1
|
Di Prima D, Reinholdt P, Kongsted J. Color Tuning in Bovine Rhodopsin through Polarizable Embedding. J Phys Chem B 2024. [PMID: 38489248 DOI: 10.1021/acs.jpcb.3c07891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2024]
Abstract
Bovine rhodopsin is among the most studied proteins in the rhodopsin family. Its primary activation mechanism is the photoisomerization of 11-cis retinal, triggered by the absorption of a UV-visible photon. Different mutants of the same rhodopsin show different absorption wavelengths due to the influence of the specific amino acid residues forming the cavity in which the retinal chromophore is embedded, and rhodopsins activated at different wavelengths are, for example, exploited in the field of optogenetics. In this letter, we present a procedure for systematically investigating color tuning in models of bovine rhodopsin and a set of its mutants embedded in a membrane bilayer. Vertical excitation energy calculations were carried out with the polarizable embedding potential for describing the environment surrounding the chromophore. We show that polarizable embedding outperformed regular electrostatic embedding in determining both the vertical excitation energies and associated oscillator strengths of the systems studied.
Collapse
Affiliation(s)
- Duccio Di Prima
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M DK-5230, Denmark
| | - Peter Reinholdt
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M DK-5230, Denmark
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M DK-5230, Denmark
| |
Collapse
|
2
|
Jobe A, Vijayan R. Orphan G protein-coupled receptors: the ongoing search for a home. Front Pharmacol 2024; 15:1349097. [PMID: 38495099 PMCID: PMC10941346 DOI: 10.3389/fphar.2024.1349097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 02/15/2024] [Indexed: 03/19/2024] Open
Abstract
G protein-coupled receptors (GPCRs) make up the largest receptor superfamily, accounting for 4% of protein-coding genes. Despite the prevalence of such transmembrane receptors, a significant number remain orphans, lacking identified endogenous ligands. Since their conception, the reverse pharmacology approach has been used to characterize such receptors. However, the multifaceted and nuanced nature of GPCR signaling poses a great challenge to their pharmacological elucidation. Considering their therapeutic relevance, the search for native orphan GPCR ligands continues. Despite limited structural input in terms of 3D crystallized structures, with advances in machine-learning approaches, there has been great progress with respect to accurate ligand prediction. Though such an approach proves valuable given that ligand scarcity is the greatest hurdle to orphan GPCR deorphanization, the future pairings of the remaining orphan GPCRs may not necessarily take a one-size-fits-all approach but should be more comprehensive in accounting for numerous nuanced possibilities to cover the full spectrum of GPCR signaling.
Collapse
Affiliation(s)
- Amie Jobe
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Ranjit Vijayan
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, United Arab Emirates
- The Big Data Analytics Center, United Arab Emirates University, Al Ain, United Arab Emirates
- Zayed Bin Sultan Center for Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| |
Collapse
|
3
|
Verma DK, Malhotra H, Woellert T, Calvert PD. Hydrophobic interaction between the TM1 and H8 is essential for rhodopsin trafficking to vertebrate photoreceptor outer segments. J Biol Chem 2023; 299:105412. [PMID: 37918805 PMCID: PMC10687059 DOI: 10.1016/j.jbc.2023.105412] [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: 05/16/2023] [Revised: 10/15/2023] [Accepted: 10/25/2023] [Indexed: 11/04/2023] Open
Abstract
A major unsolved question in vertebrate photoreceptor biology is the mechanism of rhodopsin transport to the outer segment. In rhodopsin-like class A G protein-coupled receptors, hydrophobic interactions between C-terminal α-helix 8 (H8), and transmembrane α-helix-1 (TM1) have been shown to be important for transport to the plasma membrane, however whether this interaction is important for rhodopsin transport to ciliary rod outer segments is not known. We examined the crystal structures of vertebrate rhodopsins and class A G protein-coupled receptors and found a conserved network of predicted hydrophobic interactions. In Xenopus rhodopsin (xRho), this interaction corresponds to F313, L317, and L321 in H8 and M57, V61, and L68 in TM1. To evaluate the role of H8-TM1 hydrophobic interactions in rhodopsin transport, we expressed xRho-EGFP where hydrophobic residues were mutated in Xenopus rods and evaluated the efficiency of outer segment enrichment. We found that substituting L317 and M57 with hydrophilic residues had the strongest impact on xRho mislocalization. Substituting hydrophilic amino acids at positions L68, F313, and L321 also had a significant impact. Replacing L317 with M resulted in significant mislocalization, indicating that the hydrophobic interaction between residues 317 and 57 is exquisitely sensitive. The corresponding experiment in bovine rhodopsin expressed in HEK293 cells had a similar effect, showing that the H8-TM1 hydrophobic network is essential for rhodopsin transport in mammalian species. Thus, for the first time, we show that a hydrophobic interaction between H8 and TM1 is critical for efficient rhodopsin transport to the vertebrate photoreceptor ciliary outer segment.
Collapse
Affiliation(s)
- Dipesh Kumar Verma
- Department of Ophthalmology and Visual Sciences, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Himanshu Malhotra
- Department of Ophthalmology and Visual Sciences, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Torsten Woellert
- Department of Ophthalmology and Visual Sciences, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Peter D Calvert
- Department of Ophthalmology and Visual Sciences, SUNY Upstate Medical University, Syracuse, New York, USA.
| |
Collapse
|
4
|
Hong JD, Palczewski K. A short story on how chromophore is hydrolyzed from rhodopsin for recycling. Bioessays 2023; 45:e2300068. [PMID: 37454357 PMCID: PMC10614701 DOI: 10.1002/bies.202300068] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/24/2023] [Accepted: 05/30/2023] [Indexed: 07/18/2023]
Abstract
The photocycle of visual opsins is essential to maintain the light sensitivity of the retina. The early physical observations of the rhodopsin photocycle by Böll and Kühne in the 1870s inspired over a century's worth of investigations on rhodopsin biochemistry. A single photon isomerizes the Schiff-base linked 11-cis-retinylidene chromophore of rhodopsin, converting it to the all-trans agonist to elicit phototransduction through photoactivated rhodopsin (Rho*). Schiff base hydrolysis of the agonist is a key step in the photocycle, not only diminishing ongoing phototransduction but also allowing for entry and binding of fresh 11-cis chromophore to regenerate the rhodopsin pigment and maintain light sensitivity. Many challenges have been encountered in measuring the rate of this hydrolysis, but recent advancements have facilitated studies of the hydrolysis within the native membrane environment of rhodopsin. These techniques can now be applied to study hydrolysis of agonist in other opsin proteins that mediate phototransduction or chromophore turnover. In this review, we discuss the progress that has been made in characterizing the rhodopsin photocycle and the journey to characterize the hydrolysis of its all-trans-retinylidene agonist.
Collapse
Affiliation(s)
- John D. Hong
- Gavin Herbert Eye Institute, Department of Ophthalmology, University of California Irvine, Irvine, CA 92697, USA
- Department of Chemistry, University of California Irvine, Irvine, CA 92697, USA
| | - Krzysztof Palczewski
- Gavin Herbert Eye Institute, Department of Ophthalmology, University of California Irvine, Irvine, CA 92697, USA
- Department of Chemistry, University of California Irvine, Irvine, CA 92697, USA
- Department of Physiology and Biophysics, University of California Irvine, Irvine, CA 92697, USA
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA 92697, USA
| |
Collapse
|
5
|
Wu A, Salom D, Hong JD, Tworak A, Watanabe K, Pardon E, Steyaert J, Kandori H, Katayama K, Kiser PD, Palczewski K. Structural basis for the allosteric modulation of rhodopsin by nanobody binding to its extracellular domain. Nat Commun 2023; 14:5209. [PMID: 37626045 PMCID: PMC10457330 DOI: 10.1038/s41467-023-40911-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
Rhodopsin is a prototypical G protein-coupled receptor (GPCR) critical for vertebrate vision. Research on GPCR signaling states has been facilitated using llama-derived nanobodies (Nbs), some of which bind to the intracellular surface to allosterically modulate the receptor. Extracellularly binding allosteric nanobodies have also been investigated, but the structural basis for their activity has not been resolved to date. Here, we report a library of Nbs that bind to the extracellular surface of rhodopsin and allosterically modulate the thermodynamics of its activation process. Crystal structures of Nb2 in complex with native rhodopsin reveal a mechanism of allosteric modulation involving extracellular loop 2 and native glycans. Nb2 binding suppresses Schiff base deprotonation and hydrolysis and prevents intracellular outward movement of helices five and six - a universal activation event for GPCRs. Nb2 also mitigates protein misfolding in a disease-associated mutant rhodopsin. Our data show the power of nanobodies to modulate the photoactivation of rhodopsin and potentially serve as therapeutic agents for disease-associated rhodopsin misfolding.
Collapse
Affiliation(s)
- Arum Wu
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, CA, 92697, USA
| | - David Salom
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, CA, 92697, USA
| | - John D Hong
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, CA, 92697, USA
- Department of Chemistry, University of California, Irvine, CA, 92697, USA
| | - Aleksander Tworak
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, CA, 92697, USA
| | - Kohei Watanabe
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, 466- 8555, Japan
- PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
| | - Els Pardon
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
- VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - Jan Steyaert
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
- VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, 466- 8555, Japan
- OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya, 466-8555, Japan
| | - Kota Katayama
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, 466- 8555, Japan.
- PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan.
- OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya, 466-8555, Japan.
| | - Philip D Kiser
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, CA, 92697, USA.
- Department of Physiology & Biophysics, University of California, Irvine, CA, USA.
- Department of Clinical Pharmacy Practice, University of California, Irvine, CA, USA.
- Research Service, VA Long Beach Healthcare System, Long Beach, CA, USA.
| | - Krzysztof Palczewski
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, CA, 92697, USA.
- Department of Chemistry, University of California, Irvine, CA, 92697, USA.
- Department of Physiology & Biophysics, University of California, Irvine, CA, USA.
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, 92697, USA.
| |
Collapse
|
6
|
Mattheisen JM, Limberakis C, Ruggeri RB, Dowling MS, Am Ende CW, Ceraudo E, Huber T, McClendon CL, Sakmar TP. Bioorthogonal Tethering Enhances Drug Fragment Affinity for G Protein-Coupled Receptors in Live Cells. J Am Chem Soc 2023; 145:11173-11184. [PMID: 37116188 DOI: 10.1021/jacs.3c00972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
G protein-coupled receptors (GPCRs) modulate diverse cellular signaling pathways and are important drug targets. Despite the availability of high-resolution structures, the discovery of allosteric modulators remains challenging due to the dynamic nature of GPCRs in native membranes. We developed a strategy to covalently tether drug fragments adjacent to allosteric sites in GPCRs to enhance their potency and enable fragment-based drug screening in cell-based systems. We employed genetic code expansion to site-specifically introduce noncanonical amino acids with reactive groups in C-C chemokine receptor 5 (CCR5) near an allosteric binding site for the drug maraviroc. We then used molecular dynamics simulations to design heterobifunctional maraviroc analogues consisting of a drug fragment connected by a flexible linker to a reactive moiety capable of undergoing a bioorthogonal coupling reaction. We synthesized a library of these analogues and employed the bioorthogonal inverse electron demand Diels-Alder reaction to couple the analogues to the engineered CCR5 in live cells, which were then assayed using cell-based signaling assays. Tetherable low-affinity maraviroc fragments displayed an increase in potency for CCR5 engineered with reactive unnatural amino acids that were adjacent to the maraviroc binding site. The strategy we describe to tether novel drug fragments to GPCRs should prove useful to probe allosteric or cryptic binding site functionality in fragment-based GPCR-targeted drug discovery.
