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Rodrigues MJ, Tejero O, Mühle J, Pamula F, Das I, Tsai CJ, Terakita A, Sheves M, Schertler GFX. Activating an invertebrate bistable opsin with the all-trans 6.11 retinal analog. Proc Natl Acad Sci U S A 2024; 121:e2406814121. [PMID: 39042699 PMCID: PMC11295067 DOI: 10.1073/pnas.2406814121] [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: 04/20/2024] [Accepted: 06/18/2024] [Indexed: 07/25/2024] Open
Abstract
Animal vision depends on opsins, a category of G protein-coupled receptor (GPCR) that achieves light sensitivity by covalent attachment to retinal. Typically binding as an inverse agonist, 11-cis retinal photoisomerizes to the all-trans isomer and activates the receptor, initiating downstream signaling cascades. Retinal bound to bistable opsins isomerizes back to the 11-cis state after absorption of a second photon, inactivating the receptor. Bistable opsins are essential for invertebrate vision and nonvisual light perception across the animal kingdom. While crystal structures are available for bistable opsins in the inactive state, it has proven difficult to form homogeneous populations of activated bistable opsins either via illumination or reconstitution with all-trans retinal. Here, we show that a nonnatural retinal analog, all-trans retinal 6.11 (ATR6.11), can be reconstituted with the invertebrate bistable opsin, Jumping Spider Rhodopsin-1 (JSR1). Biochemical activity assays demonstrate that ATR6.11 functions as a JSR1 agonist. ATR6.11 binding also enables complex formation between JSR1 and signaling partners. Our findings demonstrate the utility of retinal analogs for biophysical characterization of bistable opsins, which will deepen our understanding of light perception in animals.
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Affiliation(s)
- Matthew J. Rodrigues
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institute, Villigen5232, Switzerland
| | - Oliver Tejero
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institute, Villigen5232, Switzerland
- Department of Biology, ETH-Zurich, Zurich, Switzerland
| | - Jonas Mühle
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institute, Villigen5232, Switzerland
| | - Filip Pamula
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institute, Villigen5232, Switzerland
| | - Ishita Das
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, 76100Rehovot, Israel
| | - Ching-Ju Tsai
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institute, Villigen5232, Switzerland
| | - Akihisa Terakita
- Department of Biology, Graduate School of Science, Osaka Metropolitan University, Osaka558-8585, Japan
- The Osaka Metropolitan University Advanced Research Institute for Natural Science and Technology, Osaka Metropolitan University, Osaka558-8585, Japan
| | - Mordechai Sheves
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, 76100Rehovot, Israel
| | - Gebhard F. X. Schertler
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institute, Villigen5232, Switzerland
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2
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Gurevich VV. Arrestins: A Small Family of Multi-Functional Proteins. Int J Mol Sci 2024; 25:6284. [PMID: 38892473 PMCID: PMC11173308 DOI: 10.3390/ijms25116284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 05/24/2024] [Accepted: 05/31/2024] [Indexed: 06/21/2024] Open
Abstract
The first member of the arrestin family, visual arrestin-1, was discovered in the late 1970s. Later, the other three mammalian subtypes were identified and cloned. The first described function was regulation of G protein-coupled receptor (GPCR) signaling: arrestins bind active phosphorylated GPCRs, blocking their coupling to G proteins. It was later discovered that receptor-bound and free arrestins interact with numerous proteins, regulating GPCR trafficking and various signaling pathways, including those that determine cell fate. Arrestins have no enzymatic activity; they function by organizing multi-protein complexes and localizing their interaction partners to particular cellular compartments. Today we understand the molecular mechanism of arrestin interactions with GPCRs better than the mechanisms underlying other functions. However, even limited knowledge enabled the construction of signaling-biased arrestin mutants and extraction of biologically active monofunctional peptides from these multifunctional proteins. Manipulation of cellular signaling with arrestin-based tools has research and likely therapeutic potential: re-engineered proteins and their parts can produce effects that conventional small-molecule drugs cannot.
