1
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Agback T, Lesovoy D, Han X, Lomzov A, Sun R, Sandalova T, Orekhov VY, Achour A, Agback P. Combined NMR and molecular dynamics conformational filter identifies unambiguously dynamic ensembles of Dengue protease NS2B/NS3pro. Commun Biol 2023; 6:1193. [PMID: 38001280 PMCID: PMC10673835 DOI: 10.1038/s42003-023-05584-6] [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: 06/16/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
The dengue protease NS2B/NS3pro has been reported to adopt either an 'open' or a 'closed' conformation. We have developed a conformational filter that combines NMR with MD simulations to identify conformational ensembles that dominate in solution. Experimental values derived from relaxation parameters for the backbone and methyl side chains were compared with the corresponding back-calculated relaxation parameters of different conformational ensembles obtained from free MD simulations. Our results demonstrate a high prevalence for the 'closed' conformational ensemble while the 'open' conformation is absent, indicating that the latter conformation is most probably due to crystal contacts. Conversely, conformational ensembles in which the positioning of the co-factor NS2B results in a 'partially' open conformation, previously described in both MD simulations and X-ray studies, were identified by our conformational filter. Altogether, we believe that our approach allows for unambiguous identification of true conformational ensembles, an essential step for reliable drug discovery.
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Affiliation(s)
- Tatiana Agback
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, PO Box 7015, SE-750 07, Uppsala, Sweden
| | - Dmitry Lesovoy
- Department of Structural Biology, Shemyakin-Ovchinnikov, Institute of Bioorganic Chemistry RAS, 117997, Moscow, Russia
- Swedish NMR Centre, University of Gothenburg, Box 465, 40530, Gothenburg, Sweden
| | - Xiao Han
- Science for Life Laboratory, Department of Medicine, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, SE-171 76, Stockholm, Sweden
| | - Alexander Lomzov
- Laboratory of Structural Biology, Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090, Novosibirsk, Russia
| | - Renhua Sun
- Science for Life Laboratory, Department of Medicine, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, SE-171 76, Stockholm, Sweden
| | - Tatyana Sandalova
- Science for Life Laboratory, Department of Medicine, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, SE-171 76, Stockholm, Sweden
| | - Vladislav Yu Orekhov
- Swedish NMR Centre, University of Gothenburg, Box 465, 40530, Gothenburg, Sweden
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 465, 40530, Gothenburg, Sweden
| | - Adnane Achour
- Science for Life Laboratory, Department of Medicine, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, SE-171 76, Stockholm, Sweden.
| | - Peter Agback
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, PO Box 7015, SE-750 07, Uppsala, Sweden.
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2
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Pogozheva ID, Cherepanov S, Park SJ, Raghavan M, Im W, Lomize AL. Structural Modeling of Cytokine-Receptor-JAK2 Signaling Complexes Using AlphaFold Multimer. J Chem Inf Model 2023; 63:5874-5895. [PMID: 37694948 DOI: 10.1021/acs.jcim.3c00926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Homodimeric class 1 cytokine receptors include the erythropoietin (EPOR), thrombopoietin (TPOR), granulocyte colony-stimulating factor 3 (CSF3R), growth hormone (GHR), and prolactin receptors (PRLR). These cell-surface single-pass transmembrane (TM) glycoproteins regulate cell growth, proliferation, and differentiation and induce oncogenesis. An active TM signaling complex consists of a receptor homodimer, one or two ligands bound to the receptor extracellular domains, and two molecules of Janus Kinase 2 (JAK2) constitutively associated with the receptor intracellular domains. Although crystal structures of soluble extracellular domains with ligands have been obtained for all of the receptors except TPOR, little is known about the structure and dynamics of the complete TM complexes that activate the downstream JAK-STAT signaling pathway. Three-dimensional models of five human receptor complexes with cytokines and JAK2 were generated here by using AlphaFold Multimer. Given the large size of the complexes (from 3220 to 4074 residues), the modeling required a stepwise assembly from smaller parts, with selection and validation of the models through comparisons with published experimental data. The modeling of active and inactive complexes supports a general activation mechanism that involves ligand binding to a monomeric receptor followed by receptor dimerization and rotational movement of the receptor TM α-helices, causing proximity, dimerization, and activation of associated JAK2 subunits. The binding mode of two eltrombopag molecules to the TM α-helices of the active TPOR dimer was proposed. The models also help elucidate the molecular basis of oncogenic mutations that may involve a noncanonical activation route. Models equilibrated in explicit lipids of the plasma membrane are publicly available.