Collapse
Affiliation(s)
- Jordan M Mattheisen
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York 10065, United States
- Tri-Institutional PhD Program in Chemical Biology, New York, New York 10065, United States
| | - Chris Limberakis
- Pfizer Worldwide Research, Development, and Medical, Groton, Connecticut 06340, United States
| | - Roger B Ruggeri
- Pfizer Worldwide Research, Development, and Medical, Groton, Connecticut 06340, United States
| | - Matthew S Dowling
- Pfizer Worldwide Research, Development, and Medical, Groton, Connecticut 06340, United States
| | - Christopher W Am Ende
- Pfizer Worldwide Research, Development, and Medical, Groton, Connecticut 06340, United States
| | - Emilie Ceraudo
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York 10065, United States
| | - Thomas Huber
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York 10065, United States
| | - Christopher L McClendon
- Pfizer Worldwide Research, Development, and Medical, Cambridge, Massachusetts 02139, United States
| | - Thomas P Sakmar
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York 10065, United States
| |
Collapse
|
7
|
Liessmann F, Künze G, Meiler J. Improving the Modeling of Extracellular Ligand Binding Pockets in RosettaGPCR for Conformational Selection. Int J Mol Sci 2023; 24:7788. [PMID: 37175495 PMCID: PMC10178219 DOI: 10.3390/ijms24097788] [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: 04/03/2023] [Revised: 04/19/2023] [Accepted: 04/22/2023] [Indexed: 05/15/2023] Open
Abstract
G protein-coupled receptors (GPCRs) are the largest class of drug targets and undergo substantial conformational changes in response to ligand binding. Despite recent progress in GPCR structure determination, static snapshots fail to reflect the conformational space of putative binding pocket geometries to which small molecule ligands can bind. In comparative modeling of GPCRs in the absence of a ligand, often a shrinking of the orthosteric binding pocket is observed. However, the exact prediction of the flexible orthosteric binding site is crucial for adequate structure-based drug discovery. In order to improve ligand docking and guide virtual screening experiments in computer-aided drug discovery, we developed RosettaGPCRPocketSize. The algorithm creates a conformational ensemble of biophysically realistic conformations of the GPCR binding pocket between the TM bundle, which is consistent with a knowledge base of expected pocket geometries. Specifically, tetrahedral volume restraints are defined based on information about critical residues in the orthosteric binding site and their experimentally observed range of Cα-Cα-distances. The output of RosettaGPCRPocketSize is an ensemble of binding pocket geometries that are filtered by energy to ensure biophysically probable arrangements, which can be used for docking simulations. In a benchmark set, pocket shrinkage observed in the default RosettaGPCR was reduced by up to 80% and the binding pocket volume range and geometric diversity were increased. Compared to models from four different GPCR homology model databases (RosettaGPCR, GPCR-Tasser, GPCR-SSFE, and GPCRdb), the here-created models showed more accurate volumes of the orthosteric pocket when evaluated with respect to the crystallographic reference structure. Furthermore, RosettaGPCRPocketSize was able to generate an improved realistic pocket distribution. However, while being superior to other homology models, the accuracy of generated model pockets was comparable to AlphaFold2 models. Furthermore, in a docking benchmark using small-molecule ligands with a higher molecular weight between 400 and 700 Da, a higher success rate in creating native-like binding poses was observed. In summary, RosettaGPCRPocketSize can generate GPCR models with realistic orthosteric pocket volumes, which are useful for structure-based drug discovery applications.
Collapse
Affiliation(s)
- Fabian Liessmann
- Institute for Drug Discovery, Medical Faculty, Leipzig University, 04103 Leipzig, Germany; (F.L.)
| | - Georg Künze
- Institute for Drug Discovery, Medical Faculty, Leipzig University, 04103 Leipzig, Germany; (F.L.)
| | - Jens Meiler
- Institute for Drug Discovery, Medical Faculty, Leipzig University, 04103 Leipzig, Germany; (F.L.)
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA
- Center for Scalable Data Analytics and Artificial Intelligence, Leipzig University, 04105 Leipzig, Germany
| |
Collapse
|
8
|
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: 21] [Impact Index Per Article: 21.0] [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.
Collapse
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.
| |
Collapse
|
9
|
Poria D, Kolesnikov AV, Lee TJ, Salom D, Palczewski K, Kefalov VJ. Investigating the Role of Rhodopsin F45L Mutation in Mouse Rod Photoreceptor Signaling and Survival. eNeuro 2023; 10:ENEURO.0330-22.2023. [PMID: 36823167 PMCID: PMC9997694 DOI: 10.1523/eneuro.0330-22.2023] [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: 08/19/2022] [Revised: 01/16/2023] [Accepted: 01/24/2023] [Indexed: 02/25/2023] Open
Abstract
Rhodopsin is the critical receptor molecule which enables vertebrate rod photoreceptor cells to detect a single photon of light and initiate a cascade of molecular events leading to visual perception. Recently, it has been suggested that the F45L mutation in the transmembrane helix of rhodopsin disrupts its dimerization in vitro To determine whether this mutation of rhodopsin affects its signaling properties in vivo, we generated knock-in mice expressing the rhodopsin F45L mutant. We then examined the function of rods in the mutant mice versus wild-type controls, using in vivo electroretinography and transretinal and single cell suction recordings, combined with morphologic analysis and spectrophotometry. Although we did not evaluate the effect of the F45L mutation on the state of dimerization of the rhodopsin in vivo, our results revealed that F45L-mutant mice exhibit normal retinal morphology, normal rod responses as measured both in vivo and ex vivo, and normal rod dark adaptation. We conclude that the F45L mutation does not affect the signaling properties of rhodopsin in its natural setting.
Collapse
Affiliation(s)
- Deepak Poria
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, CA 92697
| | - Alexander V Kolesnikov
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, CA 92697
| | - Tae Jun Lee
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, Saint Louis, MO 63110
| | - David Salom
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, CA 92697
| | - Krzysztof Palczewski
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, CA 92697
- Department of Chemistry, University of California, Irvine, CA 92697
- Department of Physiology and Biophysics, University of California, Irvine, CA 92697
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697
| | - Vladimir J Kefalov
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, CA 92697
- Department of Physiology and Biophysics, University of California, Irvine, CA 92697
| |
Collapse
|
10
|
Leemann S, Kleinlogel S. Functional optimization of light-activatable Opto-GPCRs: Illuminating the importance of the proximal C-terminus in G-protein specificity. Front Cell Dev Biol 2023; 11:1053022. [PMID: 36936685 PMCID: PMC10014536 DOI: 10.3389/fcell.2023.1053022] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 02/14/2023] [Indexed: 03/05/2023] Open
Abstract
Introduction: G-protein coupled receptors (GPCRs) are the largest family of human receptors that transmit signals from natural ligands and pharmaceutical drugs into essentially every physiological process. One main characteristic of G-protein coupled receptors is their ability to specifically couple with different families of G-proteins, thereby triggering specific downstream signaling pathways. While an abundance of structural information is available on G-protein coupled receptorn interactions with G-proteins, little is known about the G-protein coupled receptor domains functionally mediating G-protein specificity, in particular the proximal C-terminus, the structure which cannot be predicted with high confidentiality due to its flexibility. Methods: In this study, we exploited OptoGPCR chimeras between lightgated G-protein coupled receptors (opsins) and ligand-gated G-protein coupled receptors to systematically investigate the involvement of the C-terminus steering G-protein specificity. We employed rhodopsin-beta2-adrenoceptor and melanopsin-mGluR6 chimeras in second messenger assays and developed structural models of the chimeras. Results: We discovered a dominant role of the proximal C-terminus, dictating G-protein selectivity in the melanopsin-mGluR6 chimera, whereas it is the intracellular loop 3, which steers G-protein tropism in the rhodopsin-beta2-adrenoceptor. From the functional results and structural predictions, melanopsin and mGluR6 use a different mechanism to bovine rhodopsin and b2AR to couple to a selective G-protein. Discussion: Collectively, this work adds knowledge to the G-protein coupled receptor domains mediating G-protein selectivity, ultimately paving the way to optogenetically elicited specific G-protein signaling on demand.
Collapse
|
11
|
McIntire WE. A model for how Gβγ couples Gα to GPCR. J Gen Physiol 2022; 154:213096. [PMID: 35333292 PMCID: PMC8961292 DOI: 10.1085/jgp.202112982] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 02/28/2022] [Indexed: 11/20/2022] Open
Abstract
Representing ∼5% of the human genome, G-protein-coupled receptors (GPCRs) are a primary target for drug discovery; however, the molecular details of how they couple to heterotrimeric G protein subunits are incompletely understood. Here, I propose a hypothetical initial docking model for the encounter between GPCR and Gβγ that is defined by transient interactions between the cytosolic surface of the GPCR and the prenyl moiety and the tripeptide motif, asparagine-proline-phenylalanine (NPF), in the C-terminus of the Gγ subunit. Analysis of class A GPCRs reveals a conserved NPF binding site formed by the interaction of the TM1 and H8. Functional studies using differentially prenylated proteins and peptides further suggest that the intracellular hydrophobic core of the GPCR is a prenyl binding site. Upon binding TM1 and H8 of GPCRs, the propensity of the C-terminal region of Gγ to convert into an α helix allows it to extend into the hydrophobic core of the GPCR, facilitating the GPCR active state. Conservation of the NPF motif in Gγ isoforms and interacting residues in TM1 and H8 suggest that this is a general mechanism of GPCR-G protein signaling. Analysis of the rhodopsin dimer also suggests that Gγ-rhodopsin interactions may facilitate GPCR dimer transactivation.
Collapse
Affiliation(s)
- William E McIntire
- Department of Molecular Physiology and Biological Physics, University of Virginia Health System, Charlottesville, VA
| |
Collapse
|
12
|
Zhang B, Li S, Shui W. Post-Translational Modifications of G Protein–Coupled Receptors Revealed by Proteomics and Structural Biology. Front Chem 2022; 10:843502. [PMID: 35355784 PMCID: PMC8960047 DOI: 10.3389/fchem.2022.843502] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Accepted: 02/16/2022] [Indexed: 01/20/2023] Open
Abstract
G protein–coupled receptors (GPCRs) are a protein superfamily comprising >800 members that regulate numerous cellular and physiologic responses. GPCRs represent the largest class of therapeutic targets with implications in various diseases. Although advances in GPCR structural and pharmacological research have significantly improved our knowledge of GPCR signaling mechanisms, mapping diverse post-translational modifications (PTMs) of GPCR proteins and understanding their regulatory roles have received much less attention. Mass spectrometry-based proteomics has become the most popular technology for profiling protein PTMs in a systematic manner. Herein we provide an overview of PTM types, locations, crosstalk and dynamic regulation for different GPCRs that are characterized using proteomic and/or biochemical approaches. Our main focus is on glycosylation, phosphorylation, ubiquitination and palmitoylation that are known to modulate receptor folding, biosynthesis, trafficking, dimerization and signaling. Furthermore, we discuss the locations of specific PTM sites in the structure of a given GPCR and its signaling complex to highlight the importance of PTM regulation in the molecular basis of GPCRs, which may shed new light on structure-based drug discovery.
Collapse
Affiliation(s)
- Bingjie Zhang
- iHuman Institute, ShanghaiTech University, Shanghai, China
| | - Shanshan Li
- iHuman Institute, ShanghaiTech University, Shanghai, China
| | - Wenqing Shui
- iHuman Institute, ShanghaiTech University, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- *Correspondence: Wenqing Shui,
| |
Collapse
|
13
|
Ortega JT, Jastrzebska B. Rhodopsin as a Molecular Target to Mitigate Retinitis Pigmentosa. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1371:61-77. [PMID: 34962636 DOI: 10.1007/5584_2021_682] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Retinitis pigmentosa (RP) is a group of hereditary degenerative diseases affecting 1 of 4000 people worldwide and being the most prevalent cause of visual handicap among working populations in developed countries. These disorders are mainly related to the abnormalities in the rod G protein-coupled receptor (GPCR), rhodopsin reflected in the dysregulated membrane trafficking, stability and phototransduction processes that lead to progressive loss of retina function and eventually blindness. Currently, there is no cure for RP, and the therapeutic options are limited. Targeting rhodopsin with small molecule chaperones to improve the folding and stability of the mutant receptor is one of the most promising pharmacological approaches to alleviate the pathology of RP. This review provides an update on the current knowledge regarding small molecule compounds that have been evaluated as rhodopsin modulators to be considered as leads for the development of novel therapies for RP.
