1
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Schuck RJ, Ward AE, Sahoo AR, Rybak JA, Pyron RJ, Trybala TN, Simmons TB, Baccile JA, Sgouralis I, Buck M, Lamichhane R, Barrera FN. Cholesterol inhibits assembly and activation of the EphA2 receptor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.10.598255. [PMID: 38915729 PMCID: PMC11195142 DOI: 10.1101/2024.06.10.598255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
The receptor tyrosine kinase EphA2 drives cancer malignancy by facilitating metastasis. EphA2 can be found in different self-assembly states: as a monomer, dimer, and oligomer. However, our understanding remains limited regarding which EphA2 state is responsible for driving pro-metastatic signaling. To address this limitation, we have developed SiMPull-POP, a single-molecule method for accurate quantification of membrane protein self-assembly. Our experiments revealed that a reduction of plasma membrane cholesterol strongly promoted EphA2 self-assembly. Indeed, low cholesterol caused a similar effect to the EphA2 ligand ephrinA1-Fc. These results indicate that cholesterol inhibits EphA2 assembly. Phosphorylation studies in different cell lines revealed that low cholesterol increased phospho-serine levels, the signature of oncogenic signaling. Investigation of the mechanism that cholesterol uses to inhibit the assembly and activity of EphA2 indicate an in-trans effect, where EphA2 is phosphorylated by protein kinase A downstream of beta-adrenergic receptor activity, which cholesterol also inhibits. Our study not only provides new mechanistic insights on EphA2 oncogenic function, but also suggests that cholesterol acts as a molecular safeguard mechanism that prevents uncontrolled self-assembly and activation of EphA2.
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Affiliation(s)
- Ryan J Schuck
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, USA
| | - Alyssa E Ward
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, USA
| | - Amita R Sahoo
- Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, Cleveland, USA
| | - Jennifer A Rybak
- Genome Science and Technology, University of Tennessee, Knoxville, USA
| | - Robert J Pyron
- Genome Science and Technology, University of Tennessee, Knoxville, USA
| | - Thomas N Trybala
- Department of Chemistry, University of Tennessee, Knoxville, USA
| | - Timothy B Simmons
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, USA
| | - Joshua A Baccile
- Department of Chemistry, University of Tennessee, Knoxville, USA
| | | | - Matthias Buck
- Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, Cleveland, USA
| | - Rajan Lamichhane
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, USA
| | - Francisco N Barrera
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, USA
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2
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Wirth D, Özdemir E, Wimley WC, Pasquale EB, Hristova K. Transmembrane helix interactions regulate oligomerization of the receptor tyrosine kinase EphA2. J Biol Chem 2024; 300:107441. [PMID: 38838777 DOI: 10.1016/j.jbc.2024.107441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/27/2024] [Accepted: 05/28/2024] [Indexed: 06/07/2024] Open
Abstract
The transmembrane helices of receptor tyrosine kinases (RTKs) have been proposed to switch between two different dimeric conformations, one associated with the inactive RTK and the other with the active RTK. Furthermore, recent work has demonstrated that some full-length RTKs are associated with oligomers that are larger than dimers, raising questions about the roles of the TM helices in the assembly and function of these oligomers. Here we probe the roles of the TM helices in the stability of EphA2 RTK oligomers in the plasma membrane. We employ mutagenesis to evaluate the relevance of a published NMR dimeric structure of the isolated EphA2 TM helix in the context of the full-length EphA2 in the plasma membrane. We use two fluorescence methods, Förster Resonance Energy Transfer and Fluorescence Intensity Fluctuations spectrometry, which yield complementary information about the EphA2 oligomerization process. These studies reveal that the TM helix mutations affect the stability, structure, and size of EphA2 oligomers. However, the effects are multifaceted and point to a more complex role of the TM helix than the one expected from the "TM dimer switch" model.