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Affiliation(s)
- Irina D Pogozheva
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Stanislav Cherepanov
- Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Sang-Jun Park
- Departments of Biological Sciences and Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Malini Raghavan
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Wonpil Im
- Departments of Biological Sciences and Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Andrei L Lomize
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States
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3
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Cai T, Lenoir Capello R, Pi X, Wu H, Chou JJ. Structural basis of γ chain family receptor sharing at the membrane level. Science 2023; 381:569-576. [PMID: 37535730 DOI: 10.1126/science.add1219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 06/23/2023] [Indexed: 08/05/2023]
Abstract
Common γ chain (γc) cytokine receptors, including interleukin-2 (IL-2), IL-4, IL-7, IL-9, IL-15, and IL-21 receptors, are activated upon engagement with a common γc receptor (CD132) by concomitant binding of their ectodomains to an interleukin. In this work, we find that direct interactions between the transmembrane domains (TMDs) of both the γc and the interleukin receptors (ILRs) are also required for receptor activation. Moreover, the same γc TMD can specifically recognize multiple ILR TMDs of diverse sequences within the family. Heterodimer structures of γc TMD bound to IL-7 and IL-9 receptor TMDs-determined in a lipid bilayer-like environment by nuclear magnetic resonance spectroscopy-reveal a conserved knob-into-hole mechanism of recognition that mediates receptor sharing within the membrane. Thus, signaling in the γc receptor family requires specific heterotypic interactions of the TMDs.
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Affiliation(s)
- Tiantian Cai
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Rachel Lenoir Capello
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Xiong Pi
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Hao Wu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - James J Chou
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
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4
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Pogozheva ID, Cherepanov S, Park SJ, Raghavan M, Im W, Lomize AL. Structural modeling of cytokine-receptor-JAK2 signaling complexes using AlphaFold Multimer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.14.544971. [PMID: 37398331 PMCID: PMC10312770 DOI: 10.1101/2023.06.14.544971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Homodimeric class 1 cytokine receptors include the erythropoietin (EPOR), thrombopoietin (TPOR), granulocyte colony-stimulating factor 3 (CSF3R), growth hormone (GHR), and prolactin receptors (PRLR). They are cell-surface single-pass transmembrane (TM) glycoproteins that regulate cell growth, proliferation, and differentiation and induce oncogenesis. An active TM signaling complex consists of a receptor homodimer, one or two ligands bound to the receptor extracellular domains and two molecules of Janus Kinase 2 (JAK2) constitutively associated with the receptor intracellular domains. Although crystal structures of soluble extracellular domains with ligands have been obtained for all the receptors except TPOR, little is known about the structure and dynamics of the complete TM complexes that activate the downstream JAK-STAT signaling pathway. Three-dimensional models of five human receptor complexes with cytokines and JAK2 were generated using AlphaFold Multimer. Given the large size of the complexes (from 3220 to 4074 residues), the modeling required a stepwise assembly from smaller parts with selection and validation of the models through comparisons with published experimental data. The modeling of active and inactive complexes supports a general activation mechanism that involves ligand binding to a monomeric receptor followed by receptor dimerization and rotational movement of the receptor TM α-helices causing proximity, dimerization, and activation of associated JAK2 subunits. The binding mode of two eltrombopag molecules to TM α-helices of the active TPOR dimer was proposed. The models also help elucidating the molecular basis of oncogenic mutations that may involve non-canonical activation route. Models equilibrated in explicit lipids of the plasma membrane are publicly available.
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Affiliation(s)
- Irina D. Pogozheva
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, United States
| | | | - Sang-Jun Park
- Departments of Biological Sciences and Chemistry, Lehigh University, Bethlehem, PA 18015, United States
| | - Malini Raghavan
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, United States
| | - Wonpil Im
- Departments of Biological Sciences and Chemistry, Lehigh University, Bethlehem, PA 18015, United States
| | - Andrei L. Lomize
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, United States
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5
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Martín MG, Dotti CG. Plasma membrane and brain dysfunction of the old: Do we age from our membranes? Front Cell Dev Biol 2022; 10:1031007. [PMID: 36274849 PMCID: PMC9582647 DOI: 10.3389/fcell.2022.1031007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 09/20/2022] [Indexed: 11/26/2022] Open
Abstract
One of the characteristics of aging is a gradual hypo-responsiveness of cells to extrinsic stimuli, mainly evident in the pathways that are under hormone control, both in the brain and in peripheral tissues. Age-related resistance, i.e., reduced response of receptors to their ligands, has been shown to Insulin and also to leptin, thyroid hormones and glucocorticoids. In addition, lower activity has been reported in aging for ß-adrenergic receptors, adenosine A2B receptor, and several other G-protein-coupled receptors. One of the mechanisms proposed to explain the loss of sensitivity to hormones and neurotransmitters with age is the loss of receptors, which has been observed in several tissues. Another mechanism that is finding more and more experimental support is related to the changes that occur with age in the lipid composition of the neuronal plasma membrane, which are responsible for changes in the receptors’ coupling efficiency to ligands, signal attenuation and pathway desensitization. In fact, recent works have shown that altered membrane composition—as occurs during neuronal aging—underlies reduced response to glutamate, to the neurotrophin BDNF, and to insulin, all these leading to cognition decay and epigenetic alterations in the old. In this review we present evidence that altered functions of membrane receptors due to altered plasma membrane properties may be a triggering factor in physiological decline, decreased brain function, and increased vulnerability to neuropathology in aging.
