1
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Dumont ME, Konopka JB. Comparison of Experimental Approaches Used to Determine the Structure and Function of the Class D G Protein-Coupled Yeast α-Factor Receptor. Biomolecules 2022; 12:biom12060761. [PMID: 35740886 PMCID: PMC9220813 DOI: 10.3390/biom12060761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/26/2022] [Accepted: 05/27/2022] [Indexed: 02/01/2023] Open
Abstract
The Saccharomyces cerevisiae α-factor mating pheromone receptor (Ste2p) has been studied as a model for the large medically important family of G protein-coupled receptors. Diverse yeast genetic screens and high-throughput mutagenesis of STE2 identified a large number of loss-of-function, constitutively-active, dominant-negative, and intragenic second-site suppressor mutants as well as mutations that specifically affect pheromone binding. Facile genetic manipulation of Ste2p also aided in targeted biochemical approaches, such as probing the aqueous accessibility of substituted cysteine residues in order to identify the boundaries of the seven transmembrane segments, and the use of cysteine disulfide crosslinking to identify sites of intramolecular contacts in the transmembrane helix bundle of Ste2p and sites of contacts between the monomers in a Ste2p dimer. Recent publication of a series of high-resolution cryo-EM structures of Ste2p in ligand-free, agonist-bound and antagonist-bound states now makes it possible to evaluate the results of these genetic and biochemical strategies, in comparison to three-dimensional structures showing activation-related conformational changes. The results indicate that the genetic and biochemical strategies were generally effective, and provide guidance as to how best to apply these experimental strategies to other proteins. These strategies continue to be useful in defining mechanisms of signal transduction in the context of the available structures and suggest aspects of receptor function beyond what can be discerned from the available structures.
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Affiliation(s)
- Mark E. Dumont
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA
- Correspondence: ; Tel.: +1-585-275-2466
| | - James B. Konopka
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, NY 11794-5222, USA;
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2
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Velazhahan V, Ma N, Vaidehi N, Tate CG. Activation mechanism of the class D fungal GPCR dimer Ste2. Nature 2022; 603:743-748. [PMID: 35296853 PMCID: PMC8942848 DOI: 10.1038/s41586-022-04498-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 02/01/2022] [Indexed: 02/06/2023]
Abstract
The fungal class D1 G-protein-coupled receptor (GPCR) Ste2 has a different arrangement of transmembrane helices compared with mammalian GPCRs and a distinct mode of coupling to the heterotrimeric G protein Gpa1-Ste2-Ste181. In addition, Ste2 lacks conserved sequence motifs such as DRY, PIF and NPXXY, which are associated with the activation of class A GPCRs2. This suggested that the activation mechanism of Ste2 may also differ. Here we determined structures of Saccharomyces cerevisiae Ste2 in the absence of G protein in two different conformations bound to the native agonist α-factor, bound to an antagonist and without ligand. These structures revealed that Ste2 is indeed activated differently from other GPCRs. In the inactive state, the cytoplasmic end of transmembrane helix H7 is unstructured and packs between helices H1-H6, blocking the G protein coupling site. Agonist binding results in the outward movement of the extracellular ends of H6 and H7 by 6 Å. On the intracellular surface, the G protein coupling site is formed by a 20 Å outward movement of the unstructured region in H7 that unblocks the site, and a 12 Å inward movement of H6. This is a distinct mechanism in GPCRs, in which the movement of H6 and H7 upon agonist binding facilitates G protein coupling.
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Affiliation(s)
| | - Ning Ma
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - Nagarajan Vaidehi
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - Christopher G Tate
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK.
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3
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Connelly SM, Sridharan R, Naider F, Dumont ME. Oligomerization of yeast α-factor receptor detected by fluorescent energy transfer between ligands. Biophys J 2021; 120:5090-5106. [PMID: 34627767 DOI: 10.1016/j.bpj.2021.10.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 08/26/2021] [Accepted: 10/05/2021] [Indexed: 11/26/2022] Open
Abstract
G-protein-coupled receptors (GPCRs) comprise a large superfamily of transmembrane receptors responsible for transducing responses to the binding of a wide variety of hormones, neurotransmitters, ions, and other small molecules. There is extensive evidence that GPCRs exist as homo-and hetero-oligomeric complexes; however, in many cases, the role of oligomerization and the extent to which it occurs at low physiological levels of receptor expression in cells remain unclear. We report here the use of flow cytometry to detect receptor-receptor interactions based on fluorescence resonance energy transfer between fluorescently labeled cell-impermeant ligands bound to yeast α-mating pheromone receptors that are members of the GPCR superfamily. A novel, to our knowledge, procedure was used to analyze energy transfer as a function of receptor occupancy by donor and acceptor ligands. Measurements of loss of donor fluorescence due to energy transfer in cells expressing high levels of receptors were used to calibrate measurements of enhanced acceptor emission due to energy transfer in cells expressing low levels of receptors. The procedure allows determination of energy transfer efficiencies over a 50-fold range of expression of full-length receptors at the surface of living cells without the need to create fluorescent or bioluminescent fusion proteins. Energy transfer efficiencies for fluorescently labeled derivatives of the receptor agonist α-factor do not depend on receptor expression level and are unaffected by C-terminal truncation of receptors. Fluorescently labeled derivatives of α-factor that act as receptor antagonists exhibit higher transfer efficiencies than those for labeled agonists. Although the approach cannot determine the number of receptors per oligomer, these results demonstrate that ligand-bound, native α-factor receptors exist as stable oligomers in the cell membranes of intact yeast cells at normal physiological expression levels and that the extent of oligomer formation is not dependent on the concentration of receptors in the membrane.