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Affiliation(s)
- Daniel Wirth
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Ece Özdemir
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - William C Wimley
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Elena B Pasquale
- Cancer Metabolism and Microenvironment Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Kalina Hristova
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, Maryland, USA.
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3
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Sahoo AR, Souza PCT, Meng Z, Buck M. Transmembrane dimers of type 1 receptors sample alternate configurations: MD simulations using coarse grain Martini 3 versus AlphaFold2 Multimer. Structure 2023; 31:735-745.e2. [PMID: 37075749 PMCID: PMC10833135 DOI: 10.1016/j.str.2023.03.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 02/07/2023] [Accepted: 03/23/2023] [Indexed: 04/21/2023]
Abstract
Structures and dynamics of transmembrane (TM) receptor regions are key to understanding their signaling mechanism across membranes. Here we examine configurations of TM region dimers, assembled using the recent Martini 3 force field for coarse-grain (CG) molecular dynamics simulations. At first glance, our results show only a reasonable agreement with ab initio predictions using PREDDIMER and AlphaFold2 Multimer and with nuclear magnetic resonance (NMR)-derived structures. 5 of 11 CG TM structures are similar to the NMR structures (within <3.5 Å root-mean-square deviation [RMSD]) compared with 10 and 9 using PREDDIMER and AlphaFold2, respectively (with 8 structures of the later within 1.5 Å). Surprisingly, AlphaFold2 predictions are closer to NMR structures when the 2001 instead of 2020 database is used for training. The CG simulations reveal that alternative configurations of TM dimers readily interconvert with a predominant population. The implications for transmembrane signaling are discussed, including for the development of peptide-based pharmaceuticals.
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Affiliation(s)
- Amita R Sahoo
- Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - Paulo C T Souza
- Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), CNRS & University of Lyon, 7 Passage du Vercors, 69007 Lyon, France
| | - Zhiyuan Meng
- Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - Matthias Buck
- Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA.
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4
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Hu R, Li Y, Guo Y, Li X, Du S, Liao M, Hou H, Sun H, Zhao S, Su J, Chen X, Yin M. BRD4 inhibitor suppresses melanoma metastasis via the SPINK6/EGFR-EphA2 pathway. Pharmacol Res 2023; 187:106609. [PMID: 36516883 DOI: 10.1016/j.phrs.2022.106609] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 12/07/2022] [Accepted: 12/10/2022] [Indexed: 12/14/2022]
Abstract
BET inhibition or BRD4 depletion is a promising and attractive therapy for metastatic melanoma; however, the mechanism is still unclear. Here, we indicated that BET inhibition suppressed melanoma metastasis both in vitro and in vivo and identified a new mechanism by which BET inhibitors suppress melanoma metastasis by blocking the direct interaction of BRD4 and the SPINK6 enhancer. Moreover, we demonstrated that SPINK6 activated the EGFR/EphA2 complex in melanoma and the downstream ERK1/2 and AKT pathways. Thus, these results identified the SPINK6/EGFR-EphA2 axis as a new oncogenic pathway in melanoma metastasis and support the further development of BRD4 inhibitors for the treatment of metastatic melanoma in the clinic.
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Affiliation(s)
- Rui Hu
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; Department of Dermatology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China; National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Central South University, Changsha, Hunan 410008, China
| | - Yao Li
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Ying Guo
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Central South University, Changsha, Hunan 410008, China
| | - Xin Li
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Central South University, Changsha, Hunan 410008, China
| | - Songtao Du
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Central South University, Changsha, Hunan 410008, China
| | - Mengting Liao
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Central South University, Changsha, Hunan 410008, China; Health Management of Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Huihui Hou
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Central South University, Changsha, Hunan 410008, China
| | - Hongyin Sun
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Central South University, Changsha, Hunan 410008, China
| | - Shuang Zhao
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Central South University, Changsha, Hunan 410008, China
| | - Juan Su
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Central South University, Changsha, Hunan 410008, China
| | - Xiang Chen
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Central South University, Changsha, Hunan 410008, China.
| | - Mingzhu Yin
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Central South University, Changsha, Hunan 410008, China.