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Affiliation(s)
- Mauricio G. Martín
- Cellular and Molecular Neurobiology Department, Instituto Ferreyra (INIMEC)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Córdoba (UNC), Córdoba, Argentina
- *Correspondence: Mauricio G. Martín, ; Carlos G. Dotti,
| | - Carlos G. Dotti
- Molecular Neuropathology Unit, Physiological and Pathological Processes Program, Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas (CSIC), Universidad Autónoma de Madrid (UAM), Madrid, Spain
- *Correspondence: Mauricio G. Martín, ; Carlos G. Dotti,
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6
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Aliper ET, Krylov NA, Nolde DE, Polyansky AA, Efremov RG. A Uniquely Stable Trimeric Model of SARS-CoV-2 Spike Transmembrane Domain. Int J Mol Sci 2022; 23:ijms23169221. [PMID: 36012488 PMCID: PMC9409440 DOI: 10.3390/ijms23169221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 08/13/2022] [Accepted: 08/15/2022] [Indexed: 11/16/2022] Open
Abstract
Understanding fusion mechanisms employed by SARS-CoV-2 spike protein entails realistic transmembrane domain (TMD) models, while no reliable approaches towards predicting the 3D structure of transmembrane (TM) trimers exist. Here, we propose a comprehensive computational framework to model the spike TMD only based on its primary structure. We performed amino acid sequence pattern matching and compared the molecular hydrophobicity potential (MHP) distribution on the helix surface against TM homotrimers with known 3D structures and selected an appropriate template for homology modeling. We then iteratively built a model of spike TMD, adjusting “dynamic MHP portraits” and residue variability motifs. The stability of this model, with and without palmitoyl modifications downstream of the TMD, and several alternative configurations (including a recent NMR structure), was tested in all-atom molecular dynamics simulations in a POPC bilayer mimicking the viral envelope. Our model demonstrated unique stability under the conditions applied and conforms to known basic principles of TM helix packing. The original computational framework looks promising and could potentially be employed in the construction of 3D models of TM trimers for a wide range of membrane proteins.
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Affiliation(s)
- Elena T. Aliper
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya St., 117997 Moscow, Russia
| | - Nikolay A. Krylov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya St., 117997 Moscow, Russia
- National Research University Higher School of Economics, 101000 Moscow, Russia
| | - Dmitry E. Nolde
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya St., 117997 Moscow, Russia
- National Research University Higher School of Economics, 101000 Moscow, Russia
| | - Anton A. Polyansky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya St., 117997 Moscow, Russia
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna BioCenter 5, A-1030 Vienna, Austria
| | - Roman G. Efremov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya St., 117997 Moscow, Russia
- National Research University Higher School of Economics, 101000 Moscow, Russia
- Moscow Institute of Physics and Technology (State University), 141701 Dolgoprudny, Russia
- Correspondence:
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7
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Intrinsically disordered proteins and membranes: a marriage of convenience for cell signalling? Biochem Soc Trans 2021; 48:2669-2689. [PMID: 33155649 PMCID: PMC7752083 DOI: 10.1042/bst20200467] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 10/05/2020] [Accepted: 10/08/2020] [Indexed: 02/07/2023]
Abstract
The structure-function paradigm has guided investigations into the molecules involved in cellular signalling for decades. The peripheries of this paradigm, however, start to unravel when considering the co-operation between proteins and the membrane in signalling processes. Intrinsically disordered regions hold distinct advantages over folded domains in terms of their binding promiscuity, sensitivity to their particular environment and their ease of modulation through post-translational modifications. Low sequence complexity and bias towards charged residues are also favourable for the multivalent electrostatic interactions that occur at the surfaces of lipid bilayers. This review looks at the principles behind the successful marriage between protein disorder and membranes in addition to the role of this partnership in modifying and regulating signalling in cellular processes. The HVR (hypervariable region) of small GTPases is highlighted as a well-studied example of the nuanced role a short intrinsically disordered region can play in the fine-tuning of signalling pathways.
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8
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Cheng Y, Li W, Gui R, Wang C, Song J, Wang Z, Wang X, Shen Y, Wang Z, Hao L. Dual Characters of GH-IGF1 Signaling Pathways in Radiotherapy and Post-radiotherapy Repair of Cancers. Front Cell Dev Biol 2021; 9:671247. [PMID: 34178997 PMCID: PMC8220142 DOI: 10.3389/fcell.2021.671247] [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: 02/24/2021] [Accepted: 05/17/2021] [Indexed: 12/02/2022] Open
Abstract
Radiotherapy remains one of the most important cancer treatment modalities. In the course of radiotherapy for tumor treatment, the incidental irradiation of adjacent tissues could not be completely avoided. DNA damage is one of the main factors of cell death caused by ionizing radiation, including single-strand (SSBs) and double-strand breaks (DSBs). The growth hormone-Insulin-like growth factor 1 (GH-IGF1) axis plays numerous roles in various systems by promoting cell proliferation and inhibiting apoptosis, supporting its effects in inducing the development of multiple cancers. Meanwhile, the GH-IGF1 signaling involved in DNA damage response (DDR) and DNA damage repair determines the radio-resistance of cancer cells subjected to radiotherapy and repair of adjacent tissues damaged by radiotherapy. In the present review, we firstly summarized the studies on GH-IGF1 signaling in the development of cancers. Then we discussed the adverse effect of GH-IGF1 signaling in radiotherapy to cancer cells and the favorable impact of GH-IGF1 signaling on radiation damage repair to adjacent tissues after irradiation. This review further summarized recent advances on research into the molecular mechanism of GH-IGF1 signaling pathway in these effects, expecting to specify the dual characters of GH-IGF1 signaling pathways in radiotherapy and post-radiotherapy repair of cancers, subsequently providing theoretical basis of their roles in increasing radiation sensitivity during cancer radiotherapy and repairing damage after radiotherapy.
