Mannucci
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois 60637, USA
| | - Bernard Ousmane Sane
- Graduate School of Media and Governance, Keio University, 5322 Endo, Fujisawa 252-0882, Japan
| | - Rodney Van Meter
- Faculty of Environment and Information Studies, Keio University, 5322 Endo, Fujisawa 252-0882, Japan
| | - Andrew N Cleland
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois 60637, USA
- Center for Molecular Engineering and Material Science Division, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - Liang Jiang
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois 60637, USA
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49
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Casajuana-Martin N, Navarro G, Gonzalez A, Llinas del Torrent C, Gómez-Autet M, Quintana García A, Franco R, Pardo L. A Single Point Mutation Blocks the Entrance of Ligands to the Cannabinoid CB 2 Receptor via the Lipid Bilayer. J Chem Inf Model 2022; 62:5771-5779. [PMID: 36302505 PMCID: PMC9709915 DOI: 10.1021/acs.jcim.2c00865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Molecular dynamic (MD) simulations have become a common tool to study the pathway of ligand entry to the orthosteric binding site of G protein-coupled receptors. Here, we have combined MD simulations and site-directed mutagenesis to study the binding process of the potent JWH-133 agonist to the cannabinoid CB2 receptor (CB2R). In CB2R, the N-terminus and extracellular loop 2 fold over the ligand binding pocket, blocking access to the binding cavity from the extracellular environment. We, thus, hypothesized that the binding pathway is a multistage process consisting of the hydrophobic ligand diffusing in the lipid bilayer to contact a lipid-facing vestibule, from which the ligand enters an allosteric site inside the transmembrane bundle through a tunnel formed between TMs 1 and 7 and finally moving from the allosteric to the orthosteric binding cavity. This pathway was experimentally validated by the Ala2827.36Phe mutation that blocks the entrance of the ligand, as JWH-133 was not able to decrease the forskolin-induced cAMP levels in cells expressing the mutant receptor. This proposed ligand entry pathway defines transient binding sites that are potential cavities for the design of synthetic modulators.
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Affiliation(s)
- Nil Casajuana-Martin
- Laboratory
of Computational Medicine, Biostatistics Unit, Faculty of Medicine, Universitat Autònoma Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Gemma Navarro
- Department
of Biochemistry and Physiology, Faculty of Pharmacy and Food Sciences, Universitat de Barcelona, 08028 Barcelona, Spain,Centro
de Investigación en Red, Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, 28031 Madrid, Spain
| | - Angel Gonzalez
- Laboratory
of Computational Medicine, Biostatistics Unit, Faculty of Medicine, Universitat Autònoma Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Claudia Llinas del Torrent
- Laboratory
of Computational Medicine, Biostatistics Unit, Faculty of Medicine, Universitat Autònoma Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Marc Gómez-Autet
- Laboratory
of Computational Medicine, Biostatistics Unit, Faculty of Medicine, Universitat Autònoma Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Aleix Quintana García
- Laboratory
of Computational Medicine, Biostatistics Unit, Faculty of Medicine, Universitat Autònoma Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Rafael Franco
- Centro
de Investigación en Red, Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, 28031 Madrid, Spain,Department
of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, 08028 Barcelona, Spain
| | - Leonardo Pardo
- Laboratory
of Computational Medicine, Biostatistics Unit, Faculty of Medicine, Universitat Autònoma Barcelona, 08193 Bellaterra, Barcelona, Spain,E-mail:
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50
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Yang J, Hall JE, Jose PA, Chen K, Zeng C. Comprehensive insights in GRK4 and hypertension: From mechanisms to potential therapeutics. Pharmacol Ther 2022; 239:108194. [PMID: 35487286 PMCID: PMC9728143 DOI: 10.1016/j.pharmthera.2022.108194] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 03/30/2022] [Accepted: 04/21/2022] [Indexed: 11/24/2022]
Abstract
G protein-coupled receptors (GPCRs) mediate cellular responses to diverse extracellular stimuli that play vital roles in the regulation of biology, including behavior. Abnormal G protein-coupled receptor kinase (GRK)-mediated regulation of GPCR function is involved in the pathogenesis of hypertension. Among the seven GRK subtypes, GRK4 has attracted attention because of its constitutive activity and tissue-specific expression. Increasing number of studies show that GRK4 affects blood pressure by GPCR-mediated regulation of renal and arterial function. The target receptor of GRK4 is confined not only to GPCRs, but also to other blood pressure-regulating receptors, such as the adiponectin receptor. Genetic studies in humans show that in several ethnic groups, GRK4 gene variants (R65L, A142V, and A486V) are associated with salt-sensitive or salt-resistant essential hypertension and blood pressure responses to antihypertensive medicines. In this article, we present a comprehensive overview of GRK-mediated regulation of blood pressure, focusing on the latest research progress on GRK4 and hypertension and highlighting potential and novel strategies for the prevention and treatment of hypertension.
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Affiliation(s)
- Jian Yang
- Department of Clinical Nutrition, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, PR China; Research Center for Metabolic and Cardiovascular Diseases, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China.
| | - John E Hall
- Department of Physiology and Biophysics, Mississippi Center for Obesity Research, University of Mississippi Medical Center, Jackson, MS, USA
| | - Pedro A Jose
- Division of Renal Diseases & Hypertension, The George Washington University School of Medicine & Health Sciences, Washington, DC, USA
| | - Ken Chen
- Department of Cardiology, Daping Hospital, The Third Military Medical University, Chongqing, PR China; Cardiovascular Research Center of Chongqing College, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Chongqing, PR China.
| | - Chunyu Zeng
- Department of Cardiology, Daping Hospital, The Third Military Medical University, Chongqing, PR China; Heart Center of Fujian Province, Union Hospital, Fujian Medical University, Fuzhou, PR China; Department of Cardiology, Chongqing General Hospital, Chongqing, PR China; Cardiovascular Research Center of Chongqing College, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Chongqing, PR China.
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