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Affiliation(s)
- Sara M Connelly
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York
| | - Rajashri Sridharan
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York
| | - Fred Naider
- Department of Chemistry and Macromolecular Assembly Institute, College of Staten Island of the City University of New York, Staten Island, New York; PhD Programs in Biochemistry and Chemistry, The Graduate Center of the City University of New York, New York, New York
| | - Mark E Dumont
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York.
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4
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Cevheroğlu O, Murat M, Mingu-Akmete S, Son ÇD. Ste2p Under the Microscope: the Investigation of Oligomeric States of a Yeast G Protein-Coupled Receptor. J Phys Chem B 2021; 125:9526-9536. [PMID: 34433281 DOI: 10.1021/acs.jpcb.1c05872] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Oligomerization of G protein-coupled receptors (GPCRs) may play important roles in maturation, internalization, signaling, and pharmacology of these receptors. However, the nature and extent of their oligomerization is still under debate. In our study, Ste2p, a yeast mating pheromone GPCR, was tagged with enhanced green fluorescent protein (EGFP), mCherry, and with split florescent protein fragments at the receptor C-terminus. The Förster resonance energy transfer (FRET) technique was used to detect receptors' oligomerization by calculating the energy transfer from EGFP to mCherry. Stimulation of Ste2p oligomers with the receptor ligand did not result in any significant change on observed FRET values. The bimolecular fluorescence complementation (BiFC) assay was combined with FRET to further investigate the tetrameric complexes of Ste2p. Our results suggest that in its quiescent (nonligand-activated) state, Ste2p is found at least as a tetrameric complex on the plasma membrane. Intriguingly, receptor tetramers in their active form showed a significant increase in FRET. This study provides a direct in vivo visualization of Ste2p tetramers and the pheromone effect on the extent of the receptor oligomerization.
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Affiliation(s)
- Orkun Cevheroğlu
- Stem Cell Institute, Ankara University, Cankaya, 06520 Ankara, Turkey
| | - Merve Murat
- Stem Cell Institute, Ankara University, Cankaya, 06520 Ankara, Turkey.,Department of Biological Sciences, Middle East Technical University, Cankaya, 06800 Ankara, Turkey
| | - Sara Mingu-Akmete
- Stem Cell Institute, Ankara University, Cankaya, 06520 Ankara, Turkey.,Department of Biological Sciences, Middle East Technical University, Cankaya, 06800 Ankara, Turkey
| | - Çağdaş D Son
- Department of Biological Sciences, Middle East Technical University, Cankaya, 06800 Ankara, Turkey
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5
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Paprocki J, Biener G, Stoneman M, Raicu V. In-Cell Detection of Conformational Substates of a G Protein-Coupled Receptor Quaternary Structure: Modulation of Substate Probability by Cognate Ligand Binding. J Phys Chem B 2020; 124:10062-10076. [DOI: 10.1021/acs.jpcb.0c06081] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Joel Paprocki
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53211, United States
| | - Gabriel Biener
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53211, United States
| | - Michael Stoneman
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53211, United States
| | - Valerică Raicu
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53211, United States
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53211, United States
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6
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Capturing Peptide-GPCR Interactions and Their Dynamics. Molecules 2020; 25:molecules25204724. [PMID: 33076289 PMCID: PMC7587574 DOI: 10.3390/molecules25204724] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/08/2020] [Accepted: 10/09/2020] [Indexed: 12/16/2022] Open
Abstract
Many biological functions of peptides are mediated through G protein-coupled receptors (GPCRs). Upon ligand binding, GPCRs undergo conformational changes that facilitate the binding and activation of multiple effectors. GPCRs regulate nearly all physiological processes and are a favorite pharmacological target. In particular, drugs are sought after that elicit the recruitment of selected effectors only (biased ligands). Understanding how ligands bind to GPCRs and which conformational changes they induce is a fundamental step toward the development of more efficient and specific drugs. Moreover, it is emerging that the dynamic of the ligand–receptor interaction contributes to the specificity of both ligand recognition and effector recruitment, an aspect that is missing in structural snapshots from crystallography. We describe here biochemical and biophysical techniques to address ligand–receptor interactions in their structural and dynamic aspects, which include mutagenesis, crosslinking, spectroscopic techniques, and mass-spectrometry profiling. With a main focus on peptide receptors, we present methods to unveil the ligand–receptor contact interface and methods that address conformational changes both in the ligand and the GPCR. The presented studies highlight a wide structural heterogeneity among peptide receptors, reveal distinct structural changes occurring during ligand binding and a surprisingly high dynamics of the ligand–GPCR complexes.