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Affiliation(s)
- Yunyun Cheng
- NHC Key Laboratory of Radiobiology, School of Public Health, Jilin University, Changchun, China
| | - Wanqiao Li
- NHC Key Laboratory of Radiobiology, School of Public Health, Jilin University, Changchun, China
| | - Ruirui Gui
- NHC Key Laboratory of Radiobiology, School of Public Health, Jilin University, Changchun, China
| | - Chunli Wang
- College of Animal Science, Jilin University, Changchun, China
| | - Jie Song
- College of Animal Science, Jilin University, Changchun, China
| | - Zhaoguo Wang
- College of Animal Science, Jilin University, Changchun, China
| | - Xue Wang
- The First Hospital of Jilin University, Changchun, China
| | - Yannan Shen
- NHC Key Laboratory of Radiobiology, School of Public Health, Jilin University, Changchun, China
| | - Zhicheng Wang
- NHC Key Laboratory of Radiobiology, School of Public Health, Jilin University, Changchun, China
| | - Linlin Hao
- College of Animal Science, Jilin University, Changchun, China
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9
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Kassem N, Araya-Secchi R, Bugge K, Barclay A, Steinocher H, Khondker A, Wang Y, Lenard AJ, Bürck J, Sahin C, Ulrich AS, Landreh M, Pedersen MC, Rheinstädter MC, Pedersen PA, Lindorff-Larsen K, Arleth L, Kragelund BB. Order and disorder-An integrative structure of the full-length human growth hormone receptor. SCIENCE ADVANCES 2021; 7:7/27/eabh3805. [PMID: 34193419 PMCID: PMC8245047 DOI: 10.1126/sciadv.abh3805] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 05/18/2021] [Indexed: 05/13/2023]
Abstract
Because of its small size (70 kilodalton) and large content of structural disorder (>50%), the human growth hormone receptor (hGHR) falls between the cracks of conventional high-resolution structural biology methods. Here, we study the structure of the full-length hGHR in nanodiscs with small-angle x-ray scattering (SAXS) as the foundation. We develop an approach that combines SAXS, x-ray diffraction, and NMR spectroscopy data obtained on individual domains and integrate these through molecular dynamics simulations to interpret SAXS data on the full-length hGHR in nanodiscs. The hGHR domains reorient freely, resulting in a broad structural ensemble, emphasizing the need to take an ensemble view on signaling of relevance to disease states. The structure provides the first experimental model of any full-length cytokine receptor in a lipid membrane and exemplifies how integrating experimental data from several techniques computationally may access structures of membrane proteins with long, disordered regions, a widespread phenomenon in biology.
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Affiliation(s)
- Noah Kassem
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes vej 5, 2200 Copenhagen N, Denmark
| | - Raul Araya-Secchi
- X-ray and Neutron Science, The Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
| | - Katrine Bugge
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes vej 5, 2200 Copenhagen N, Denmark
| | - Abigail Barclay
- X-ray and Neutron Science, The Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
| | - Helena Steinocher
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes vej 5, 2200 Copenhagen N, Denmark
| | - Adree Khondker
- Department of Physics and Astronomy, McMaster University, Hamilton, ON, Canada
| | - Yong Wang
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes vej 5, 2200 Copenhagen N, Denmark
| | - Aneta J Lenard
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes vej 5, 2200 Copenhagen N, Denmark
| | - Jochen Bürck
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), POB 3640, 76021 Karlsruhe, Germany
| | - Cagla Sahin
- Department of Microbiology, Tumor, and Cell Biology, Karolinska Institutet, Stockholm 171 65, Sweden
| | - Anne S Ulrich
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), POB 3640, 76021 Karlsruhe, Germany
| | - Michael Landreh
- Department of Microbiology, Tumor, and Cell Biology, Karolinska Institutet, Stockholm 171 65, Sweden
| | - Martin Cramer Pedersen
- X-ray and Neutron Science, The Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Per Amstrup Pedersen
- Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100 Copenhagen, Denmark
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes vej 5, 2200 Copenhagen N, Denmark.
| | - Lise Arleth
- X-ray and Neutron Science, The Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark.
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes vej 5, 2200 Copenhagen N, Denmark.