Collapse
Affiliation(s)
- Joseph T Ortega
- Department of Pharmacology, School of Medicine, Cleveland Center for Membrane and Structural Biology, Case Western Reserve University, Cleveland, OH, USA
| | - Beata Jastrzebska
- Department of Pharmacology, School of Medicine, Cleveland Center for Membrane and Structural Biology, Case Western Reserve University, Cleveland, OH, USA.
| |
Collapse
|
14
|
Guérin DMA, Digilio A, Branda MM. Dimeric Rhodopsin R135L Mutant-Transducin-like Complex Sheds Light on Retinitis Pigmentosa Misfunctions. J Phys Chem B 2021; 125:12958-12971. [PMID: 34793169 DOI: 10.1021/acs.jpcb.1c06348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Rhodopsin (RHO) is a light-sensitive pigment in the retina and the main prototypical protein of the G-protein-coupled receptor (GCPR) family. After receiving a light stimulus, RHO and its cofactor retinylidene undergo a series of structural changes that initiate an intricate transduction mechanism. Along with RHO, other partner proteins play key roles in the signaling pathway. These include transducin, a GTPase, kinases that phosphorylate RHO, and arrestin (Arr), which ultimately stops the signaling process and promotes RHO regeneration. A large number of RHO genetic mutations may lead to very severe retinal dysfunction and eventually to impaired dark adaptation disease called autosomal dominant retinitis pigmentosa (adRP). In this study, we used molecular dynamics (MD) simulations to evaluate the different behaviors of the dimeric form of wild-type RHO (WT dRHO) and its mutant at position 135 of arginine to leucine (dR135L), both in the free (noncomplexed) and in complex with the transducin-like protein (Gtl). Gtl is a heterotrimeric model composed of a mixture of human and bovine G proteins. Our calculations allow us to explain how the mutation causes structural changes in the RHO dimer and how this can affect the signal that transducin generates when it is bound to RHO. Moreover, the structural modifications induced by the R135L mutation can also account for other misfunctions observed in the up- and downstream signaling pathways. The mechanism of these dysfunctions, together with the transducin activity reduction, provides structure-based explanations of the impairment of some key processes that lead to adRP.
Collapse
Affiliation(s)
- Diego M A Guérin
- Department of Biochemistry and Molecular Biology, University of the Basque Country (EHU) and Instituto Biofisika (CSIC, UPV/EHU), Barrio Sarriena S/N, 48940 Leioa, Vizcaya, Spain
| | - Ayelen Digilio
- Department of Physics, National University of San Luis (UNSL), Av. Ejército de los Andes 950, 5700 San Luis, Argentina
| | - María Marta Branda
- Institute of Applied Physics (CONICET-UNSL), Av. Ejercito de los Andes 950, 5700 San Luis, Argentina
| |
Collapse
|
15
|
Tse LH, Wong YH. Modeling the Heterodimer Interfaces of Melatonin Receptors. Front Cell Neurosci 2021; 15:725296. [PMID: 34690701 PMCID: PMC8529217 DOI: 10.3389/fncel.2021.725296] [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: 06/15/2021] [Accepted: 08/16/2021] [Indexed: 11/16/2022] Open
Abstract
Melatonin receptors are Class A G protein-coupled receptors (GPCRs) that regulate a plethora of physiological activities in response to the rhythmic secretion of melatonin from the pineal gland. Melatonin is a key regulator in the control of circadian rhythm and has multiple functional roles in retinal physiology, memory, immunomodulation and tumorigenesis. The two subtypes of human melatonin receptors, termed MT1 and MT2, utilize overlapping signaling pathways although biased signaling properties have been reported in some cellular systems. With the emerging concept of GPCR dimerization, melatonin receptor heterodimers have been proposed to participate in system-biased signaling. Here, we used computational approaches to map the dimerization interfaces of known heterodimers of melatonin receptors, including MT1/MT2, MT1/GPR50, MT2/GPR50, and MT2/5-HT2C. By homology modeling and membrane protein docking analyses, we have identified putative preferred interface interactions within the different pairs of melatonin receptor dimers and provided plausible structural explanations for some of the unique pharmacological features of specific heterodimers previously reported. A thorough understanding of the molecular basis of melatonin receptor heterodimers may enable the development of new therapeutic approaches against aliments involving these heterodimeric receptors.
Collapse
Affiliation(s)
- Lap Hang Tse
- Division of Life Science and the Biotechnology Research Institute, Hong Kong University of Science and Technology, Hong Kong, SAR China
| | - Yung Hou Wong
- Division of Life Science and the Biotechnology Research Institute, Hong Kong University of Science and Technology, Hong Kong, SAR China.,State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, Hong Kong University of Science and Technology, Hong Kong, SAR China.,Hong Kong Center for Neurodegenerative Diseases, Hong Kong Science Park, Hong Kong, SAR China
| |
Collapse
|
16
|
Lamprakis C, Andreadelis I, Manchester J, Velez-Vega C, Duca JS, Cournia Z. Evaluating the Efficiency of the Martini Force Field to Study Protein Dimerization in Aqueous and Membrane Environments. J Chem Theory Comput 2021; 17:3088-3102. [PMID: 33913726 DOI: 10.1021/acs.jctc.0c00507] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Protein-protein complex assembly is one of the major drivers of biological response. Understanding the mechanisms of protein oligomerization/dimerization would allow one to elucidate how these complexes participate in biological activities and could ultimately lead to new approaches in designing novel therapeutic agents. However, determining the exact association pathways and structures of such complexes remains a challenge. Here, we use parallel tempering metadynamics simulations in the well-tempered ensemble to evaluate the performance of Martini 2.2P and Martini open-beta 3 (Martini 3) force fields in reproducing the structure and energetics of the dimerization process of membrane proteins and proteins in an aqueous solution in reasonable accuracy and throughput. We find that Martini 2.2P systematically overestimates the free energy of association by estimating large barriers in distinct areas, which likely leads to overaggregation when multiple monomers are present. In comparison, the less viscous Martini 3 results in a systematic underestimation of the free energy of association for proteins in solution, while it performs well in describing the association of membrane proteins. In all cases, the near-native dimer complexes are identified as minima in the free energy surface albeit not always as the lowest minima. In the case of Martini 3, we find that the spurious supramolecular protein aggregation present in Martini 2.2P multimer simulations is alleviated and thus this force field may be more suitable for the study of protein oligomerization. We propose that the use of enhanced sampling simulations with a refined coarse-grained force field and appropriately defined collective variables is a robust approach for studying the protein dimerization process, although one should be cautious of the ranking of energy minima.
Collapse
Affiliation(s)
- Christos Lamprakis
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527 Athens, Greece
| | - Ioannis Andreadelis
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527 Athens, Greece
| | - John Manchester
- Computer-Aided Drug Discovery, Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Camilo Velez-Vega
- Computer-Aided Drug Discovery, Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - José S Duca
- Computer-Aided Drug Discovery, Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Zoe Cournia
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527 Athens, Greece
| |
Collapse
|
17
|
Fang X, Peden AA, van Eeden FJM, Malicki JJ. Identification of additional outer segment targeting signals in zebrafish rod opsin. J Cell Sci 2021; 134:jcs.254995. [PMID: 33589494 DOI: 10.1242/jcs.254995] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 02/01/2021] [Indexed: 11/20/2022] Open
Abstract
In vertebrate photoreceptors, opsins are highly concentrated in a morphologically distinct ciliary compartment known as the outer segment (OS). Opsin is synthesized in the cell body and transported to the OS at a remarkable rate of 100 to 1000 molecules per second. Opsin transport defects contribute to photoreceptor loss and blindness in human ciliopathies. Previous studies revealed that the rhodopsin C-terminal tail, of 44 amino acids, is sufficient to mediate OS targeting in Xenopus photoreceptors. Here, we show that, although the Xenopus C-terminus retains this function in zebrafish, the homologous zebrafish sequence is not sufficient to target opsin to the OS. This functional difference is largely caused by a change of a single amino acid present in Xenopus but not in other vertebrates examined. Furthermore, we find that sequences in the third intracellular cytoplasmic loop (IC3) and adjacent regions of transmembrane helices 6 and 7 are also necessary for opsin transport in zebrafish. Combined with the cytoplasmic tail, these sequences are sufficient to target opsin to the ciliary compartment.
Collapse
Affiliation(s)
- Xiaoming Fang
- Bateson Centre and Department of Biomedical Science, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK
| | - Andrew A Peden
- Department of Biomedical Science, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK
| | - Fredericus J M van Eeden
- Bateson Centre and Department of Biomedical Science, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK
| | - Jarema J Malicki
- Bateson Centre and Department of Biomedical Science, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK
| |
Collapse
|
18
|
Fanelli F, Felline A, Marigo V. Structural aspects of rod opsin and their implication in genetic diseases. Pflugers Arch 2021; 473:1339-1359. [PMID: 33728518 DOI: 10.1007/s00424-021-02546-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 02/17/2021] [Accepted: 02/22/2021] [Indexed: 01/04/2023]
Abstract
Vision in dim-light conditions is triggered by photoactivation of rhodopsin, the visual pigment of rod photoreceptor cells. Rhodopsin is made of a protein, the G protein coupled receptor (GPCR) opsin, and the chromophore 11-cis-retinal. Vertebrate rod opsin is the GPCR best characterized at the atomic level of detail. Since the release of the first crystal structure 20 years ago, a huge number of structures have been released that, in combination with valuable spectroscopic determinations, unveiled most aspects of the photobleaching process. A number of spontaneous mutations of rod opsin have been found linked to vision-impairing diseases like autosomal dominant or autosomal recessive retinitis pigmentosa (adRP or arRP, respectively) and autosomal congenital stationary night blindness (adCSNB). While adCSNB is mainly caused by constitutive activation of rod opsin, RP shows more variegate determinants affecting different aspects of rod opsin function. The vast majority of missense rod opsin mutations affects folding and trafficking and is linked to adRP, an incurable disease that awaits light on its molecular structure determinants. This review article summarizes all major structural information available on vertebrate rod opsin conformational states and the insights gained so far into the structural determinants of adCSNB and adRP linked to rod opsin mutations. Strategies to design small chaperones with therapeutic potential for selected adRP rod opsin mutants will be discussed as well.
Collapse
Affiliation(s)
- Francesca Fanelli
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 103, 41125, Modena, Italy. .,Center for Neuroscience and Neurotechnology, University of Modena and Reggio Emilia, via Campi 287, Modena, 41125, Italy.
| | - Angelo Felline
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 103, 41125, Modena, Italy
| | - Valeria Marigo
- Center for Neuroscience and Neurotechnology, University of Modena and Reggio Emilia, via Campi 287, Modena, 41125, Italy.,Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 287, 41125, Modena, Italy
| |
Collapse
|
19
|
Park PSH. Supramolecular organization of rhodopsin in rod photoreceptor cell membranes. Pflugers Arch 2021; 473:1361-1376. [PMID: 33591421 DOI: 10.1007/s00424-021-02522-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 01/12/2021] [Accepted: 01/18/2021] [Indexed: 11/30/2022]
Abstract
Rhodopsin is the light receptor in rod photoreceptor cells that initiates scotopic vision. Studies on the light receptor span well over a century, yet questions about the organization of rhodopsin within the photoreceptor cell membrane still persist and a consensus view on the topic is still elusive. Rhodopsin has been intensely studied for quite some time, and there is a wealth of information to draw from to formulate an organizational picture of the receptor in native membranes. Early experimental evidence in apparent support for a monomeric arrangement of rhodopsin in rod photoreceptor cell membranes is contrasted and reconciled with more recent visual evidence in support of a supramolecular organization of rhodopsin. What is known so far about the determinants of forming a supramolecular structure and possible functional roles for such an organization are also discussed. Many details are still missing on the structural and functional properties of the supramolecular organization of rhodopsin in rod photoreceptor cell membranes. The emerging picture presented here can serve as a springboard towards a more in-depth understanding of the topic.
Collapse
Affiliation(s)
- Paul S-H Park
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA.
| |
Collapse
|
20
|
Mazzotta S, Governa P, Borgonetti V, Marcolongo P, Nanni C, Gamberucci A, Manetti F, Pessina F, Carullo G, Brizzi A, Aiello F. Pinocembrin and its linolenoyl ester derivative induce wound healing activity in HaCaT cell line potentially involving a GPR120/FFA4 mediated pathway. Bioorg Chem 2021; 108:104657. [PMID: 33556697 DOI: 10.1016/j.bioorg.2021.104657] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 01/07/2021] [Accepted: 01/12/2021] [Indexed: 12/17/2022]
Abstract
Wound healing represents an urgent need from the clinical point of view. Several diseases result in wound conditions which are difficult to treat, such as in the case of diabetic foot ulcer. Starting from there, the medicinal research has focused on various targets over the years, including GPCRs as new wound healing drug targets. In line with this, GPR120, known to be an attractive target in type 2 diabetes drug discovery, was studied to finalize the development of new wound healing agents. Pinocembrin (HW0) was evaluated as a suitable compound for interacting with GPR120, and was hybridized with fatty acids, which are known endogenous GPR120 ligands, to enhance the wound healing potential and GPR120 interactions. HW0 and its 7-linolenoyl derivative (HW3) were found to be innovative wound healing agents. Immunofluorescence and functional assays suggested that their activity was mediated by GPR120, and docking simulations showed that the compounds could share the same pocket occupied by the known GPR120 agonist, TUG-891.