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7
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Naider F, Becker JM. A Paradigm for Peptide Hormone-GPCR Analyses. Molecules 2020; 25:E4272. [PMID: 32961885 PMCID: PMC7570734 DOI: 10.3390/molecules25184272] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/16/2020] [Accepted: 09/17/2020] [Indexed: 01/14/2023] Open
Abstract
Work from our laboratories over the last 35 years that has focused on Ste2p, a G protein-coupled receptor (GPCR), and its tridecapeptide ligand α-factor is reviewed. Our work utilized the yeast Saccharomyces cerevisiae as a model system for understanding peptide-GPCR interactions. It explored the structure and function of synthetic α-factor analogs and biosynthetic receptor domains, as well as designed mutations of Ste2p. The results and conclusions are described using the nuclear magnetic resonance interrogation of synthetic Ste2p transmembrane domains (TMs), the fluorescence interrogation of agonist and antagonist binding, the biochemical crosslinking of peptide analogs to Ste2p, and the phenotypes of receptor mutants. We identified the ligand-binding domain in Ste2p, the functional assemblies of TMs, unexpected and interesting ligand analogs; gained insights into the bound α-factor structure; and unraveled the function and structures of various Ste2p domains, including the N-terminus, TMs, loops connecting the TMs, and the C-terminus. Our studies showed interactions between specific residues of Ste2p in an active state, but not resting state, and the effect of ligand activation on the dimerization of Ste2p. We show that, using a battery of different biochemical and genetic approaches, deep insight can be gained into the structure and conformational dynamics of GPCR-peptide interactions in the absence of a crystal structure.
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Affiliation(s)
- Fred Naider
- Department of Chemistry, College of Staten Island, CUNY, 2800 Victory Blvd, Staten Island, NY 10314, USA
| | - Jeffrey M. Becker
- Department of Microbiology, University of Tennessee, 610 Ken and Blaire Mossman Building, 1311 Cumberland Avenue, Knoxville, TN 37996, USA
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8
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Seidel L, Zarzycka B, Katritch V, Coin I. Exploring Pairwise Chemical Crosslinking To Study Peptide-Receptor Interactions. Chembiochem 2019; 20:683-692. [PMID: 30565820 DOI: 10.1002/cbic.201800582] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Indexed: 01/29/2023]
Abstract
Pairwise crosslinking is a powerful technique to characterize interactions between G protein coupled receptors and their ligands in the live cell. In this work, the "thiol trapping" method, which exploits the proximity-enhanced reaction between haloacetamides and cysteine, is examined to identify intermolecular pairs of vicinal positions. By incorporating cysteine into the corticotropin-releasing factor receptor and either α-chloro- or α-bromoacetamide groups into its ligands, it is shown that thiol trapping provides highly reproducible signals and a low background, and represents a valid alternative to classical "disulfide trapping". The method is advantageous if reducing agents are required during sample analysis. Moreover, it can provide partially distinct spatial constraints, thus giving access to a wider dataset for molecular modeling. Finally, by applying recombinant mini-Gs, GTPγS, and Gαs-depleted HEK293 cells to modulate Gs coupling, it is shown that yields of crosslinking increase in the presence of elevated levels of Gs.
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Affiliation(s)
- Lisa Seidel
- Faculty of Life Sciences, Institute of Biochemistry, University of Leipzig, Bruederstrasse 34, 04103, Leipzig, Germany
| | - Barbara Zarzycka
- Department of Biological Sciences, Bridge Institute, University of Southern California, 1002 Childs Way, MCB 317, Los Angeles, CA, 90089-3502, USA
| | - Vsevolod Katritch
- Department of Biological Sciences, Bridge Institute, University of Southern California, 1002 Childs Way, MCB 317, Los Angeles, CA, 90089-3502, USA.,Department of Chemistry, Bridge Institute, University of Southern California, 1002 Childs Way, MCB 317, Los Angeles, CA, 90089-3502, USA
| | - Irene Coin
- Faculty of Life Sciences, Institute of Biochemistry, University of Leipzig, Bruederstrasse 34, 04103, Leipzig, Germany
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9
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Uddin MS, Naider F, Becker JM. Dynamic roles for the N-terminus of the yeast G protein-coupled receptor Ste2p. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:2058-2067. [PMID: 28754538 DOI: 10.1016/j.bbamem.2017.07.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 07/13/2017] [Accepted: 07/24/2017] [Indexed: 12/11/2022]
Abstract
The Saccharomyces cerevisiae α-factor receptor Ste2p has been used extensively as a model to understand the molecular mechanism of signal transduction by G protein-coupled receptors (GPCRs). Single and double cysteine mutants of Ste2p were created and served as surrogates to detect intramolecular interactions and dimerization of Ste2p using disulfide cross-linking methodology. When a mutation was introduced into the phylogenetically conserved tyrosine residue at position 26 (Y26C) in the N-terminus of Ste2p, dimerization was increased greatly. The amount of dimer formed by this Y26C mutant was greatly reduced by ligand binding even though the ligand binding site is far removed from the N-terminus; the lowering of the dimer formation was consistent with a conformational change in the N-terminus of the receptor upon activation. Dimerization was decreased by double mutations Y26C/V109C or Y26C/T114C indicating that Y26 is in close proximity to V109 and T114 of extracellular loop 1 in native Ste2p. Combined with earlier studies, these results indicate previously unrecognized roles for the N-terminus of Ste2p, and perhaps of GPCRs in general, and reveal a specific N-terminus residue or region, that is involved in GPCR signaling, intrareceptor interactions, and receptor dimerization.