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10
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Chhabra Y, Lee CMM, Müller AF, Brooks AJ. GHR signalling: Receptor activation and degradation mechanisms. Mol Cell Endocrinol 2021; 520:111075. [PMID: 33181235 DOI: 10.1016/j.mce.2020.111075] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 11/01/2020] [Accepted: 11/03/2020] [Indexed: 12/21/2022]
Abstract
Growth hormone (GH) actions via initiating cell signalling through the GH receptor (GHR) are important for many physiological processes, in addition to its well-known role in regulating growth. The activation of JAK-STAT signalling by GH is well characterized, however knowledge on GH activation of SRC family kinases (SFKs) is still limited. In this review we summarise the collective knowledge on the activation, regulation, and downstream signalling of GHR. We highlight studies on GH activation of SFKs and the important outcome of this signalling pathway with a focus on the different degradation mechanisms that can regulate GHR availability since this is an area that warrants further study considering its role in tumour progression.
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Affiliation(s)
- Yash Chhabra
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD, 4102, Australia; Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21231, USA
| | - Christine M M Lee
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD, 4102, Australia
| | - Alexandra Franziska Müller
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD, 4102, Australia
| | - Andrew J Brooks
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD, 4102, Australia.
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11
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Geisler M, Hegedűs T. A twist in the ABC: regulation of ABC transporter trafficking and transport by FK506-binding proteins. FEBS Lett 2020; 594:3986-4000. [PMID: 33125703 DOI: 10.1002/1873-3468.13983] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 10/02/2020] [Accepted: 10/15/2020] [Indexed: 01/07/2023]
Abstract
Post-transcriptional regulation of ATP-binding cassette (ABC) proteins has been so far shown to encompass protein phosphorylation, maturation, and ubiquitination. Yet, recent accumulating evidence implicates FK506-binding proteins (FKBPs), a type of peptidylprolyl cis-trans isomerase (PPIase) proteins, in ABC transporter regulation. In this perspective article, we summarize current knowledge on ABC transporter regulation by FKBPs, which seems to be conserved over kingdoms and ABC subfamilies. We uncover striking functional similarities but also differences between regulatory FKBP-ABC modules in plants and mammals. We dissect a PPIase- and HSP90-dependent and independent impact of FKBPs on ABC biogenesis and transport activity. We propose and discuss a putative new mode of transient ABC transporter regulation by cis-trans isomerization of X-prolyl bonds.
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Affiliation(s)
- Markus Geisler
- Department of Biology, University of Fribourg, Switzerland
| | - Tamás Hegedűs
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
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12
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Kuznetsov AS, Zamaletdinov MF, Bershatsky YV, Urban AS, Bocharova OV, Bennasroune A, Maurice P, Bocharov EV, Efremov RG. Dimeric states of transmembrane domains of insulin and IGF-1R receptors: Structures and possible role in activation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183417. [PMID: 32710851 DOI: 10.1016/j.bbamem.2020.183417] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 06/21/2020] [Accepted: 07/07/2020] [Indexed: 01/07/2023]
Abstract
Despite the biological significance of insulin signaling, the molecular mechanisms of activation of the insulin receptor (IR) and other proteins from its family remain elusive. Current hypothesis on signal transduction suggests ligand-triggered structural changes in the extracellular domain followed by transmembrane (TM) domains closure and dimerization leading to trans-autophosphorylation and kinase activity in intracellular segments of the receptor. Using NMR spectroscopy, we detected dimerization of isolated TM segments of IR in different membrane-mimicking environments and observed multiple signals of NH groups of protein backbone possibly corresponding to several dimer conformations. Taking available experimental data as constraints, several atomistic models of dimeric TM domains of IR and insulin-like growth factor 1 (IGF-1R) receptors were elaborated. Molecular dynamics simulations of IR ectodomain revealed noticeable collective movements potentially responsible for closure of the C-termini of FnIII-3 domains and spatial approaching of TM helices upon insulin-induced receptor activation. In addition, we demonstrated that the intracellular part of the receptor does not impose restrictions on the positioning of TM helices in the membrane. Finally, we used two independent structure prediction methods to generate a series of dimer conformations followed by their cluster analysis and dimerization free energy estimation to select the best dimer models. Biological relevance of the later was further tested via comparison of the hydrophobic organization of TM helices for both wild-type receptors and their mutants. Based on these data, the ability of several segments from other proteins to functionally replace IR and/or IGF-1R TM domains was explained.