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3
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Smylla TK, Wagner K, Huber A. The Role of Reversible Phosphorylation of Drosophila Rhodopsin. Int J Mol Sci 2022; 23:ijms232314674. [PMID: 36499010 PMCID: PMC9740569 DOI: 10.3390/ijms232314674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/18/2022] [Accepted: 11/21/2022] [Indexed: 11/27/2022] Open
Abstract
Vertebrate and fly rhodopsins are prototypical GPCRs that have served for a long time as model systems for understanding GPCR signaling. Although all rhodopsins seem to become phosphorylated at their C-terminal region following activation by light, the role of this phosphorylation is not uniform. Two major functions of rhodopsin phosphorylation have been described: (1) inactivation of the activated rhodopsin either directly or by facilitating binding of arrestins in order to shut down the visual signaling cascade and thus eventually enabling a high-temporal resolution of the visual system. (2) Facilitating endocytosis of activated receptors via arrestin binding that in turn recruits clathrin to the membrane for clathrin-mediated endocytosis. In vertebrate rhodopsins the shutdown of the signaling cascade may be the main function of rhodopsin phosphorylation, as phosphorylation alone already quenches transducin activation and, in addition, strongly enhances arrestin binding. In the Drosophila visual system rhodopsin phosphorylation is not needed for receptor inactivation. Its role here may rather lie in the recruitment of arrestin 1 and subsequent endocytosis of the activated receptor. In this review, we summarize investigations of fly rhodopsin phosphorylation spanning four decades and contextualize them with regard to the most recent insights from vertebrate phosphorylation barcode theory.
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4
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van Mazijk R, Haarman AEG, Hoefsloot LH, Polling JR, van Tienhoven M, Klaver CCW, Verhoeven VJM, Loudon SE, Thiadens AAHJ, Kievit AJA. Early onset X-linked female limited high myopia in three multigenerational families caused by novel mutations in the ARR3 gene. Hum Mutat 2022; 43:380-388. [PMID: 35001458 PMCID: PMC9303208 DOI: 10.1002/humu.24327] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 11/06/2021] [Accepted: 12/15/2021] [Indexed: 11/09/2022]
Abstract
This study describes the clinical spectrum and genetic background of high myopia caused by mutations in the ARR3 gene. We performed an observational case series of three multigenerational families with high myopia (SER≤-6D), from the departments of Clinical Genetics and Ophthalmology of a tertiary Dutch hospital. Whole-exome sequencing (WES) with a vision-related gene panel was performed, followed by a full open exome sequencing. We identified three Caucasian families with high myopia caused by three different pathogenic variants in the ARR3 gene (c.214C>T, p.Arg72*; c.767+1G>A; p.?; c.848delG, p.(Gly283fs)). Myopia was characterized by a high severity (<-8D), an early onset (<6 years), progressive nature, and a moderate to bad atropine treatment response. Remarkably, a female limited inheritance pattern was present in all three families accordant with previous reports. The frequency of a pathogenic variant in the ARR3 gene in our diagnostic WES cohort was 5%. To conclude, we identified three families with early onset, therapy-resistant, high myopia with a female-limited inheritance pattern, caused by a mutation in the ARR3 gene. The singular mode of inheritance might be explained by metabolic interference due to X-inactivation. Identification of this type of high myopia will improve prompt myopia treatment, monitoring, and genetic counseling.