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Affiliation(s)
- M Seraj Uddin
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Fred Naider
- Department of Chemistry and Macromolecular Assemblies Institute, College of Staten Island, CUNY, New York, New York 10314, United States; Ph.D. Programs in Biochemistry and Chemistry, The Graduate Center of the City University of New York, New York, NY 10016, United States
| | - Jeffrey M Becker
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee 37996, United States.
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10
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Cai Y, Liu Y, Culhane KJ, DeVree BT, Yang Y, Sunahara RK, Yan ECY. Purification of family B G protein-coupled receptors using nanodiscs: Application to human glucagon-like peptide-1 receptor. PLoS One 2017; 12:e0179568. [PMID: 28609478 PMCID: PMC5469476 DOI: 10.1371/journal.pone.0179568] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 05/31/2017] [Indexed: 12/16/2022] Open
Abstract
Family B G protein-coupled receptors (GPCRs) play vital roles in hormone-regulated homeostasis. They are drug targets for metabolic diseases, including type 2 diabetes and osteoporosis. Despite their importance, the signaling mechanisms for family B GPCRs at the molecular level remain largely unexplored due to the challenges in purification of functional receptors in sufficient amount for biophysical characterization. Here, we purified the family B GPCR human glucagon-like peptide-1 (GLP-1) receptor (GLP1R), whose agonists, e.g. exendin-4, are used for the treatment of type 2 diabetes mellitus. The receptor was expressed in HEK293S GnTl- cells using our recently developed protocol. The protocol incorporates the receptor into the native-like lipid environment of reconstituted high density lipoprotein (rHDL) particles, also known as nanodiscs, immediately after the membrane solubilization step followed by chromatographic purification, minimizing detergent contact with the target receptor to reduce denaturation and prolonging stabilization of receptor in lipid bilayers without extra steps of reconstitution. This method yielded purified GLP1R in nanodiscs that could bind to GLP-1 and exendin-4 and activate Gs protein. This nanodisc purification method can potentially be a general strategy to routinely obtain purified family B GPCRs in the 10s of microgram amounts useful for spectroscopic analysis of receptor functions and activation mechanisms.
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Affiliation(s)
- Yingying Cai
- Department of Chemistry, Yale University, New Haven, Connecticut, United States of America
| | - Yuting Liu
- Department of Chemistry, Yale University, New Haven, Connecticut, United States of America
| | - Kelly J. Culhane
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
| | - Brian T. DeVree
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Yang Yang
- Nanobiology Institute, Yale University, New Haven, Connecticut, United States of America
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Roger K. Sunahara
- Department of Pharmacology, University of California at San Diego, La Jolla, California, United States of America
| | - Elsa C. Y. Yan
- Department of Chemistry, Yale University, New Haven, Connecticut, United States of America
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11
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Cevheroğlu O, Kumaş G, Hauser M, Becker JM, Son ÇD. The yeast Ste2p G protein-coupled receptor dimerizes on the cell plasma membrane. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:698-711. [PMID: 28073700 DOI: 10.1016/j.bbamem.2017.01.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 12/23/2016] [Accepted: 01/05/2017] [Indexed: 12/17/2022]
Abstract
Dimerization of G protein-coupled receptors (GPCR) may play an important role in maturation, internalization, signaling and/or pharmacology of these receptors. However, the location where dimerization occurs is still under debate. In our study, variants of Ste2p, a yeast mating pheromone GPCR, were tagged with split EGFP (enhanced green fluorescent protein) fragments inserted between transmembrane domain seven and the C-terminus or appended to the C-terminus. Bimolecular Fluorescence Complementation (BiFC) assay was used to determine where receptor dimerization occurred during protein trafficking by monitoring generation of EGFP fluorescence, which occurred upon GPCR dimerization. Our results suggest that these tagged receptors traffic to the membrane as monomers, undergo dimerization or higher ordered oligomerization predominantly on the plasma membrane, and are internalized as dimers/oligomers. This study is the first to provide direct in vivo visualization of GPCR dimerization/oligomerization, during trafficking to and from the plasma membrane.