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Affiliation(s)
- Andrey S Kuznetsov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences RAS, str. Miklukho-Maklaya 16/10, Moscow 117997, Russian Federation; National Research University Higher School of Economics, Myasnitskaya ul. 20, Moscow 101000, Russian Federation; Moscow Institute of Physics and Technology, Institutsky per., 9, Dolgoprudnyi 141700, Russian Federation
| | - Miftakh F Zamaletdinov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences RAS, str. Miklukho-Maklaya 16/10, Moscow 117997, Russian Federation; Lomonosov Moscow State University, Leninskiye Gory, 1, Moscow 119991, Russian Federation
| | - Yaroslav V Bershatsky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences RAS, str. Miklukho-Maklaya 16/10, Moscow 117997, Russian Federation; Moscow Institute of Physics and Technology, Institutsky per., 9, Dolgoprudnyi 141700, Russian Federation
| | - Anatoly S Urban
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences RAS, str. Miklukho-Maklaya 16/10, Moscow 117997, Russian Federation; Moscow Institute of Physics and Technology, Institutsky per., 9, Dolgoprudnyi 141700, Russian Federation
| | - Olga V Bocharova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences RAS, str. Miklukho-Maklaya 16/10, Moscow 117997, Russian Federation; Moscow Institute of Physics and Technology, Institutsky per., 9, Dolgoprudnyi 141700, Russian Federation
| | - Amar Bennasroune
- UMR CNRS 7369 Matrice Extracellulaire et Dynamique Cellulaire (MEDyC), Université de Reims Champagne Ardenne (URCA), UFR Sciences Exactes et Naturelles, Reims, France
| | - Pascal Maurice
- UMR CNRS 7369 Matrice Extracellulaire et Dynamique Cellulaire (MEDyC), Université de Reims Champagne Ardenne (URCA), UFR Sciences Exactes et Naturelles, Reims, France
| | - Eduard V Bocharov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences RAS, str. Miklukho-Maklaya 16/10, Moscow 117997, Russian Federation; Moscow Institute of Physics and Technology, Institutsky per., 9, Dolgoprudnyi 141700, Russian Federation
| | - Roman G Efremov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences RAS, str. Miklukho-Maklaya 16/10, Moscow 117997, Russian Federation; National Research University Higher School of Economics, Myasnitskaya ul. 20, Moscow 101000, Russian Federation; Moscow Institute of Physics and Technology, Institutsky per., 9, Dolgoprudnyi 141700, Russian Federation.
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13
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Seiffert P, Bugge K, Nygaard M, Haxholm GW, Martinsen JH, Pedersen MN, Arleth L, Boomsma W, Kragelund BB. Orchestration of signaling by structural disorder in class 1 cytokine receptors. Cell Commun Signal 2020; 18:132. [PMID: 32831102 PMCID: PMC7444064 DOI: 10.1186/s12964-020-00626-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 07/08/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Class 1 cytokine receptors (C1CRs) are single-pass transmembrane proteins responsible for transmitting signals between the outside and the inside of cells. Remarkably, they orchestrate key biological processes such as proliferation, differentiation, immunity and growth through long disordered intracellular domains (ICDs), but without having intrinsic kinase activity. Despite these key roles, their characteristics remain rudimentarily understood. METHODS The current paper asks the question of why disorder has evolved to govern signaling of C1CRs by reviewing the literature in combination with new sequence and biophysical analyses of chain properties across the family. RESULTS We uncover that the C1CR-ICDs are fully disordered and brimming with SLiMs. Many of these short linear motifs (SLiMs) are overlapping, jointly signifying a complex regulation of interactions, including network rewiring by isoforms. The C1CR-ICDs have unique properties that distinguish them from most IDPs and we forward the perception that the C1CR-ICDs are far from simple strings with constitutively bound kinases. Rather, they carry both organizational and operational features left uncovered within their disorder, including mechanisms and complexities of regulatory functions. CONCLUSIONS Critically, the understanding of the fascinating ability of these long, completely disordered chains to orchestrate complex cellular signaling pathways is still in its infancy, and we urge a perceptional shift away from the current simplistic view towards uncovering their full functionalities and potential. Video abstract.
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Affiliation(s)
- Pernille Seiffert
- REPIN, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Katrine Bugge
- REPIN, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Mads Nygaard
- REPIN, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Gitte W. Haxholm
- REPIN, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Jacob H. Martinsen
- REPIN, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Martin N. Pedersen
- Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100 Copenhagen Ø, Denmark
| | - Lise Arleth
- Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100 Copenhagen Ø, Denmark
| | - Wouter Boomsma
- Department of Computer Science, University of Copenhagen, Universitetsparken 1, 2100 Copenhagen Ø, Denmark
| | - Birthe B. Kragelund
- REPIN, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark
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14
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Metcalfe RD, Putoczki TL, Griffin MDW. Structural Understanding of Interleukin 6 Family Cytokine Signaling and Targeted Therapies: Focus on Interleukin 11. Front Immunol 2020; 11:1424. [PMID: 32765502 PMCID: PMC7378365 DOI: 10.3389/fimmu.2020.01424] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 06/02/2020] [Indexed: 12/12/2022] Open
Abstract
Cytokines are small signaling proteins that have central roles in inflammation and cell survival. In the half-century since the discovery of the first cytokines, the interferons, over fifty cytokines have been identified. Amongst these is interleukin (IL)-6, the first and prototypical member of the IL-6 family of cytokines, nearly all of which utilize the common signaling receptor, gp130. In the last decade, there have been numerous advances in our understanding of the structural mechanisms of IL-6 family signaling, particularly for IL-6 itself. However, our understanding of the detailed structural mechanisms underlying signaling by most IL-6 family members remains limited. With the emergence of new roles for IL-6 family cytokines in disease and, in particular, roles of IL-11 in cardiovascular disease, lung disease, and cancer, there is an emerging need to develop therapeutics that can progress to clinical use. Here we outline our current knowledge of the structural mechanism of signaling by the IL-6 family of cytokines. We discuss how this knowledge allows us to understand the mechanism of action of currently available inhibitors targeting IL-6 family cytokine signaling, and most importantly how it allows for improved opportunities to pharmacologically disrupt cytokine signaling. We focus specifically on the need to develop and understand inhibitors that disrupt IL-11 signaling.