Collapse
Affiliation(s)
- Sarah Mazzotta
- Department of Pharmaceutical Sciences, Via Luigi Mangiagalli 25, 20133 Milano, Italy
| | - Paolo Governa
- Department of Biotechnology, Chemistry and Pharmacy - DoE 2018-2022, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Vittoria Borgonetti
- Department of Neuroscience, Psychology, Pharmacology and Child Health (NEUROFARBA), University of Florence, Viale Pieraccini 6, 50139 Firenze, Italy
| | - Paola Marcolongo
- Department of Molecular and Developmental Medicine, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Claudio Nanni
- Department of Molecular and Developmental Medicine, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Alessandra Gamberucci
- Department of Molecular and Developmental Medicine, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Fabrizio Manetti
- Department of Biotechnology, Chemistry and Pharmacy - DoE 2018-2022, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy.
| | - Federica Pessina
- Department of Molecular and Developmental Medicine, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy.
| | - Gabriele Carullo
- Department of Biotechnology, Chemistry and Pharmacy - DoE 2018-2022, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy.
| | - Antonella Brizzi
- Department of Biotechnology, Chemistry and Pharmacy - DoE 2018-2022, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Francesca Aiello
- Department of Pharmacy, Health and Nutritional Sciences - DoE 2018-2022, University of Calabria, Ed. Polifunzionale, 87036 Arcavacata di Rende (CS), Italy
| |
Collapse
|
21
|
Abe H, Kawasaki A, Takeda T, Hoshino N, Matsuda W, Seki S, Akutagawa T. Switching of Electron and Ion Conductions by Reversible H 2O Sorption in n-Type Organic Semiconductors. ACS APPLIED MATERIALS & INTERFACES 2020; 12:37391-37399. [PMID: 32814389 DOI: 10.1021/acsami.0c09501] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Polar H2O molecules generally act as trapping sites and suppress the electron mobility of n-type organic semiconductors, making chemical design of H2O-tolerant and responsive n-type semiconductors an important step toward multifunctional electron-ion coupling devices. The introduction of effective electrostatic interactions between potassium ions (K+) and carboxylate (-COO-) anions into the electron-transporting naphthalenediimide π-framework enables the design of high-performance H2O-tolerant n-type semiconductors with a reversible H2O adsorption-desorption ability, where the electron mobility and K+ ionic conductivity were coupled with the reversible H2O sorption behavior. The reversible H2O adsorption into the crystals enhanced the electron mobility from 0.04 to 0.28 cm2 V-1 s-1, whereas the K+ ionic conductivity decreased from 3.4 × 10-5 to 4.7 × 10-7 S cm-1. Because this reversible electron-ion conducting switch is responsive to H2O sorption behavior, it is a strong candidate for H2O gating carrier transport systems.
Collapse
Affiliation(s)
- Haruka Abe
- Graduate School of Engineering, Tohoku University, Sendai 980-8579, Japan
| | - Ayumi Kawasaki
- Graduate School of Engineering, Tohoku University, Sendai 980-8579, Japan
| | - Takashi Takeda
- Graduate School of Engineering, Tohoku University, Sendai 980-8579, Japan
- Institute of Multidisciplinary Research for Advanced Materials (IMRAM), Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Norihisa Hoshino
- Graduate School of Engineering, Tohoku University, Sendai 980-8579, Japan
- Institute of Multidisciplinary Research for Advanced Materials (IMRAM), Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Wakana Matsuda
- Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Shu Seki
- Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Tomoyuki Akutagawa
- Graduate School of Engineering, Tohoku University, Sendai 980-8579, Japan
- Institute of Multidisciplinary Research for Advanced Materials (IMRAM), Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
| |
Collapse
|
22
|
Kaneshige Y, Hayashi F, Morigaki K, Tanimoto Y, Yamashita H, Fujii M, Awazu A. Affinity of rhodopsin to raft enables the aligned oligomer formation from dimers: Coarse-grained molecular dynamics simulation of disk membranes. PLoS One 2020; 15:e0226123. [PMID: 32032370 PMCID: PMC7006936 DOI: 10.1371/journal.pone.0226123] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 01/13/2020] [Indexed: 12/16/2022] Open
Abstract
The visual photopigment protein rhodopsin (Rh) is a typical G protein-coupled receptor (GPCR) that initiates the phototransduction cascade in retinal disk membrane of rod-photoreceptor cells. Rh molecule has a tendency to form dimer, and the dimer tends to form rows, which is suggested to heighten phototransduction efficiency in single-photon regime. In addition, the dimerization confers Rh an affinity for lipid raft, i.e. raftophilicity. However, the mechanism by which Rh-dimer raftophilicity contributes to the organization of the higher order structure remains unknown. In this study, we performed coarse-grained molecular dynamics simulations of a disk membrane model containing unsaturated lipids, saturated lipids with cholesterol, and Rh-dimers. We described the Rh-dimers by two-dimensional particle populations where the palmitoyl moieties of each Rh exhibits raftophilicity. We simulated the structuring of Rh in a disk for two types of Rh-dimer, i.e., the most and second most stable Rh dimers, which exposes the raftophilic regions at the dimerization-interface (H1/H8 dimer) and two edges away from the interface (H4/H5 dimer), respectively. Our simulations revealed that only the H1/H8 dimer could form a row structure. A small number of raftophilic lipids recruited to and intercalated in a narrow space between H1/H8 dimers stabilize the side-by-side interaction between dimers in a row. Our results implicate that the nano-sized lipid raft domains act as a “glue” to organize the long row structures of Rh-dimers.
Collapse
Affiliation(s)
- Yukito Kaneshige
- Department of Mathematical and Life Sciences, Hiroshima University, Kagamiyama, Higashi-Hiroshima, Japan
| | - Fumio Hayashi
- Graduate School of Science, Kobe University, Rokkodaicho, Nada, Kobe, Japan
| | - Kenichi Morigaki
- Biosignal Research Center, Kobe University, Rokkodaicho, Nada, Kobe, Japan
| | - Yasushi Tanimoto
- Graduate School of Science, Kobe University, Rokkodaicho, Nada, Kobe, Japan
| | - Hayato Yamashita
- Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka, Japan
| | - Masashi Fujii
- Department of Mathematical and Life Sciences, Hiroshima University, Kagamiyama, Higashi-Hiroshima, Japan
| | - Akinori Awazu
- Department of Mathematical and Life Sciences, Hiroshima University, Kagamiyama, Higashi-Hiroshima, Japan
- * E-mail:
| |
Collapse
|
23
|
Imamoto Y, Kojima K, Oka T, Maeda R, Shichida Y. Conformational Differences among Metarhodopsin I, Metarhodopsin II, and Opsin Probed by Wide-Angle X-ray Scattering. J Phys Chem B 2019; 123:9134-9142. [PMID: 31580080 DOI: 10.1021/acs.jpcb.9b08311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Among the photoproducts of vertebrate rhodopsin, only metarhodopsin II (Meta-II) preferentially adopts the active structure in which transmembrane helices are rearranged. Light-induced helical rearrangement of rhodopsin in membrane-embedded form was directly monitored by wide-angle X-ray scattering (WAXS) using nanodiscs. The change in the WAXS curve for the formation of Meta-II was characterized by a peak at 0.2 Å-1 and a valley at 0.6 Å-1, which were not observed in metarhodopsin I and opsin. However, acid-induced active opsin (Opsin*) showed a 0.2 Å-1 peak, but no 0.6 Å-1 valley. Analyses using the model structures based on the crystal structures of dark state and Meta-II suggest that the outward movement of helix VI occurred in Opsin*. However, the displaced helices III and V in Meta-II resulting from the disruption of cytoplasmic ionic lock were restored in Opsin*, which is likely to destabilize the G-protein-activating structure of opsin.
Collapse
Affiliation(s)
- Yasushi Imamoto
- Department of Biophysics, Graduate School of Science , Kyoto University , Kyoto 606-8502 , Japan
| | - Keiichi Kojima
- Department of Biophysics, Graduate School of Science , Kyoto University , Kyoto 606-8502 , Japan
| | | | - Ryo Maeda
- Department of Biophysics, Graduate School of Science , Kyoto University , Kyoto 606-8502 , Japan
| | - Yoshinori Shichida
- Research Organization for Science and Technology , Ritsumeikan University , Kusatsu , Shiga 525-8577 , Japan
| |
Collapse
|
24
|
Feldman TB, Ivankov OI, Kuklin AI, Murugova TN, Yakovleva MA, Smitienko OA, Kolchugina IB, Round A, Gordeliy VI, Belushkin AV, Ostrovsky MA. Small-angle neutron and X-ray scattering analysis of the supramolecular organization of rhodopsin in photoreceptor membrane. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:183000. [DOI: 10.1016/j.bbamem.2019.05.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 05/24/2019] [Accepted: 05/28/2019] [Indexed: 01/16/2023]
|
25
|
Zhao DY, Pöge M, Morizumi T, Gulati S, Van Eps N, Zhang J, Miszta P, Filipek S, Mahamid J, Plitzko JM, Baumeister W, Ernst OP, Palczewski K. Cryo-EM structure of the native rhodopsin dimer in nanodiscs. J Biol Chem 2019; 294:14215-14230. [PMID: 31399513 PMCID: PMC6768649 DOI: 10.1074/jbc.ra119.010089] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 08/02/2019] [Indexed: 02/03/2023] Open
Abstract
Imaging of rod photoreceptor outer-segment disc membranes by atomic force microscopy and cryo-electron tomography has revealed that the visual pigment rhodopsin, a prototypical class A G protein-coupled receptor (GPCR), can organize as rows of dimers. GPCR dimerization and oligomerization offer possibilities for allosteric regulation of GPCR activity, but the detailed structures and mechanism remain elusive. In this investigation, we made use of the high rhodopsin density in the native disc membranes and of a bifunctional cross-linker that preserves the native rhodopsin arrangement by covalently tethering rhodopsins via Lys residue side chains. We purified cross-linked rhodopsin dimers and reconstituted them into nanodiscs for cryo-EM analysis. We present cryo-EM structures of the cross-linked rhodopsin dimer as well as a rhodopsin dimer reconstituted into nanodiscs from purified monomers. We demonstrate the presence of a preferential 2-fold symmetrical dimerization interface mediated by transmembrane helix 1 and the cytoplasmic helix 8 of rhodopsin. We confirmed this dimer interface by double electron-electron resonance measurements of spin-labeled rhodopsin. We propose that this interface and the arrangement of two protomers is a prerequisite for the formation of the observed rows of dimers. We anticipate that the approach outlined here could be extended to other GPCRs or membrane receptors to better understand specific receptor dimerization mechanisms.
Collapse
Affiliation(s)
- Dorothy Yanling Zhao
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Matthias Pöge
- Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Takefumi Morizumi
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Sahil Gulati
- Gavin Herbert Eye Institute and the Department of Ophthalmology, University of California, Irvine, California 92697
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio 44106
| | - Ned Van Eps
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Jianye Zhang
- Gavin Herbert Eye Institute and the Department of Ophthalmology, University of California, Irvine, California 92697
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio 44106
| | - Przemyslaw Miszta
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw 02-093, Poland
| | - Slawomir Filipek
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw 02-093, Poland
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Jürgen M Plitzko
- Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Wolfgang Baumeister
- Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Oliver P Ernst
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Krzysztof Palczewski
- Gavin Herbert Eye Institute and the Department of Ophthalmology, University of California, Irvine, California 92697
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio 44106
| |
Collapse
|
26
|
Botta J, Bibic L, Killoran P, McCormick PJ, Howell LA. Design and development of stapled transmembrane peptides that disrupt the activity of G-protein-coupled receptor oligomers. J Biol Chem 2019; 294:16587-16603. [PMID: 31467080 PMCID: PMC6851324 DOI: 10.1074/jbc.ra119.009160] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 08/08/2019] [Indexed: 12/23/2022] Open
Abstract
Membrane proteins can associate into larger complexes. Examples include receptor tyrosine complexes, ion channels, transporters, and G protein–coupled receptors (GPCRs). For the latter, there is abundant evidence indicating that GPCRs assemble into complexes, through both homo- and heterodimerization. However, the tools for studying and disrupting these complexes, GPCR or otherwise, are limited. Here, we have developed stabilized interference peptides for this purpose. We have previously reported that tetrahydrocannabinol-mediated cognitive impairment arises from homo- or heterooligomerization between the GPCRs cannabinoid receptor type 1 (CB1R) and 5-hydroxytryptamine 2A (5-HT2AR) receptors. Here, to disrupt this interaction through targeting CB1–5-HT2A receptor heteromers in HEK293 cells and using an array of biochemical techniques, including calcium and cAMP measurements, bimolecular fluorescence complementation assays, and CD-based helicity assessments, we developed a NanoLuc binary technology (NanoBiT)-based reporter assay to screen a small library of aryl-carbon–stapled transmembrane-mimicking peptides produced by solid-phase peptide synthesis. We found that these stapling peptides have increased α-helicity and improved proteolytic resistance without any loss of disrupting activity in vitro, suggesting that this approach may also have utility in vivo. In summary, our results provide proof of concept for using NanoBiT to study membrane protein complexes and for stabilizing disrupting peptides to target such membrane complexes through hydrocarbon-mediated stapling. We propose that these peptides could be developed to target previously undruggable GPCR heteromers.