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Affiliation(s)
- Orkun Cevheroğlu
- Department of Biological Sciences, Middle East Technical University, Universiteler Mah. Dumlupinar Blv. No: 1, 06800 Cankaya, Ankara, Turkey; Department of Microbiology, University of Tennessee, Knoxville, TN 37996, United States
| | - Gözde Kumaş
- Department of Biological Sciences, Middle East Technical University, Universiteler Mah. Dumlupinar Blv. No: 1, 06800 Cankaya, Ankara, Turkey
| | - Melinda Hauser
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996, United States
| | - Jeffrey M Becker
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996, United States
| | - Çağdaş D Son
- Department of Biological Sciences, Middle East Technical University, Universiteler Mah. Dumlupinar Blv. No: 1, 06800 Cankaya, Ankara, Turkey.
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12
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Stoneman MR, Paprocki JD, Biener G, Yokoi K, Shevade A, Kuchin S, Raicu V. Quaternary structure of the yeast pheromone receptor Ste2 in living cells. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1859:1456-1464. [PMID: 27993568 DOI: 10.1016/j.bbamem.2016.12.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 12/05/2016] [Accepted: 12/08/2016] [Indexed: 12/15/2022]
Abstract
Transmembrane proteins known as G protein-coupled receptors (GPCRs) have been shown to form functional homo- or hetero-oligomeric complexes, although agreement has been slow to emerge on whether homo-oligomerization plays functional roles. Here we introduce a platform to determine the identity and abundance of differing quaternary structures formed by GPCRs in living cells following changes in environmental conditions, such as changes in concentrations. The method capitalizes on the intrinsic capability of FRET spectrometry to extract oligomer geometrical information from distributions of FRET efficiencies (or FRET spectrograms) determined from pixel-level imaging of cells, combined with the ability of the statistical ensemble approaches to FRET to probe the proportion of different quaternary structures (such as dimers, rhombus or parallelogram shaped tetramers, etc.) from averages over entire cells. Our approach revealed that the yeast pheromone receptor Ste2 forms predominantly tetramers at average expression levels of 2 to 25 molecules per pixel (2.8·10-6 to 3.5·10-5molecules/nm2), and a mixture of tetramers and octamers at expression levels of 25-100 molecules per pixel (3.5·10-5 to 1.4·10-4molecules/nm2). Ste2 is a class D GPCR found in the yeast Saccharomyces cerevisiae of the mating type a, and binds the pheromone α-factor secreted by cells of the mating type α. Such investigations may inform development of antifungal therapies targeting oligomers of pheromone receptors. The proposed FRET imaging platform may be used to determine the quaternary structure sub-states and stoichiometry of any GPCR and, indeed, any membrane protein in living cells. This article is part of a Special Issue entitled: Interactions between membrane receptors in cellular membranes edited by Kalina Hristova.
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Affiliation(s)
- Michael R Stoneman
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA.
| | - Joel D Paprocki
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Gabriel Biener
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Koki Yokoi
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Aishwarya Shevade
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Sergei Kuchin
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Valerică Raicu
- Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA; Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA.
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13
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Sridharan R, Connelly SM, Naider F, Dumont ME. Variable Dependence of Signaling Output on Agonist Occupancy of Ste2p, a G Protein-coupled Receptor in Yeast. J Biol Chem 2016; 291:24261-24279. [PMID: 27646004 DOI: 10.1074/jbc.m116.733006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Revised: 09/04/2016] [Indexed: 12/22/2022] Open
Abstract
We report here on the relationship between ligand binding and signaling responses in the yeast pheromone response pathway, a well characterized G protein-coupled receptor system. Responses to agonist (α-factor) by cells expressing widely varying numbers of receptors depend primarily on fractional occupancy, not the absolute number of agonist-bound receptors. Furthermore, the concentration of competitive antagonist required to inhibit α-factor-dependent signaling is more than 10-fold higher than predicted based on the known ligand affinities. Thus, responses to a particular number of agonist-bound receptors can vary greatly, depending on whether there are unoccupied or antagonist-bound receptors present on the same cell surface. This behavior does not appear to be due to pre-coupling of receptors to G protein or to the Sst2p regulator of G protein signaling. The results are consistent with a signaling response that is determined by the integration of positive signals from agonist-occupied receptors and inhibitory signals from unoccupied receptors, where the inhibitory signals can be diminished by antagonist binding.