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Affiliation(s)
- Ralph van Mazijk
- Department of Clinical Genetics, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Annechien E G Haarman
- Department of Ophthalmology, Erasmus Medical Centre, Rotterdam, The Netherlands.,Department of Epidemiology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Lies H Hoefsloot
- Department of Clinical Genetics, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Jan R Polling
- Department of Ophthalmology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | | | - Caroline C W Klaver
- Department of Ophthalmology, Erasmus Medical Centre, Rotterdam, The Netherlands.,Department of Epidemiology, Erasmus Medical Centre, Rotterdam, The Netherlands.,Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands.,Institute of Molecular and Clinical Ophthalmology, University of Basel, Basel, Switzerland
| | - Virginie J M Verhoeven
- Department of Clinical Genetics, Erasmus Medical Centre, Rotterdam, The Netherlands.,Department of Ophthalmology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Sjoukje E Loudon
- Department of Ophthalmology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | | | - Anneke J A Kievit
- Department of Clinical Genetics, Erasmus Medical Centre, Rotterdam, The Netherlands
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5
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James EI, Murphree TA, Vorauer C, Engen JR, Guttman M. Advances in Hydrogen/Deuterium Exchange Mass Spectrometry and the Pursuit of Challenging Biological Systems. Chem Rev 2021; 122:7562-7623. [PMID: 34493042 PMCID: PMC9053315 DOI: 10.1021/acs.chemrev.1c00279] [Citation(s) in RCA: 102] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
Solution-phase hydrogen/deuterium
exchange (HDX) coupled to mass
spectrometry (MS) is a widespread tool for structural analysis across
academia and the biopharmaceutical industry. By monitoring the exchangeability
of backbone amide protons, HDX-MS can reveal information about higher-order
structure and dynamics throughout a protein, can track protein folding
pathways, map interaction sites, and assess conformational states
of protein samples. The combination of the versatility of the hydrogen/deuterium
exchange reaction with the sensitivity of mass spectrometry has enabled
the study of extremely challenging protein systems, some of which
cannot be suitably studied using other techniques. Improvements over
the past three decades have continually increased throughput, robustness,
and expanded the limits of what is feasible for HDX-MS investigations.
To provide an overview for researchers seeking to utilize and derive
the most from HDX-MS for protein structural analysis, we summarize
the fundamental principles, basic methodology, strengths and weaknesses,
and the established applications of HDX-MS while highlighting new
developments and applications.
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Affiliation(s)
- Ellie I James
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Taylor A Murphree
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Clint Vorauer
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - John R Engen
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
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6
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Avsar SY, Kapinos LE, Schoenenberger CA, Schertler GFX, Mühle J, Meger B, Lim RYH, Ostermaier MK, Lesca E, Palivan CG. Immobilization of arrestin-3 on different biosensor platforms for evaluating GPCR binding. Phys Chem Chem Phys 2020; 22:24086-24096. [PMID: 33079118 DOI: 10.1039/d0cp01464h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
G protein-coupled receptors (GPCRs) are a large and ubiquitous family of membrane receptors of great pharmacological interest. Cell-based assays are the primary tool for assessing GPCR interactions and activation but their design and intrinsic complexity limit their application. Biosensor-based assays that directly and specifically report GPCR-protein binding (e.g. arrestin or G protein) could provide a good alternative. We present an approach based on the stable immobilization of different arrestin-3 proteins (wild type, and two mutants, mutant X (arrestin-3 I386A) and mutant Y (arrestin-3 R393E)) via histidine tags on NTA(Ni2+)-coated sensors in a defined orientation. Using biolayer interferometry (BLI), surface plasmon resonance (SPR), and quartz crystal microbalance with dissipation (QCM-D), we were able to follow the interaction between the different arrestin-3 proteins and a representative GPCR, jumping spider rhodopsin-1 (JSR1), in a label-free manner in real-time. The interactions were quantified as binding affinity, association and dissociation rate constants. The combination of surface-based biosensing methods indicated that JSR1 showed the strongest binding to arrestin mutant Y. Taken together, this work introduces direct label-free, biosensor-based screening approaches that can be easily adapted for testing interactions of proteins and other compounds with different GPCRs.
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Affiliation(s)
- Saziye Yorulmaz Avsar
- Department of Chemistry and the Swiss Nanoscience Institute, University of Basel, 4002 Basel, Switzerland.
| | - Larisa E Kapinos
- Biozentrum and the Swiss Nanoscience Institute, University of Basel, 4056 Basel, Switzerland
| | - Cora-Ann Schoenenberger
- Department of Chemistry and the Swiss Nanoscience Institute, University of Basel, 4002 Basel, Switzerland.