Collapse
Affiliation(s)
- Joaquín Botta
- Centre for Endocrinology, William Harvey Research Institute, Bart's and the London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, United Kingdom.,School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom
| | - Lucka Bibic
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom
| | - Patrick Killoran
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, James Parsons Building, Byrom Street, Liverpool L3 3AF, United Kingdom
| | - Peter J McCormick
- Centre for Endocrinology, William Harvey Research Institute, Bart's and the London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, United Kingdom
| | - Lesley A Howell
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom
| |
Collapse
|
27
|
Getter T, Gulati S, Zimmerman R, Chen Y, Vinberg F, Palczewski K. Stereospecific modulation of dimeric rhodopsin. FASEB J 2019; 33:9526-9539. [PMID: 31121099 PMCID: PMC6662988 DOI: 10.1096/fj.201900443rr] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 04/23/2019] [Indexed: 11/11/2022]
Abstract
The classic concept that GPCRs function as monomers has been challenged by the emerging evidence of GPCR dimerization and oligomerization. Rhodopsin (Rh) is the only GPCR whose native oligomeric arrangement was revealed by atomic force microscopy demonstrating that Rh exists as a dimer. However, the role of Rh dimerization in retinal physiology is currently unknown. In this study, we identified econazole and sulconazole, two small molecules that disrupt Rh dimer contacts, by implementing a cell-based high-throughput screening assay. Racemic mixtures of identified lead compounds were separated and tested for their stereospecific binding to Rh using UV-visible spectroscopy and intrinsic fluorescence of tryptophan (Trp) 265 after illumination. By following the changes in UV-visible spectra and Trp265 fluorescence in vitro, we found that binding of R-econazole modulates the formation of Meta III and quenches the intrinsic fluorescence of Trp265. In addition, electrophysiological ex vivo recording revealed that R-econazole slows photoresponse kinetics, whereas S-econazole decreased the sensitivity of rods without effecting the kinetics. Thus, this study contributes new methodology to identify compounds that disrupt the dimerization of GPCRs in general and validates the first active compounds that disrupt the Rh dimer specifically.-Getter, T., Gulati, S., Zimmerman, R., Chen, Y., Vinberg, F., Palczewski, K. Stereospecific modulation of dimeric rhodopsin.
Collapse
Affiliation(s)
- Tamar Getter
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California–Irvine, California, USA
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Sahil Gulati
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California–Irvine, California, USA
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio, USA
- Department of Physiology and Biophysics, University of California–Irvine, Irvine, California, USA
| | - Remy Zimmerman
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California–Irvine, California, USA
| | - Yuanyuan Chen
- Department of Ophthalmology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- McGowan Institute of Regenerative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Frans Vinberg
- Department of Ophthalmology and Visual Sciences, University of Utah, Salt Lake City, Utah, USA
| | - Krzysztof Palczewski
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California–Irvine, California, USA
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio, USA
- Department of Physiology and Biophysics, University of California–Irvine, Irvine, California, USA
| |
Collapse
|
28
|
Wink LH, Baker DL, Cole JA, Parrill AL. A benchmark study of loop modeling methods applied to G protein-coupled receptors. J Comput Aided Mol Des 2019; 33:573-595. [PMID: 31123958 PMCID: PMC6628340 DOI: 10.1007/s10822-019-00196-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 03/12/2019] [Indexed: 11/25/2022]
Abstract
G protein-coupled receptors (GPCR) are important drug discovery targets. Despite progress, many GPCR structures have not yet been solved. For these targets, comparative modeling is used in virtual ligand screening to prioritize experimental efforts. However, the structure of extracellular loop 2 (ECL2) is often poorly predicted. This is significant due to involvement of ECL2 in ligand binding for many Class A GPCR. Here we examine the performance of loop modeling protocols available in the Rosetta (cyclic coordinate descent [CCD], KIC with fragments [KICF] and next generation KIC [NGK]) and Molecular Operating Environment (MOE) software suites (de novo search). ECL2 from GPCR crystal structures served as the structure prediction targets and were divided into four sets depending on loop length. Results suggest that KICF and NGK sampled and scored more loop models with sub-angstrom and near-atomic accuracy than CCD or de novo search for loops of 24 or fewer residues. None of the methods were able to sample loop conformations with near-atomic accuracy for the longest targets ranging from 25 to 32 residues based on 1000 models generated. For these long loop targets, increased conformational sampling is necessary. The strongly conserved disulfide bond between Cys3.25 and Cys45.50 in ECL2 proved an effective filter. Setting an upper limit of 5.1 Å on the S-S distance improved the lowest RMSD model included in the top 10 scored structures in Groups 1-4 on average between 0.33 and 1.27 Å. Disulfide bond formation and geometry optimization of ECL2 provided an additional incremental benefit in structure quality.
Collapse
Affiliation(s)
- Lee H Wink
- Department of Chemistry, The University of Memphis, Memphis, TN, 38152, USA
| | - Daniel L Baker
- Department of Chemistry, The University of Memphis, Memphis, TN, 38152, USA
| | - Judith A Cole
- Department of Biological Sciences, The University of Memphis, Memphis, TN, 38152, USA
| | - Abby L Parrill
- Department of Chemistry, The University of Memphis, Memphis, TN, 38152, USA.
| |
Collapse
|
29
|
Yang M, Luo J, Zeng Z, Yang L, Xu L, Li Y. In silico profiling the interaction mechanism of 2,5-diketopiperazine derivatives as oxytocin antagonists. J Mol Graph Model 2019; 89:178-191. [PMID: 30904734 DOI: 10.1016/j.jmgm.2019.03.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 03/03/2019] [Accepted: 03/04/2019] [Indexed: 02/03/2023]
Abstract
Oxytocin plays a vital role in the occurrence of preterm birth by interacting with oxytocin receptor (OTR), and thus OTR antagonists provide effective approaches for the treatment of early birth. Presently, for purpose of exploring the structural traits affecting the antagonism potency, the up-to-date largest set of 121 2,5-diketopiperazine derivatives as OTR antagonists was subjected to ligand-based three-dimensional quantitative structure-activity (3D-QSAR) analysis applying comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) methods. The resultant optimal CoMSIA model displays proper validity and predictability with cross-validated correlation coefficient Q2 = 0.614, non-cross-validated correlation coefficient R2ncv = 0.969 and predicted correlation coefficient R2pre = 0.912 for the test set of compounds, respectively. In addition, docking study was carried out for further elucidating the binding modes of OTR antagonists. The final docking cavity was located among the TM2-TM7 helices of the target protein and proved to be the same as described by other scholars' researches of other type of OTR antagonists. The major amino acids forming the cavity are Q92, Q96, K116, Q119, V120, M123, G196, I201, Q295, W288, F311 and M315. Representative compound 118 forms two H-bonds with Q119 and two H-bonds with Q295, with also a π - π stacking effect with F311, respectively. Meanwhile, as a supplementary tool to study the antagonists' conformation in the binding cavity, molecular dynamics (MD) simulation was also performed to further elucidate the changes in the ligand-receptor complex. We hope that the obtained models and information may help to provide an insight into the interaction mechanism of OTR antagonists and facilitate the design and optimization of novel antagonists for preventing premature birth.
Collapse
Affiliation(s)
- Ming Yang
- School of Nursing, Guangzhou University of Chinese Medicine, Guangzhou, 510006, Guangzhou, China.
| | - Jianghe Luo
- School of Nursing, Guangzhou University of Chinese Medicine, Guangzhou, 510006, Guangzhou, China
| | - Zhumei Zeng
- School of Nursing, Guangzhou University of Chinese Medicine, Guangzhou, 510006, Guangzhou, China
| | - Ling Yang
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Limian Xu
- Department of Gynaecology and Obstetrics, Affiliated Hospital 1, Guangzhou University of Chinese Medicine, Guangzhou, 510006, Guangzhou, China
| | - Yan Li
- ChinaKey Laboratory of Xinjiang Endemic Phytomedicine Resources, Pharmacy School, Shihezi University, Shihezi, 832002, Xinjiang, China.
| |
Collapse
|
30
|
Edward Zhou X, Melcher K, Eric Xu H. Structural biology of G protein-coupled receptor signaling complexes. Protein Sci 2019; 28:487-501. [PMID: 30311978 PMCID: PMC6371222 DOI: 10.1002/pro.3526] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 09/30/2018] [Accepted: 10/01/2018] [Indexed: 12/13/2022]
Abstract
G protein-coupled receptors (GPCRs) constitute the largest family of cell surface receptors that mediate numerous cell signaling pathways, and are targets of more than one-third of clinical drugs. Thanks to the advancement of novel structural biology technologies, high-resolution structures of GPCRs in complex with their signaling transducers, including G-protein and arrestin, have been determined. These 3D complex structures have significantly improved our understanding of the molecular mechanism of GPCR signaling and provided a structural basis for signaling-biased drug discovery targeting GPCRs. Here we summarize structural studies of GPCR signaling complexes with G protein and arrestin using rhodopsin as a model system, and highlight the key features of GPCR conformational states in biased signaling including the sequence motifs of receptor TM6 that determine selective coupling of G proteins, and the phosphorylation codes of GPCRs for arrestin recruitment. We envision the future of GPCR structural biology not only to solve more high-resolution complex structures but also to show stepwise GPCR signaling complex assembly and disassembly and dynamic process of GPCR signal transduction.
Collapse
Affiliation(s)
- X. Edward Zhou
- Center for Cancer and Cell Biology, Innovation and Integration ProgramVan Andel Research InstituteGrand RapidsMichigan
| | - Karsten Melcher
- Center for Cancer and Cell Biology, Innovation and Integration ProgramVan Andel Research InstituteGrand RapidsMichigan
| | - H. Eric Xu
- Center for Cancer and Cell Biology, Innovation and Integration ProgramVan Andel Research InstituteGrand RapidsMichigan
- Key Laboratory of Receptor Research, VARI‐SIMM Center, Center for Structure and Function of Drug TargetsShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
| |
Collapse
|
31
|
Katayama K, Gulati S, Ortega JT, Alexander NS, Sun W, Shenouda MM, Palczewski K, Jastrzebska B. Specificity of the chromophore-binding site in human cone opsins. J Biol Chem 2019; 294:6082-6093. [PMID: 30770468 DOI: 10.1074/jbc.ra119.007587] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 02/13/2019] [Indexed: 01/21/2023] Open
Abstract
The variable composition of the chromophore-binding pocket in visual receptors is essential for vision. The visual phototransduction starts with the cis-trans isomerization of the retinal chromophore upon absorption of photons. Despite sharing the common 11-cis-retinal chromophore, rod and cone photoreceptors possess distinct photochemical properties. Thus, a detailed molecular characterization of the chromophore-binding pocket of these receptors is critical to understanding the differences in the photochemistry of vision between rods and cones. Unlike for rhodopsin (Rh), the crystal structures of cone opsins remain to be determined. To obtain insights into the specific chromophore-protein interactions that govern spectral tuning in human visual pigments, here we harnessed the unique binding properties of 11-cis-6-membered-ring-retinal (11-cis-6mr-retinal) with human blue, green, and red cone opsins. To unravel the specificity of the chromophore-binding pocket of cone opsins, we applied 11-cis-6mr-retinal analog-binding analyses to human blue, green, and red cone opsins. Our results revealed that among the three cone opsins, only blue cone opsin can accommodate the 11-cis-6mr-retinal in its chromophore-binding pocket, resulting in the formation of a synthetic blue pigment (B6mr) that absorbs visible light. A combination of primary sequence alignment, molecular modeling, and mutagenesis experiments revealed the specific amino acid residue 6.48 (Tyr-262 in blue cone opsins and Trp-281 in green and red cone opsins) as a selectivity filter in human cone opsins. Altogether, the results of our study uncover the molecular basis underlying the binding selectivity of 11-cis-6mr-retinal to the cone opsins.