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Affiliation(s)
- Rajashri Sridharan
- From the Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642
| | - Sara M Connelly
- From the Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642
| | - Fred Naider
- the Department of Chemistry and Macromolecular Assembly Institute, College of Staten Island of the City University of New York, Staten Island, New York 10314, and.,the Ph.D. Programs in Biochemistry and Chemistry, Graduate Center of the City University of New York, New York, New York 10016
| | - Mark E Dumont
- From the Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642,
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14
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Di Roberto RB, Chang B, Trusina A, Peisajovich SG. Evolution of a G protein-coupled receptor response by mutations in regulatory network interactions. Nat Commun 2016; 7:12344. [PMID: 27487915 PMCID: PMC4976203 DOI: 10.1038/ncomms12344] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 06/24/2016] [Indexed: 12/17/2022] Open
Abstract
All cellular functions depend on the concerted action of multiple proteins organized in complex networks. To understand how selection acts on protein networks, we used the yeast mating receptor Ste2, a pheromone-activated G protein-coupled receptor, as a model system. In Saccharomyces cerevisiae, Ste2 is a hub in a network of interactions controlling both signal transduction and signal suppression. Through laboratory evolution, we obtained 21 mutant receptors sensitive to the pheromone of a related yeast species and investigated the molecular mechanisms behind this newfound sensitivity. While some mutants show enhanced binding affinity to the foreign pheromone, others only display weakened interactions with the network's negative regulators. Importantly, the latter changes have a limited impact on overall pathway regulation, despite their considerable effect on sensitivity. Our results demonstrate that a new receptor–ligand pair can evolve through network-altering mutations independently of receptor–ligand binding, and suggest a potential role for such mutations in disease. Co-evolution of a new receptor-ligand pair will affect the downstream signal transduction network. Here, the authors use experimental evolution of yeast mating receptor Ste2 to show the effect of enhanced binding affinity and weakened interactions with the network's negative regulators on protein evolution.
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Affiliation(s)
- Raphaël B Di Roberto
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, Ontario, Canada M5S 3G5
| | - Belinda Chang
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, Ontario, Canada M5S 3G5
| | - Ala Trusina
- Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, Copenhagen Ø 2100, Denmark
| | - Sergio G Peisajovich
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, Ontario, Canada M5S 3G5
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Abstract
Experiments are described that allowed cross-linking of analogs of a 13-amino acid peptide into the binding site of a model G protein-coupled receptor. Syntheses of peptide analogs that were used for photochemical or chemical cross-linking were carried out using solid-phase peptide synthesis. Chemical cross-linking utilized 3,4-dihydroxy-l-phenylalanine-incorporated peptides and subsequent periodate-mediated activation, whereas photochemical cross-linking was mediated by p-benzoyl-l-phenylalanine (Bpa)-labeled peptides and UV-initiated activation. Mass spectrometry was employed to locate the site(s) in the receptor that formed the cross-links to the ligand. We also describe a method called unnatural amino acid replacement that allowed capture of a peptide ligand into the receptor. In this method, the receptor was genetically modified by replacement of a natural amino acid with Bpa. The modified receptor was UV-irradiated to capture the ligand. The approaches described are applicable to other peptide-binding proteins and can reveal the ligand-binding site in atomic detail.
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Affiliation(s)
| | - Fred Naider
- Chemistry Department, College of Staten Island, City University of New York
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One motif to bind them: A small-XXX-small motif affects transmembrane domain 1 oligomerization, function, localization, and cross-talk between two yeast GPCRs. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:3036-51. [DOI: 10.1016/j.bbamem.2014.08.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Revised: 08/13/2014] [Accepted: 08/14/2014] [Indexed: 12/21/2022]
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18
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Cohen LS, Fracchiolla KE, Becker J, Naider F. Invited review GPCR structural characterization: Using fragments as building blocks to determine a complete structure. Biopolymers 2014; 102:223-43. [DOI: 10.1002/bip.22490] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Revised: 03/24/2014] [Accepted: 03/27/2014] [Indexed: 12/30/2022]
Affiliation(s)
- Leah S. Cohen
- Department of Chemistry; The College of Staten Island, City University of New York (CUNY); Staten Island NY 10314
| | - Katrina E. Fracchiolla
- Department of Chemistry; The College of Staten Island, City University of New York (CUNY); Staten Island NY 10314
| | - Jeff Becker
- Department of Microbiology; University of Tennessee; Knoxville TN 37996
| | - Fred Naider
- Department of Chemistry; The College of Staten Island, City University of New York (CUNY); Staten Island NY 10314
- Department of Biochemistry; The Graduate Center; CUNY NY 10016-4309
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19
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Quaternary Structure Predictions and Structural Communication Features of GPCR Dimers. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2013; 117:105-42. [DOI: 10.1016/b978-0-12-386931-9.00005-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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20
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Fukutani Y, Ishii J, Noguchi K, Kondo A, Yohda M. An improved bioluminescence-based signaling assay for odor sensing with a yeast expressing a chimeric olfactory receptor. Biotechnol Bioeng 2012; 109:3143-51. [DOI: 10.1002/bit.24589] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Revised: 06/03/2012] [Accepted: 06/12/2012] [Indexed: 12/30/2022]
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Uddin MS, Kim H, Deyo A, Naider F, Becker JM. Identification of residues involved in homodimer formation located within a β-strand region of the N-terminus of a Yeast G protein-coupled receptor. J Recept Signal Transduct Res 2012; 32:65-75. [PMID: 22268895 DOI: 10.3109/10799893.2011.647352] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
G protein-coupled receptors (GPCRs) are members of a superfamily of cell surface signaling proteins that play critical roles in many physiological functions; malfunction of these proteins is associated with multiple diseases. Understanding the structure-function relationships of these proteins is important, therefore, for GPCR-based drug discovery. The yeast Saccharomyces cerevisiae tridecapeptide pheromone α-factor receptor Ste2p has been studied as a model to explore the structure-function relationships of this important class of cell surface receptors. Although transmembrane domains of GPCRs have been examined extensively, the extracellular N-terminus and loop regions have received less attention. We have used substituted cysteine accessibility method to probe the solvent accessibility of single cysteine residues engineered to replace residues Gly20 through Gly33 of the N-terminus of Ste2p. Unexpectedly, our analyses revealed that the residues Ser22, Ile24, Tyr26, and Ser28 in the N-terminus were solvent inaccessible, whereas all other residues of the targeted region were solvent accessible. The periodicity of accessibility from residues Ser22-Ser28 is indicative of an underlying structure consistent with a β-strand that was predicted computationally in this region. Moreover, a number of these Cys-substituted Ste2p receptors (G20C, S22C, I24C, Y26C, S28C and Y30C) were found to form increased dimers compared to the Cys-less Ste2p. Based on these data, we propose that part of the N-terminus of Ste2p is structured and that this structure forms a dimer interface for Ste2p molecules. Dimerization mediated by the N-terminus was affected by ligand binding, indicating an unanticipated conformational change in the N-terminus upon receptor activation.