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Affiliation(s)
- Riley D Metcalfe
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Technology Institute, The University of Melbourne, Parkville, VIC, Australia
| | - Tracy L Putoczki
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Michael D W Griffin
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Technology Institute, The University of Melbourne, Parkville, VIC, Australia
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15
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Kassem N, Kassem MM, Pedersen SF, Pedersen PA, Kragelund BB. Yeast recombinant production of intact human membrane proteins with long intrinsically disordered intracellular regions for structural studies. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183272. [PMID: 32169592 DOI: 10.1016/j.bbamem.2020.183272] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 03/08/2020] [Accepted: 03/09/2020] [Indexed: 01/07/2023]
Abstract
Membrane proteins exist in lipid bilayers and mediate solute transport, signal transduction, cell-cell communication and energy conversion. Their activities are fundamental for life, which make them prominent subjects of study, but access to only a limited number of high-resolution structures complicates their mechanistic understanding. The absence of such structures relates mainly to difficulties in expressing and purifying high quality membrane protein samples in large quantities. An additional layer of complexity stems from the presence of intra- and/or extra-cellular domains constituted by unstructured intrinsically disordered regions (IDR), which can be hundreds of residues long. Although IDRs form key interaction hubs that facilitate biological processes, these are regularly removed to enable structural studies. To advance mechanistic insight into intact intrinsically disordered membrane proteins, we have developed a protocol for their purification. Using engineered yeast cells for optimized expression and purification, we have purified to homogeneity two very different human membrane proteins each with >300 residues long IDRs; the sodium proton exchanger 1 and the growth hormone receptor. Subsequent to their purification we have further explored their incorporation into membrane scaffolding protein nanodiscs, which will enable future structural studies.
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Affiliation(s)
- Noah Kassem
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Maher M Kassem
- Machine Learning, Department of Computer Science, University of Copenhagen, Universitetsparken 5, DK-2100, Copenhagen Ø, Denmark
| | - Stine F Pedersen
- Cell Biology and Physiology, Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100 Copenhagen Ø, Denmark
| | - Per Amstrup Pedersen
- Cell Biology and Physiology, Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100 Copenhagen Ø, Denmark.
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark.
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16
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Westerfield JM, Barrera FN. Membrane receptor activation mechanisms and transmembrane peptide tools to elucidate them. J Biol Chem 2019; 295:1792-1814. [PMID: 31879273 DOI: 10.1074/jbc.rev119.009457] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Single-pass membrane receptors contain extracellular domains that respond to external stimuli and transmit information to intracellular domains through a single transmembrane (TM) α-helix. Because membrane receptors have various roles in homeostasis, signaling malfunctions of these receptors can cause disease. Despite their importance, there is still much to be understood mechanistically about how single-pass receptors are activated. In general, single-pass receptors respond to extracellular stimuli via alterations in their oligomeric state. The details of this process are still the focus of intense study, and several lines of evidence indicate that the TM domain (TMD) of the receptor plays a central role. We discuss three major mechanistic hypotheses for receptor activation: ligand-induced dimerization, ligand-induced rotation, and receptor clustering. Recent observations suggest that receptors can use a combination of these activation mechanisms and that technical limitations can bias interpretation. Short peptides derived from receptor TMDs, which can be identified by screening or rationally developed on the basis of the structure or sequence of their targets, have provided critical insights into receptor function. Here, we explore recent evidence that, depending on the target receptor, TMD peptides cannot only inhibit but also activate target receptors and can accommodate novel, bifunctional designs. Furthermore, we call for more sharing of negative results to inform the TMD peptide field, which is rapidly transforming into a suite of unique tools with the potential for future therapeutics.
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Affiliation(s)
- Justin M Westerfield
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996
| | - Francisco N Barrera
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996.
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17
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Paul MD, Hristova K. The transition model of RTK activation: A quantitative framework for understanding RTK signaling and RTK modulator activity. Cytokine Growth Factor Rev 2019; 49:23-31. [PMID: 31711797 DOI: 10.1016/j.cytogfr.2019.10.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 10/10/2019] [Indexed: 01/15/2023]
Abstract
Here, we discuss the transition model of receptor tyrosine kinase (RTK) activation, which is derived from biophysical investigations of RTK interactions and signaling. The model postulates that (1) RTKs can interact laterally to form dimers even in the absence of ligand, (2) different unliganded RTK dimers have different stabilities, (3) ligand binding stabilizes the RTK dimers, and (4) ligand binding causes structural changes in the RTK dimer. The model is grounded in the principles of physical chemistry and provides a framework to understand RTK activity and to make predictions in quantitative terms. It can guide basic research aimed at uncovering the mechanism of RTK activation and, in the long run, can empower the search for modulators of RTK function.
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Affiliation(s)
- Michael D Paul
- Department of Materials Science and Engineering, Institute for NanoBioTechnology, and Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, 21218, United States
| | - Kalina Hristova
- Department of Materials Science and Engineering, Institute for NanoBioTechnology, and Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, 21218, United States.