Collapse
Affiliation(s)
- Kota Katayama
- From the Department of Pharmacology, Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106; Department of Life Science and Applied Chemistry, Showa-ku, Nagoya 466-8555, Japan; OptoBio Technology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Sahil Gulati
- Gavin Herbert Eye Institute and the Department of Ophthalmology, University of California, Irvine, California 92697
| | - Joseph T Ortega
- From the Department of Pharmacology, Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106
| | - Nathan S Alexander
- From the Department of Pharmacology, Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106
| | - Wenyu Sun
- Polgenix Inc., Cleveland, Ohio 44106
| | - Marina M Shenouda
- From the Department of Pharmacology, Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106
| | - Krzysztof Palczewski
- Gavin Herbert Eye Institute and the Department of Ophthalmology, University of California, Irvine, California 92697; Polgenix Inc., Cleveland, Ohio 44106.
| | - Beata Jastrzebska
- From the Department of Pharmacology, Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106.
| |
Collapse
|
32
|
Maroteaux L, Béchade C, Roumier A. Dimers of serotonin receptors: Impact on ligand affinity and signaling. Biochimie 2019; 161:23-33. [PMID: 30685449 DOI: 10.1016/j.biochi.2019.01.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 01/16/2019] [Indexed: 01/03/2023]
Abstract
Membrane receptors often form complexes with other membrane proteins that directly interact with different effectors of the signal transduction machinery. G-protein-coupled receptors (GPCRs) were for long time considered as single pharmacological entities. However, evidence for oligomerization appeared for various classes and subtypes of GPCRs. This review focuses on metabotropic serotonin (5-hydroxytryptamine, 5-HT) receptors, which belong to the rhodopsin-like class A of GPCRs, and will summarize the convergent evidence that homo- and hetero-dimers containing 5-HT receptors exist in transfected cells and in-vivo. We will show that complexes involving 5-HT receptors may acquire new signal transduction pathways and new physiological roles. In some cases, these complexes participate in disease-specific deregulations, that can be differentially affected by various drugs. Hence, selecting receptor complex-specific responses of these heterodimers may constitute an emerging strategy likely to improve beneficial therapeutic effects.
Collapse
Affiliation(s)
- Luc Maroteaux
- INSERM UMR-S839, S1270, Paris, 75005, France; Sorbonne Université, Paris, 75005, France; Institut du Fer à Moulin, Paris, 75005, France.
| | - Catherine Béchade
- INSERM UMR-S839, S1270, Paris, 75005, France; Sorbonne Université, Paris, 75005, France; Institut du Fer à Moulin, Paris, 75005, France
| | - Anne Roumier
- INSERM UMR-S839, S1270, Paris, 75005, France; Sorbonne Université, Paris, 75005, France; Institut du Fer à Moulin, Paris, 75005, France
| |
Collapse
|
33
|
Sharma A, Kumar R, Aier I, Semwal R, Tyagi P, Varadwaj P. Sense of Smell: Structural, Functional, Mechanistic Advancements and Challenges in Human Olfactory Research. Curr Neuropharmacol 2019; 17:891-911. [PMID: 30520376 PMCID: PMC7052838 DOI: 10.2174/1570159x17666181206095626] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 11/08/2018] [Accepted: 11/28/2018] [Indexed: 02/07/2023] Open
Abstract
Olfaction, the sense of smell detects and discriminate odors as well as social cues which influence our innate responses. The olfactory system in human beings is found to be weak as compared to other animals; however, it seems to be very precise. It can detect and discriminate millions of chemical moieties (odorants) even in minuscule quantities. The process initiates with the binding of odorants to specialized olfactory receptors, encoded by a large family of Olfactory Receptor (OR) genes belonging to the G-protein-coupled receptor superfamily. Stimulation of ORs converts the chemical information encoded in the odorants, into respective neuronal action-potentials which causes depolarization of olfactory sensory neurons. The olfactory bulb relays this signal to different parts of the brain for processing. Odors are encrypted using a combinatorial approach to detect a variety of chemicals and encode their unique identity. The discovery of functional OR genes and proteins provided an important information to decipher the genomic, structural and functional basis of olfaction. ORs constitute 17 gene families, out of which 4 families were reported to contain more than hundred members each. The olfactory machinery is not limited to GPCRs; a number of non- GPCRs is also employed to detect chemosensory stimuli. The article provides detailed information about such olfaction machinery, structures, transduction mechanism, theories of odor perception, and challenges in the olfaction research. It covers the structural, functional and computational studies carried out in the olfaction research in the recent past.
Collapse
Affiliation(s)
| | | | | | | | | | - Pritish Varadwaj
- Address correspondence to this author at the Department of Applied Science, Indian Institute of Information Technology, Allahabad, Uttar Pradesh, India; E-mail:
| |
Collapse
|
34
|
Structural biology of 11- cis-retinaldehyde production in the classical visual cycle. Biochem J 2018; 475:3171-3188. [PMID: 30352831 DOI: 10.1042/bcj20180193] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 09/20/2018] [Accepted: 09/26/2018] [Indexed: 12/21/2022]
Abstract
The vitamin A derivative 11-cis-retinaldehyde plays a pivotal role in vertebrate vision by serving as the chromophore of rod and cone visual pigments. In the initial step of vision, a photon is absorbed by this chromophore resulting in its isomerization to an all-trans state and consequent activation of the visual pigment and phototransduction cascade. Spent chromophore is released from the pigments through hydrolysis. Subsequent photon detection requires the delivery of regenerated 11-cis-retinaldehyde to the visual pigment. This trans-cis conversion is achieved through a process known as the visual cycle. In this review, we will discuss the enzymes, binding proteins and transporters that enable the visual pigment renewal process with a focus on advances made during the past decade in our understanding of their structural biology.
Collapse
|
35
|
Mallory DP, Gutierrez E, Pinkevitch M, Klinginsmith C, Comar WD, Roushar FJ, Schlebach JP, Smith AW, Jastrzebska B. The Retinitis Pigmentosa-Linked Mutations in Transmembrane Helix 5 of Rhodopsin Disrupt Cellular Trafficking Regardless of Oligomerization State. Biochemistry 2018; 57:5188-5201. [PMID: 30085663 DOI: 10.1021/acs.biochem.8b00403] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
G protein-coupled receptors can exist as dimers and higher-order oligomers in biological membranes. The specific oligomeric assembly of these receptors is believed to play a major role in their function, and the disruption of native oligomers has been implicated in specific human pathologies. Computational predictions and biochemical analyses suggest that two molecules of rhodopsin (Rho) associate through the interactions involving its fifth transmembrane helix (TM5). Interestingly, there are several pathogenic loss-of-function mutations within TM5 that face the lipid bilayer in a manner that could potentially influence the dimerization of Rho. Though several of these mutations are known to induce misfolding, the pathogenic defects associated with V209M and F220C Rho remain unclear. In this work, we utilized a variety of biochemical and biophysical approaches to elucidate the effects of these mutations on the dimerization, folding, trafficking, and function of Rho in relation to other pathogenic TM5 variants. Chemical cross-linking, bioluminescence energy transfer, and pulsed-interleaved excitation fluorescence cross-correlation spectroscopy experiments revealed that each of these mutants exhibits a wild type-like propensity to self-associate within the plasma membrane. However, V209M and F220C each exhibit subtle defects in cellular trafficking. Together, our results suggest that the RP pathology associated with the expression of the V209M and F220C mutants could arise from defects in folding and cellular trafficking rather than the disruption of dimerization, as has been previously proposed.
Collapse
Affiliation(s)
- D Paul Mallory
- Department of Chemistry , University of Akron , 190 Buchtel Common , Akron , Ohio 44325 , United States
| | - Elizabeth Gutierrez
- Department of Pharmacology, Cleveland Center for Membrane and Structural Biology, School of Medicine , Case Western Reserve University , 10900 Euclid Avenue , Cleveland , Ohio 44106 , United States
| | - Margaret Pinkevitch
- Department of Chemistry , University of Akron , 190 Buchtel Common , Akron , Ohio 44325 , United States
| | - Christie Klinginsmith
- Department of Chemistry , University of Akron , 190 Buchtel Common , Akron , Ohio 44325 , United States
| | - William D Comar
- Department of Chemistry , University of Akron , 190 Buchtel Common , Akron , Ohio 44325 , United States
| | - Francis J Roushar
- Department of Chemistry , Indiana University , 800 East Kirkwood Avenue , Bloomington , Indiana 47405-7102 , United States
| | - Jonathan P Schlebach
- Department of Chemistry , Indiana University , 800 East Kirkwood Avenue , Bloomington , Indiana 47405-7102 , United States
| | - Adam W Smith
- Department of Chemistry , University of Akron , 190 Buchtel Common , Akron , Ohio 44325 , United States
| | - Beata Jastrzebska
- Department of Pharmacology, Cleveland Center for Membrane and Structural Biology, School of Medicine , Case Western Reserve University , 10900 Euclid Avenue , Cleveland , Ohio 44106 , United States
| |
Collapse
|
36
|
Stenkamp RE. Identifying G protein-coupled receptor dimers from crystal packings. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2018; 74:655-670. [PMID: 29968675 DOI: 10.1107/s2059798318008136] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 06/01/2018] [Indexed: 12/20/2022]
Abstract
Dimers of G protein-coupled receptors (GPCRs) are believed to be important for signaling with their associated G proteins. Low-resolution electron microscopy has shown rhodopsin dimers in native retinal membranes, and CXCR4 dimers have been found in several different crystal structures. Evidence for dimers of other GPCRs is more indirect. An alternative to computational modeling studies is to search for parallel dimers in the packing environments of the reported crystal structures of GPCRs. Two major structural types of GPCR dimers exist (as predicted by others), but there is considerable structural variation within each cluster. The different structural variants described here might reflect different functional properties and should provide a range of model structures for computational and experimental examination.
Collapse
Affiliation(s)
- Ronald E Stenkamp
- Departments of Biological Structure and Biochemistry, Biomolecular Structure Center, University of Washington, Box 357420, Seattle, WA 98195, USA
| |
Collapse
|
37
|
Lemos A, Melo R, Preto AJ, Almeida JG, Moreira IS, Cordeiro MNDS. In Silico Studies Targeting G-protein Coupled Receptors for Drug Research Against Parkinson's Disease. Curr Neuropharmacol 2018; 16:786-848. [PMID: 29521236 PMCID: PMC6080095 DOI: 10.2174/1570159x16666180308161642] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 02/16/2018] [Accepted: 02/02/2018] [Indexed: 11/22/2022] Open
Abstract
Parkinson's Disease (PD) is a long-term neurodegenerative brain disorder that mainly affects the motor system. The causes are still unknown, and even though currently there is no cure, several therapeutic options are available to manage its symptoms. The development of novel antiparkinsonian agents and an understanding of their proper and optimal use are, indeed, highly demanding. For the last decades, L-3,4-DihydrOxyPhenylAlanine or levodopa (L-DOPA) has been the gold-standard therapy for the symptomatic treatment of motor dysfunctions associated to PD. However, the development of dyskinesias and motor fluctuations (wearing-off and on-off phenomena) associated with long-term L-DOPA replacement therapy have limited its antiparkinsonian efficacy. The investigation for non-dopaminergic therapies has been largely explored as an attempt to counteract the motor side effects associated with dopamine replacement therapy. Being one of the largest cell membrane protein families, G-Protein-Coupled Receptors (GPCRs) have become a relevant target for drug discovery focused on a wide range of therapeutic areas, including Central Nervous System (CNS) diseases. The modulation of specific GPCRs potentially implicated in PD, excluding dopamine receptors, may provide promising non-dopaminergic therapeutic alternatives for symptomatic treatment of PD. In this review, we focused on the impact of specific GPCR subclasses, including dopamine receptors, adenosine receptors, muscarinic acetylcholine receptors, metabotropic glutamate receptors, and 5-hydroxytryptamine receptors, on the pathophysiology of PD and the importance of structure- and ligand-based in silico approaches for the development of small molecules to target these receptors.