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Affiliation(s)
- M Seraj Uddin
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA
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Fanelli F, De Benedetti PG. Update 1 of: computational modeling approaches to structure-function analysis of G protein-coupled receptors. Chem Rev 2011; 111:PR438-535. [PMID: 22165845 DOI: 10.1021/cr100437t] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Francesca Fanelli
- Dulbecco Telethon Institute, University of Modena and Reggio Emilia, via Campi 183, 41125 Modena, Italy.
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Umanah GKE, Huang LY, Maccarone JM, Naider F, Becker JM. Changes in conformation at the cytoplasmic ends of the fifth and sixth transmembrane helices of a yeast G protein-coupled receptor in response to ligand binding. Biochemistry 2011; 50:6841-54. [PMID: 21728340 DOI: 10.1021/bi200254h] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The third intracellular loop (IL3) of G protein-coupled receptors (GPCRs) is an important contact domain between GPCRs and their G proteins. Previously, the IL3 of Ste2p, a Saccharomyces cerevisiae GPCR, was suggested to undergo a conformational change upon activation as detected by differential protease susceptibility in the presence and absence of ligand. In this study using disulfide cross-linking experiments we show that the Ste2p cytoplasmic ends of helix 5 (TM5) and helix 6 (TM6) that flank the amino and carboxyl sides of IL3 undergo conformational changes upon ligand binding, whereas the center of the IL3 loop does not. Single Cys substitution of residues in the middle of IL3 led to receptors that formed high levels of cross-linked Ste2p, whereas Cys substitution at the interface of IL3 and the contiguous cytoplasmic ends of TM5 and TM6 resulted in minimal disulfide-mediated cross-linked receptor. The alternating pattern of residues involved in cross-linking suggested the presence of a 3(10) helix in the middle of IL3. Agonist (WHWLQLKPGQPNleY) induced Ste2p activation reduced cross-linking mediated by Cys substitutions at the cytoplasmic ends of TM5 and TM6 but not by residues in the middle of IL3. Thus, the cytoplasmic ends of TM5 and TM6 undergo conformational change upon ligand binding. An α-factor antagonist (des-Trp, des-His-α-factor) did not influence disulfide-mediated Ste2p cross-linking, suggesting that the interaction of the N-terminus of α-factor with Ste2p is critical for inducing conformational changes at TM5 and TM6. We propose that the changes in conformation revealed for residues at the ends of TM5 and TM6 are affected by the presence of G protein but not G protein activation. This study provides new information about role of specific residues of a GPCR in signal transduction and how peptide ligand binding activates the receptor.
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Affiliation(s)
- George K E Umanah
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee 37996, United States
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Jones SK, Bennett RJ. Fungal mating pheromones: choreographing the dating game. Fungal Genet Biol 2011; 48:668-76. [PMID: 21496492 PMCID: PMC3100450 DOI: 10.1016/j.fgb.2011.04.001] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2010] [Revised: 02/23/2011] [Accepted: 04/05/2011] [Indexed: 01/11/2023]
Abstract
Pheromones are ubiquitous from bacteria to mammals - a testament to their importance in regulating inter-cellular communication. In fungal species, they play a critical role in choreographing interactions between mating partners during the program of sexual reproduction. Here, we describe how fungal pheromones are synthesized, their interactions with G protein-coupled receptors, and the signals propagated by this interaction, using Saccharomyces cerevisiae as a reference point. Divergence from this model system is compared amongst the ascomycetes and basidiomycetes, which reveals the wealth of information that has been gleaned from studying pheromone-driven processes across a wide spectrum of the fungal kingdom.