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18
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Basu R, Kopchick JJ. The effects of growth hormone on therapy resistance in cancer. CANCER DRUG RESISTANCE (ALHAMBRA, CALIF.) 2019; 2:827-846. [PMID: 32382711 PMCID: PMC7204541 DOI: 10.20517/cdr.2019.27] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Pituitary derived and peripherally produced growth hormone (GH) is a crucial mediator of longitudinal growth, organ development, metabolic regulation with tissue specific, sex specific, and age-dependent effects. GH and its cognate receptor (GHR) are expressed in several forms of cancer and have been validated as an anti-cancer target through a large body of in vitro, in vivo and epidemiological analyses. However, the underlying molecular mechanisms of GH action in cancer prognosis and therapeutic response had been sparse until recently. This review assimilates the critical details of GH-GHR mediated therapy resistance across different cancer types, distilling the therapeutic implications based on our current understanding of these effects.
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Affiliation(s)
- Reetobrata Basu
- Ohio University Heritage College of Osteopathic Medicine (OU-HCOM), Ohio University, Athens, OH 45701, USA.,Edison Biotechnology Institute, Ohio University, Athens, OH 45701, USA
| | - John J Kopchick
- Ohio University Heritage College of Osteopathic Medicine (OU-HCOM), Ohio University, Athens, OH 45701, USA.,Edison Biotechnology Institute, Ohio University, Athens, OH 45701, USA
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19
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Oncogenic basic amino acid insertions at the extracellular juxtamembrane region of IL7RA cause receptor hypersensitivity. Blood 2019; 133:1259-1263. [DOI: 10.1182/blood-2018-09-872945] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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20
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Panina IS, Chugunov AO, Efremov RG. Lipid II as a Target for Novel Antibiotics: Structural and Molecular Dynamics Studies. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2019. [DOI: 10.1134/s1068162019010126] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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21
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Polyansky AA, Bocharov EV, Velghe AI, Kuznetsov AS, Bocharova OV, Urban AS, Arseniev AS, Zagrovic B, Demoulin JB, Efremov RG. Atomistic mechanism of the constitutive activation of PDGFRA via its transmembrane domain. Biochim Biophys Acta Gen Subj 2018; 1863:82-95. [PMID: 30253204 DOI: 10.1016/j.bbagen.2018.09.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 09/12/2018] [Accepted: 09/16/2018] [Indexed: 12/14/2022]
Abstract
Single-point mutations in the transmembrane (TM) region of receptor tyrosine kinases (RTKs) can lead to abnormal ligand-independent activation. We use a combination of computational modeling, NMR spectroscopy and cell experiments to analyze in detail the mechanism of how TM domains contribute to the activation of wild-type (WT) PDGFRA and its oncogenic V536E mutant. Using a computational framework, we scan all positions in PDGFRA TM helix for identification of potential functional mutations for the WT and the mutant and reveal the relationship between the receptor activity and TM dimerization via different interfaces. This strategy also allows us design a novel activating mutation in the WT (I537D) and a compensatory mutation in the V536E background eliminating its constitutive activity (S541G). We show both computationally and experimentally that single-point mutations in the TM region reshape the TM dimer ensemble and delineate the structural and dynamic determinants of spontaneous activation of PDGFRA via its TM domain. Our atomistic picture of the coupling between TM dimerization and PDGFRA activation corroborates the data obtained for other RTKs and provides a foundation for developing novel modulators of the pathological activity of PDGFRA.
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Affiliation(s)
- Anton A Polyansky
- MM Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russia; Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria.
| | - Eduard V Bocharov
- MM Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russia; Moscow Institute of Physics and Technology (State University), Institutskiy Pereulok 9, Dolgoprudny, Moscow region 141700, Russia; National Research Centre "Kurchatov Institute", Akad. Kurchatova pl. 1, Moscow 123182, Russia
| | - Amélie I Velghe
- de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, 1200 Brussels, Belgium
| | - Andrey S Kuznetsov
- MM Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russia; Moscow Institute of Physics and Technology (State University), Institutskiy Pereulok 9, Dolgoprudny, Moscow region 141700, Russia; Higher School of Economics, Myasnitskaya 20, 101000 Moscow, Russia
| | - Olga V Bocharova
- MM Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russia; Moscow Institute of Physics and Technology (State University), Institutskiy Pereulok 9, Dolgoprudny, Moscow region 141700, Russia
| | - Anatoly S Urban
- MM Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russia; Moscow Institute of Physics and Technology (State University), Institutskiy Pereulok 9, Dolgoprudny, Moscow region 141700, Russia
| | - Alexander S Arseniev
- MM Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russia; Moscow Institute of Physics and Technology (State University), Institutskiy Pereulok 9, Dolgoprudny, Moscow region 141700, Russia
| | - Bojan Zagrovic
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria
| | - Jean-Baptiste Demoulin
- de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, 1200 Brussels, Belgium.
| | - Roman G Efremov
- MM Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russia; Moscow Institute of Physics and Technology (State University), Institutskiy Pereulok 9, Dolgoprudny, Moscow region 141700, Russia; Higher School of Economics, Myasnitskaya 20, 101000 Moscow, Russia
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