Collapse
Affiliation(s)
- Agostinho Lemos
- LAQV/REQUIMTE, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007Porto, Portugal
- GIGA Cyclotron Research Centre In Vivo Imaging, University of Liège, 4000Liège, Belgium
| | - Rita Melo
- CNC - Center for Neuroscience and Cell Biology, Faculty of Medicine, University of Coimbra, Rua Larga, 3004-517Coimbra, Portugal
- Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10 (ao km 139,7), 2695-066 Bobadela LRS, Portugal
| | - Antonio Jose Preto
- CNC - Center for Neuroscience and Cell Biology, Faculty of Medicine, University of Coimbra, Rua Larga, 3004-517Coimbra, Portugal
| | - Jose Guilherme Almeida
- CNC - Center for Neuroscience and Cell Biology, Faculty of Medicine, University of Coimbra, Rua Larga, 3004-517Coimbra, Portugal
| | - Irina Sousa Moreira
- CNC - Center for Neuroscience and Cell Biology, Faculty of Medicine, University of Coimbra, Rua Larga, 3004-517Coimbra, Portugal
- Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Utrecht, 3584CH, The Netherlands
| | - Maria Natalia Dias Soeiro Cordeiro
- LAQV/REQUIMTE, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007Porto, Portugal
| |
Collapse
|
38
|
El Hage K, Brickel S, Hermelin S, Gaulier G, Schmidt C, Bonacina L, van Keulen SC, Bhattacharyya S, Chergui M, Hamm P, Rothlisberger U, Wolf JP, Meuwly M. Implications of short time scale dynamics on long time processes. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2017; 4:061507. [PMID: 29308419 PMCID: PMC5741438 DOI: 10.1063/1.4996448] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 09/15/2017] [Indexed: 05/02/2023]
Abstract
This review provides a comprehensive overview of the structural dynamics in topical gas- and condensed-phase systems on multiple length and time scales. Starting from vibrationally induced dissociation of small molecules in the gas phase, the question of vibrational and internal energy redistribution through conformational dynamics is further developed by considering coupled electron/proton transfer in a model peptide over many orders of magnitude. The influence of the surrounding solvent is probed for electron transfer to the solvent in hydrated I-. Next, the dynamics of a modified PDZ domain over many time scales is analyzed following activation of a photoswitch. The hydration dynamics around halogenated amino acid side chains and their structural dynamics in proteins are relevant for iodinated TyrB26 insulin. Binding of nitric oxide to myoglobin is a process for which experimental and computational analyses have converged to a common view which connects rebinding time scales and the underlying dynamics. Finally, rhodopsin is a paradigmatic system for multiple length- and time-scale processes for which experimental and computational methods provide valuable insights into the functional dynamics. The systems discussed here highlight that for a comprehensive understanding of how structure, flexibility, energetics, and dynamics contribute to functional dynamics, experimental studies in multiple wavelength regions and computational studies including quantum, classical, and more coarse grained levels are required.
Collapse
Affiliation(s)
- Krystel El Hage
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
| | - Sebastian Brickel
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
| | - Sylvain Hermelin
- Department of Applied Physics (GAP), University of Geneva, 22 Ch. de Pinchat, 1211 Geneva 4, Switzerland
| | - Geoffrey Gaulier
- Department of Applied Physics (GAP), University of Geneva, 22 Ch. de Pinchat, 1211 Geneva 4, Switzerland
| | - Cédric Schmidt
- Department of Applied Physics (GAP), University of Geneva, 22 Ch. de Pinchat, 1211 Geneva 4, Switzerland
| | - Luigi Bonacina
- Department of Applied Physics (GAP), University of Geneva, 22 Ch. de Pinchat, 1211 Geneva 4, Switzerland
| | - Siri C van Keulen
- Institute of Chemical Sciences and Engineering, EPFL, Lausanne, Switzerland
| | | | - Majed Chergui
- Institute of Chemical Sciences and Engineering, EPFL, Lausanne, Switzerland
| | - Peter Hamm
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | | | - Jean-Pierre Wolf
- Department of Applied Physics (GAP), University of Geneva, 22 Ch. de Pinchat, 1211 Geneva 4, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
| |
Collapse
|
39
|
Pediani JD, Ward RJ, Marsango S, Milligan G. Spatial Intensity Distribution Analysis: Studies of G Protein-Coupled Receptor Oligomerisation. Trends Pharmacol Sci 2017; 39:175-186. [PMID: 29032835 PMCID: PMC5783713 DOI: 10.1016/j.tips.2017.09.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 09/04/2017] [Accepted: 09/14/2017] [Indexed: 02/08/2023]
Abstract
Spatial intensity distribution analysis (SpIDA) is a recently developed approach for determining quaternary structure information on fluorophore-labelled proteins of interest in situ. It can be applied to live or fixed cells and native tissue. Using confocal images, SpIDA generates fluorescence intensity histograms that are analysed by super-Poissonian distribution functions to obtain density and quantal brightness values of the fluorophore-labelled protein of interest. This allows both expression level and oligomerisation state of the protein to be determined. We describe the application of SpIDA to investigate the oligomeric state of G protein-coupled receptors (GPCRs) at steady state and following cellular challenge, and consider how SpIDA may be used to explore GPCR quaternary organisation in pathophysiology and to stratify medicines. GPCRs may exist and function as monomers: however, abundant evidence suggests they can form dimers/oligomers. This concept has implications for drug discovery as it may offer opportunities to modulate the effects of known pharmaceuticals or identify new drug therapies. A variety of approaches have been applied to this issue from traditional biochemical techniques, via resonance energy transfer approaches to recently developed image analysis-based techniques such as SpIDA. This uses mathematical analysis of confocal microscopy images to generate quantal brightness and density information for a fluorophore-tagged receptor. SpIDA can be applied to live or fixed cells and native tissue. SpIDA has been applied to GPCRs from each of the major subfamilies to explore their oligomerisation status at steady state and their regulation by receptor density and ligand binding.
Collapse
Affiliation(s)
- John D Pediani
- Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Richard J Ward
- Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Sara Marsango
- Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Graeme Milligan
- Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK.
| |
Collapse
|
40
|
Clark LD, Dikiy I, Chapman K, Rödström KE, Aramini J, LeVine MV, Khelashvili G, Rasmussen SG, Gardner KH, Rosenbaum DM. Ligand modulation of sidechain dynamics in a wild-type human GPCR. eLife 2017; 6:28505. [PMID: 28984574 PMCID: PMC5650471 DOI: 10.7554/elife.28505] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 09/20/2017] [Indexed: 11/13/2022] Open
Abstract
GPCRs regulate all aspects of human physiology, and biophysical studies have deepened our understanding of GPCR conformational regulation by different ligands. Yet there is no experimental evidence for how sidechain dynamics control allosteric transitions between GPCR conformations. To address this deficit, we generated samples of a wild-type GPCR (A2AR) that are deuterated apart from 1H/13C NMR probes at isoleucine δ1 methyl groups, which facilitated 1H/13C methyl TROSY NMR measurements with opposing ligands. Our data indicate that low [Na+] is required to allow large agonist-induced structural changes in A2AR, and that patterns of sidechain dynamics substantially differ between agonist (NECA) and inverse agonist (ZM241385) bound receptors, with the inverse agonist suppressing fast ps-ns timescale motions at the G protein binding site. Our approach to GPCR NMR creates a framework for exploring how different regions of a receptor respond to different ligands or signaling proteins through modulation of fast ps-ns sidechain dynamics.
Collapse
Affiliation(s)
- Lindsay D Clark
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, United States.,Molecular Biophysics Graduate Program, The University of Texas Southwestern Medical Center, Dallas, United States
| | - Igor Dikiy
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, United States
| | - Karen Chapman
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, United States
| | - Karin Ej Rödström
- Department of Neuroscience and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - James Aramini
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, United States
| | - Michael V LeVine
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, United States.,Institute for Computational Bioscience, Weill Cornell Medical College, New York, United States
| | - George Khelashvili
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, United States.,Institute for Computational Bioscience, Weill Cornell Medical College, New York, United States
| | - Søren Gf Rasmussen
- Department of Neuroscience and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Kevin H Gardner
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, United States.,Department of Chemistry and Biochemistry, City College of New York, New York, United States.,Biochemistry, Chemistry and Biology PhD Programs, Graduate Center, City University of New York, New York, United States
| | - Daniel M Rosenbaum
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, United States.,Molecular Biophysics Graduate Program, The University of Texas Southwestern Medical Center, Dallas, United States
| |
Collapse
|
41
|
Felce JH, Latty SL, Knox RG, Mattick SR, Lui Y, Lee SF, Klenerman D, Davis SJ. Receptor Quaternary Organization Explains G Protein-Coupled Receptor Family Structure. Cell Rep 2017; 20:2654-2665. [PMID: 28903045 PMCID: PMC5608970 DOI: 10.1016/j.celrep.2017.08.072] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 07/14/2017] [Accepted: 08/23/2017] [Indexed: 12/15/2022] Open
Abstract
The organization of Rhodopsin-family G protein-coupled receptors (GPCRs) at the cell surface is controversial. Support both for and against the existence of dimers has been obtained in studies of mostly individual receptors. Here, we use a large-scale comparative study to examine the stoichiometric signatures of 60 receptors expressed by a single human cell line. Using bioluminescence resonance energy transfer- and single-molecule microscopy-based assays, we found that a relatively small fraction of Rhodopsin-family GPCRs behaved as dimers and that these receptors otherwise appear to be monomeric. Overall, the analysis predicted that fewer than 20% of ∼700 Rhodopsin-family receptors form dimers. The clustered distribution of the dimers in our sample and a striking correlation between receptor organization and GPCR family size that we also uncover each suggest that receptor stoichiometry might have profoundly influenced GPCR expansion and diversification.
Collapse
Affiliation(s)
- James H Felce
- Radcliffe Department of Medicine and Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Sarah L Latty
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Rachel G Knox
- Radcliffe Department of Medicine and Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Susan R Mattick
- Radcliffe Department of Medicine and Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Yuan Lui
- Radcliffe Department of Medicine and Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Steven F Lee
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - David Klenerman
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK.
| | - Simon J Davis
- Radcliffe Department of Medicine and Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
| |
Collapse
|
42
|
Recent advances in biophysical studies of rhodopsins - Oligomerization, folding, and structure. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1512-1521. [PMID: 28844743 DOI: 10.1016/j.bbapap.2017.08.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Revised: 08/06/2017] [Accepted: 08/11/2017] [Indexed: 12/19/2022]
Abstract
Retinal-binding proteins, mainly known as rhodopsins, function as photosensors and ion transporters in a wide range of organisms. From halobacterial light-driven proton pump, bacteriorhodopsin, to bovine photoreceptor, visual rhodopsin, they have served as prototypical α-helical membrane proteins in a large number of biophysical studies and aided in the development of many cutting-edge techniques of structural biology and biospectroscopy. In the last decade, microbial and animal rhodopsin families have expanded significantly, bringing into play a number of new interesting structures and functions. In this review, we will discuss recent advances in biophysical approaches to retinal-binding proteins, primarily microbial rhodopsins, including those in optical spectroscopy, X-ray crystallography, nuclear magnetic resonance, and electron paramagnetic resonance, as applied to such fundamental biological aspects as protein oligomerization, folding, and structure.
Collapse
|
43
|
Gacasan SB, Baker DL, Parrill AL. G protein-coupled receptors: the evolution of structural insight. AIMS BIOPHYSICS 2017; 4:491-527. [PMID: 29951585 DOI: 10.3934/biophy.2017.3.491] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
G protein-coupled receptors (GPCR) comprise a diverse superfamily of over 800 proteins that have gained relevance as biological targets for pharmaceutical drug design. Although these receptors have been investigated for decades, three-dimensional structures of GPCR have only recently become available. In this review, we focus on the technological advancements that have facilitated efforts to gain insights into GPCR structure. Progress in these efforts began with the initial crystal structure determination of rhodopsin (PDB: 1F88) in 2000 and has continued to the most recently published structure of the A1AR (PDB: 5UEN) in 2017. Numerous experimental developments over the past two decades have opened the door for widespread GPCR structural characterization. These efforts have resulted in the determination of three-dimensional structures for over 40 individual GPCR family members. Herein we present a comprehensive list and comparative analysis of over 180 individual GPCR structures. This includes a summary of different GPCR functional states crystallized with agonists, dual agonists, partial agonists, inverse agonists, antagonists, and allosteric modulators.