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Affiliation(s)
- Stephen K. Jones
- Graduate Program in Molecular Biology, Cellular Biology, and Biochemistry, Brown University, Providence, RI 02912
| | - Richard J. Bennett
- Graduate Program in Molecular Biology, Cellular Biology, and Biochemistry, Brown University, Providence, RI 02912
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02912
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Abstract
The unique chemistry of oxygen has been both a resource and threat for life on Earth for at least the last 2.4 billion years. Reduction of oxygen to water allows extraction of more metabolic energy from organic fuels than is possible through anaerobic glycolysis. On the other hand, partially reduced oxygen can react indiscriminately with biomolecules to cause genetic damage, disease, and even death. Organisms in all three superkingdoms of life have developed elaborate mechanisms to protect against such oxidative damage and to exploit reactive oxygen species as sensors and signals in myriad processes. The sulfur amino acids, cysteine and methionine, are the main targets of reactive oxygen species in proteins. Oxidative modifications to cysteine and methionine can have profound effects on a protein's activity, structure, stability, and subcellular localization. Non-reversible oxidative modifications (oxidative damage) may contribute to molecular, cellular, and organismal aging and serve as signals for repair, removal, or programmed cell death. Reversible oxidation events can function as transient signals of physiological status, extracellular environment, nutrient availability, metabolic state, cell cycle phase, immune function, or sensory stimuli. Because of its chemical similarity to sulfur and stronger nucleophilicity and acidity, selenium is an extremely efficient catalyst of reactions between sulfur and oxygen. Most of the biological activity of selenium is due to selenoproteins containing selenocysteine, the 21st genetically encoded protein amino acid. The most abundant selenoproteins in mammals are the glutathione peroxidases (five to six genes) that reduce hydrogen peroxide and lipid hydroperoxides at the expense of glutathione and serve to limit the strength and duration of reactive oxygen signals. Thioredoxin reductases (three genes) use nicotinamide adenine dinucleotide phosphate to reduce oxidized thioredoxin and its homologs, which regulate a plethora of redox signaling events. Methionine sulfoxide reductase B1 reduces methionine sulfoxide back to methionine using thioredoxin as a reductant. Several selenoproteins in the endoplasmic reticulum are involved in the regulation of protein disulfide formation and unfolded protein response signaling, although their precise biological activities have not been determined. The most widely distributed selenoprotein family in Nature is represented by the highly conserved thioredoxin-like selenoprotein W and its homologs that have not yet been assigned specific biological functions. Recent evidence suggests selenoprotein W and the six other small thioredoxin-like mammalian selenoproteins may serve to transduce hydrogen peroxide signals into regulatory disulfide bonds in specific target proteins.
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Affiliation(s)
- Wayne Chris Hawkes
- USDA Agricultural Research Service, Western Human Nutrition Research Center, University of California at Davis, Davis, USA
| | - Zeynep Alkan
- USDA Agricultural Research Service, Western Human Nutrition Research Center, University of California at Davis, Davis, USA
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Current awareness on yeast. Yeast 2010. [DOI: 10.1002/yea.1717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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Park G, Masi T, Choi CK, Kim H, Becker JM, Sparer TE. Screening for novel constitutively active CXCR2 mutants and their cellular effects. Methods Enzymol 2010; 485:481-97. [PMID: 21050933 DOI: 10.1016/b978-0-12-381296-4.00026-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Chemokines play an important role in inflammatory, developmental, and homeostatic processes. Deregulation of this system results in various diseases including tumorigenesis and cancer metastasis. Deregulation can occur when constitutively active mutant (CAM) chemokine receptors are locked in the "on" position. This can lead to cellular transformation/tumorigenesis. The CXC chemokine receptor 2 (CXCR2) is a G-protein-coupled receptor (GPCR) expressed on neutrophils, some monocytes, endothelial cells, and some epithelial cells. CXCR2 activation with CXC chemokines induces leukocyte migration, trafficking, leukocyte degranulation, cellular differentiation, and angiogenesis. Activation of CXCR2 can lead to cellular transformation. We hypothesized that CAM CXCR2s may play a role in cancer development. In order to identify CXCR2 CAMs, potential mutant CXCR2 receptors were screened using a modified Saccharomyces cerevisiae high-throughput system. S. cerevisiae has been used successfully to identify GPCR/G-protein interactions and autocrine selection for peptide agonists. The CXCR2 CAMs identified from this screen were characterized in mammalian cells. Their ability to transform cells in vitro was shown using foci formation, soft-agar growth, impedance measurement assays, and in vivo tumor growth following hind flank inoculation into mice. Signaling pathways contributing to cellular transformation were identified using luciferase reporter assays. Studying constitutively active GPCRs is an approach to "capturing" pluridimensional GPCRs in a "locked" activation state. In order to address the residues necessary for CXCR2 activation, we used S. cerevisiae for screening novel CAMs and characterized them using mammalian reporter assays.
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Affiliation(s)
- Giljun Park
- The University of Tennessee, Department of Microbiology, Knoxville, Tennessee, USA
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