| | - Gebhard F X Schertler
- Department of Biology and Chemistry, Laboratory of Biomolecular Research, Paul Scherrer Institute, 5303 Villigen-PSI, Switzerland. and Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Jonas Mühle
- Department of Biology and Chemistry, Laboratory of Biomolecular Research, Paul Scherrer Institute, 5303 Villigen-PSI, Switzerland.
| | - Benoit Meger
- Department of Biology and Chemistry, Laboratory of Biomolecular Research, Paul Scherrer Institute, 5303 Villigen-PSI, Switzerland.
| | - Roderick Y H Lim
- Biozentrum and the Swiss Nanoscience Institute, University of Basel, 4056 Basel, Switzerland
| | | | - Elena Lesca
- Department of Biology and Chemistry, Laboratory of Biomolecular Research, Paul Scherrer Institute, 5303 Villigen-PSI, Switzerland. and Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Cornelia G Palivan
- Department of Chemistry and the Swiss Nanoscience Institute, University of Basel, 4002 Basel, Switzerland.
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7
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Min K, Yoon HJ, Park JY, Baidya M, Dwivedi-Agnihotri H, Maharana J, Chaturvedi M, Chung KY, Shukla AK, Lee HH. Crystal Structure of β-Arrestin 2 in Complex with CXCR7 Phosphopeptide. Structure 2020; 28:1014-1023.e4. [PMID: 32579945 DOI: 10.1016/j.str.2020.06.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 04/02/2020] [Accepted: 06/03/2020] [Indexed: 12/21/2022]
Abstract
β-Arrestins (βarrs) critically regulate G-protein-coupled receptor (GPCR) signaling and trafficking. βarrs have two isoforms, βarr1 and βarr2. Receptor phosphorylation is a key determinant for the binding of βarrs, and understanding the intricate details of receptor-βarr interaction is the next frontier in GPCR structural biology. The high-resolution structure of active βarr1 in complex with a phosphopeptide derived from GPCR has been revealed, but that of βarr2 remains elusive. Here, we present a 2.3-Å crystal structure of βarr2 in complex with a phosphopeptide (C7pp) derived from the carboxyl terminus of CXCR7. The structural analysis of C7pp-bound βarr2 reveals key differences from the previously determined active conformation of βarr1. One of the key differences is that C7pp-bound βarr2 shows a relatively small inter-domain rotation. Antibody-fragment-based conformational sensor and hydrogen/deuterium exchange experiments further corroborated the structural features of βarr2 and suggested that βarr2 adopts a range of inter-domain rotations.
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Affiliation(s)
- Kyungjin Min
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Hye-Jin Yoon
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Ji Young Park
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Mithu Baidya
- Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur 208016, India
| | | | - Jagannath Maharana
- Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur 208016, India
| | - Madhu Chaturvedi
- Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur 208016, India
| | - Ka Young Chung
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea.
| | - Arun K Shukla
- Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur 208016, India.
| | - Hyung Ho Lee
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 08826, Republic of Korea.
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8
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Gurevich VV, Gurevich EV. Targeting arrestin interactions with its partners for therapeutic purposes. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2019; 121:169-197. [PMID: 32312421 DOI: 10.1016/bs.apcsb.2019.11.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Most vertebrates express four arrestin subtypes: two visual ones in photoreceptor cells and two non-visuals expressed ubiquitously. The latter two interact with hundreds of G protein-coupled receptors, certain receptors of other types, and numerous non-receptor partners. Arrestins have no enzymatic activity and work by interacting with other proteins, often assembling multi-protein signaling complexes. Arrestin binding to every partner affects cell signaling, including pathways regulating cell survival, proliferation, and death. Thus, targeting individual arrestin interactions has therapeutic potential. This requires precise identification of protein-protein interaction sites of both participants and the choice of the side of each interaction which would be most advantageous to target. The interfaces involved in each interaction can be disrupted by small molecule therapeutics, as well as by carefully selected peptides of the other partner that do not participate in the interactions that should not be targeted.
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Affiliation(s)
- Vsevolod V Gurevich
- Department of Pharmacology, Vanderbilt University, Nashville, TN, United States
| | - Eugenia V Gurevich
- Department of Pharmacology, Vanderbilt University, Nashville, TN, United States
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