Collapse
Affiliation(s)
- Samantha B Gacasan
- Department of Chemistry, University of Memphis, 3744 Walker Ave, Memphis, TN 38152, USA
| | - Daniel L Baker
- Department of Chemistry, University of Memphis, 3744 Walker Ave, Memphis, TN 38152, USA
| | - Abby L Parrill
- Department of Chemistry, University of Memphis, 3744 Walker Ave, Memphis, TN 38152, USA
| |
Collapse
|
44
|
Seno K, Hayashi F. Palmitoylation is a prerequisite for dimerization-dependent raftophilicity of rhodopsin. J Biol Chem 2017; 292:15321-15328. [PMID: 28747438 DOI: 10.1074/jbc.m117.804880] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 07/23/2017] [Indexed: 01/07/2023] Open
Abstract
The visual photopigment rhodopsin (Rh) is a prototypical G protein-coupled receptor (GPCR) responsible for initiation of the phototransduction cascade in rod photoreceptors. Similar to other GPCRs, Rh can form dimers or even higher oligomers and tends to have a supramolecular organization that is likely important in the dim light response. Rh also exhibits high affinity for lipid rafts (i.e. raftophilicity) upon light-dependent binding with the cognate G protein transducin (Gt), suggesting the presence of lipid raft-like domains in the retinal disk membrane and their importance in phototransduction. However, the relationship between Rh oligomerization and lipid rafts in the disk membrane remains to be explored. Given previous findings that Gt binds to dimeric Rh and that Rh is posttranslationally modified with two highly raftophilic palmitoyl moieties, we hypothesized that Rh becomes raftophilic upon dimerization. Here, using biochemical assays, we found that Rh*-Gt complexes in the detergent-resistant membrane are partially resistant to cholesterol depletion by methyl-β-cyclodextrin and that the Rh-to-Gt stoichiometry in this methyl-β-cyclodextrin-resistant complex is 2:1. Next, we found that IgG-mediated Rh-Rh cross-linking renders Rh highly raftophilic, supporting the premise that Rh becomes raftophilic upon dimerization. Rh depalmitoylation via reduction of thioester linkages blocked the translocation of IgG-cross-linked Rh to the detergent-resistant membrane, highlighting that the two palmitoyl moieties are important for the dimerization-dependent raftophilicity of Rh. These results indicate that palmitoylated GPCRs such as Rh can acquire raftophilicity upon G protein-stabilized dimerization and thereby organize receptor-cluster rafts by recruiting raftophilic lipids.
Collapse
Affiliation(s)
- Keiji Seno
- From the Department of Biology, Faculty of Medicine, and.,International Mass Imaging Center, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka 431-3192, Japan and
| | - Fumio Hayashi
- the Department of Biology, Graduate School of Science, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| |
Collapse
|
45
|
Lee Y, Basith S, Choi S. Recent Advances in Structure-Based Drug Design Targeting Class A G Protein-Coupled Receptors Utilizing Crystal Structures and Computational Simulations. J Med Chem 2017; 61:1-46. [PMID: 28657745 DOI: 10.1021/acs.jmedchem.6b01453] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
G protein-coupled receptors (GPCRs) represent the largest and most physiologically important integral membrane protein family, and these receptors respond to a wide variety of physiological and environmental stimuli. GPCRs are among the most critical therapeutic targets for numerous human diseases, and approximately one-third of the currently marketed drugs target this receptor family. The recent breakthroughs in GPCR structural biology have significantly contributed to our understanding of GPCR function, ligand binding, and pharmacological action as well as to the design of new drugs. This perspective highlights the latest advances in GPCR structures with a focus on the receptor-ligand interactions of each receptor family in class A nonrhodopsin GPCRs as well as the structural features for their activation, biased signaling, and allosteric mechanisms. The current state-of-the-art methodologies of structure-based drug design (SBDD) approaches in the GPCR research field are also discussed.
Collapse
Affiliation(s)
- Yoonji Lee
- National Leading Research Laboratory (NLRL) of Molecular Modeling & Drug Design, College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University , Seoul 03760, Republic of Korea
| | - Shaherin Basith
- National Leading Research Laboratory (NLRL) of Molecular Modeling & Drug Design, College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University , Seoul 03760, Republic of Korea
| | - Sun Choi
- National Leading Research Laboratory (NLRL) of Molecular Modeling & Drug Design, College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University , Seoul 03760, Republic of Korea
| |
Collapse
|
46
|
Brookes JC. Quantum effects in biology: golden rule in enzymes, olfaction, photosynthesis and magnetodetection. Proc Math Phys Eng Sci 2017; 473:20160822. [PMID: 28588400 DOI: 10.1098/rspa.2016.0822] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 05/02/2017] [Indexed: 02/07/2023] Open
Abstract
Despite certain quantum concepts, such as superposition states, entanglement, 'spooky action at a distance' and tunnelling through insulating walls, being somewhat counterintuitive, they are no doubt extremely useful constructs in theoretical and experimental physics. More uncertain, however, is whether or not these concepts are fundamental to biology and living processes. Of course, at the fundamental level all things are quantum, because all things are built from the quantized states and rules that govern atoms. But when does the quantum mechanical toolkit become the best tool for the job? This review looks at four areas of 'quantum effects in biology'. These are biosystems that are very diverse in detail but possess some commonality. They are all (i) effects in biology: rates of a signal (or information) that can be calculated from a form of the 'golden rule' and (ii) they are all protein-pigment (or ligand) complex systems. It is shown, beginning with the rate equation, that all these systems may contain some degree of quantumeffect, and where experimental evidence is available, it is explored to determine how the quantum analysis aids in understanding of the process.
Collapse
Affiliation(s)
- Jennifer C Brookes
- London Centre for Nanotechnology, University College London, 17-19 Gordon Street, London WC1E 6BT, UK
| |
Collapse
|
47
|
Hofrnann L, Alexander NS, Sun W, Zhang J, Orban T, Palczewski K. Hydrogen/Deuterium Exchange Mass Spectrometry of Human Green Opsin Reveals a Conserved Pro-Pro Motif in Extracellular Loop 2 of Monostable Visual G Protein-Coupled Receptors. Biochemistry 2017; 56:2338-2348. [PMID: 28402104 PMCID: PMC5501310 DOI: 10.1021/acs.biochem.7b00165] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Opsins comprise the protein component of light sensitive G protein-coupled receptors (GPCRs) in the retina of the eye that are responsible for the transduction of light into a biochemical signal. Here, we used hydrogen/deuterium (H/D) exchange coupled with mass spectrometry to map conformational changes in green cone opsin upon light activation. We then compared these findings with those reported for rhodopsin. The extent of H/D exchange in green cone opsin was greater than in rhodopsin in the dark and bleached states, suggesting a higher structural heterogeneity for green cone opsin. Further analysis revealed that green cone opsin exists as a dimer in both dark (inactive) and bleached (active) states, and that the predicted glycosylation sites at N32 and N34 are indeed glycosylated. Comparison of deuterium uptake between inactive and active states of green cone opsin also disclosed a reduced solvent accessibility of the extracellular N-terminal region and an increased accessibility of the chromophore binding site. Increased H/D exchange at the extracellular side of transmembrane helix four (TM4) combined with an analysis of sequence alignments revealed a conserved Pro-Pro motif in extracellular loop 2 (EL2) of monostable visual GPCRs. These data present new insights into the locus of chromophore release at the extracellular side of TM4 and TM5 and provide a foundation for future functional evaluation.
Collapse
Affiliation(s)
- Lukas Hofrnann
- Department of Pharmacology and Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Nathan S. Alexander
- Department of Pharmacology and Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Wenyu Sun
- Department of Pharmacology and Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Jianye Zhang
- Department of Pharmacology and Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Tivadar Orban
- Department of Pharmacology and Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Krzysztof Palczewski
- Department of Pharmacology and Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| |
Collapse
|
48
|
Kamiya M, Hayashi S. Photoactivation Intermediates of a G-Protein Coupled Receptor Rhodopsin Investigated by a Hybrid Molecular Simulation. J Phys Chem B 2017; 121:3842-3852. [PMID: 28240904 DOI: 10.1021/acs.jpcb.6b13050] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Rhodopsin is a G-protein coupled receptor functioning as a photoreceptor for vision through photoactivation of a covalently bound ligand of a retinal protonated Schiff base chromophore. Despite the availability of structural information on the inactivated and activated forms of the receptor, the transition processes initiated by the photoabsorption have not been well understood. Here we theoretically examined the photoactivation processes by means of molecular dynamics (MD) simulations and ab initio quantum mechanical/molecular mechanical (QM/MM) free energy geometry optimizations which enabled accurate geometry determination of the ligand molecule in ample statistical conformational samples of the protein. Structures of the intermediate states of the activation process, blue-shifted intermediate and Lumi, as well as the dark state first generated by MD simulations and then refined by the QM/MM free energy geometry optimizations were characterized by large displacement of the β-ionone ring of retinal along with change in the hydrogen bond of the protonated Schiff base. The ab initio calculations of vibrational and electronic spectroscopic properties of those states well reproduced the experimental observations and successfully identified the molecular origins underlying the spectroscopic features. The structural evolution in the formation of the intermediates provides a molecular insight into the efficient activation processes of the receptor.
Collapse
Affiliation(s)
- Motoshi Kamiya
- Department of Chemistry, Graduate School of Science, Kyoto University , Kyoto 606-8502, Japan
| | - Shigehiko Hayashi
- Department of Chemistry, Graduate School of Science, Kyoto University , Kyoto 606-8502, Japan
| |
Collapse
|
49
|
Methods used to study the oligomeric structure of G-protein-coupled receptors. Biosci Rep 2017; 37:BSR20160547. [PMID: 28062602 PMCID: PMC5398257 DOI: 10.1042/bsr20160547] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 01/05/2017] [Accepted: 01/06/2017] [Indexed: 02/02/2023] Open
Abstract
G-protein-coupled receptors (GPCRs), which constitute the largest family of cell surface receptors, were originally thought to function as monomers, but are now recognized as being able to act in a wide range of oligomeric states and indeed, it is known that the oligomerization state of a GPCR can modulate its pharmacology and function. A number of experimental techniques have been devised to study GPCR oligomerization including those based upon traditional biochemistry such as blue-native PAGE (BN-PAGE), co-immunoprecipitation (Co-IP) and protein-fragment complementation assays (PCAs), those based upon resonance energy transfer, FRET, time-resolved FRET (TR-FRET), FRET spectrometry and bioluminescence resonance energy transfer (BRET). Those based upon microscopy such as FRAP, total internal reflection fluorescence microscopy (TIRFM), spatial intensity distribution analysis (SpIDA) and various single molecule imaging techniques. Finally with the solution of a growing number of crystal structures, X-ray crystallography must be acknowledged as an important source of discovery in this field. A different, but in many ways complementary approach to the use of more traditional experimental techniques, are those involving computational methods that possess obvious merit in the study of the dynamics of oligomer formation and function. Here, we summarize the latest developments that have been made in the methods used to study GPCR oligomerization and give an overview of their application.
Collapse
|
50
|
Beta 2-adrenergic receptor homodimers: Role of transmembrane domain 1 and helix 8 in dimerization and cell surface expression. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1859:1445-1455. [PMID: 27993566 DOI: 10.1016/j.bbamem.2016.12.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 12/05/2016] [Accepted: 12/08/2016] [Indexed: 11/22/2022]
Abstract
Even though there are hundreds of reports in the published literature supporting the hypothesis that G protein-coupled receptors (GPCR) form and function as dimers this remains a highly controversial area of research and mechanisms governing homodimer formation are poorly understood. Crystal structures revealing homodimers have been reported for many different GPCR. For adrenergic receptors, a potential dimer interface involving transmembrane domain 1 (TMD1) and helix 8 (H8) was identified in crystal structures of the beta1-adrenergic (β1-AR) and β2-AR. The purpose of this study was to investigate a potential role for TMD1 and H8 in dimerization and plasma membrane expression of functional β2-AR. Charged residues at the base of TMD1 and in the distal portion of H8 were replaced, singly and in combination, with non-polar residues or residues of opposite charge. Wild type and mutant β2-AR, tagged with YFP and expressed in HEK293 cells, were evaluated for plasma membrane expression and function. Homodimer formation was evaluated using bioluminescence resonance energy transfer, bimolecular fluorescence complementation, and fluorescence correlation spectroscopy. Amino acid substitutions at the base of TMD1 and in the distal portion of H8 disrupted homodimer formation and caused receptors to be retained in the endoplasmic reticulum. Mutations in the proximal region of H8 did not disrupt dimerization but did interfere with plasma membrane expression. This study provides biophysical evidence linking a potential TMD1/H8 interface with ER export and the expression of functional β2-AR on the plasma membrane. This article is part of a Special Issue entitled: Interactions between membrane receptors in cellular membranes edited by Kalina Hristova.
Collapse
|