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5
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Wirth D, Paul MD, Pasquale EB, Hristova K. Direct quantification of ligand-induced lipid and protein microdomains with distinctive signaling properties. CHEMSYSTEMSCHEM 2022; 4:e202200011. [PMID: 36337751 PMCID: PMC9634703 DOI: 10.1002/syst.202200011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Indexed: 11/08/2022]
Abstract
Lipid rafts are ordered lipid domains that are enriched in saturated lipids, such as the ganglioside GM1. While lipid rafts are believed to exist in cells and to serve as signaling platforms through their enrichment in signaling components, they have not been directly observed in the plasma membrane without treatments that artificially cluster GM1 into large lattices. Here, we report that microscopic GM1-enriched domains can form, in the plasma membrane of live mammalian cells expressing the EphA2 receptor tyrosine kinase in response to its ligand ephrinA1-Fc. The GM1-enriched microdomains form concomitantly with EphA2-enriched microdomains. To gain insight into how plasma membrane heterogeneity controls signaling, we quantify the degree of EphA2 segregation and study initial EphA2 signaling steps in both EphA2-enriched and EphA2-depleted domains. By measuring dissociation constants, we demonstrate that the propensity of EphA2 to oligomerize is similar in EphA2-enriched and -depleted domains. However, surprisingly, EphA2 interacts preferentially with its downstream effector SRC in EphA2-depleted domains. The ability to induce microscopic GM1-enriched domains in live cells using a ligand for a transmembrane receptor will give us unprecedented opportunities to study the biophysical chemistry of lipid rafts.
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Affiliation(s)
- Daniel Wirth
- Department of Materials Science and Engineering, Johns Hopkins University, 3400 Charles Street, Baltimore, MD 21218
| | - Michael D. Paul
- Program in Molecular Biophysics, Johns Hopkins University, 3400 Charles Street, Baltimore, MD 21218
| | - Elena B. Pasquale
- Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Road, La Jolla, CA 92037
| | - Kalina Hristova
- Department of Materials Science and Engineering, Johns Hopkins University, 3400 Charles Street, Baltimore, MD 21218
- Program in Molecular Biophysics, Johns Hopkins University, 3400 Charles Street, Baltimore, MD 21218
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6
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Bioengineered System for High Throughput Screening of Kv1 Ion Channel Blockers. Bioengineering (Basel) 2021; 8:bioengineering8110187. [PMID: 34821753 PMCID: PMC8614864 DOI: 10.3390/bioengineering8110187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/03/2021] [Accepted: 11/10/2021] [Indexed: 12/12/2022] Open
Abstract
Screening drug candidates for their affinity and selectivity for a certain binding site is a crucial step in developing targeted therapy. Here, we created a screening assay for receptor binding that can be easily scaled up and automated for the high throughput screening of Kv channel blockers. It is based on the expression of the KcsA-Kv1 hybrid channel tagged with a fluorescent protein in the E. coli membrane. In order to make this channel accessible for the soluble compounds, E. coli were transformed into spheroplasts by disruption of the cellular peptidoglycan envelope. The assay was evaluated using a hybrid KcsA-Kv1.3 potassium channel tagged with a red fluorescent protein (TagRFP). The binding of Kv1.3 channel blockers was measured by flow cytometry either by using their fluorescent conjugates or by determining the ability of unconjugated compounds to displace fluorescently labeled blockers with a known affinity. A fraction of the occupied receptor was calculated with a dedicated pipeline available as a Jupyter notebook. Measured binding constants for agitoxin-2, charybdotoxin and kaliotoxin were in firm agreement with the earlier published data. By using a mid-range flow cytometer with manual sample handling, we measured and analyzed up to ten titration curves (eight data points each) in one day. Finally, we considered possibilities for multiplexing, scaling and automation of the assay.
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7
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Single-molecule fluorescence vistas of how lipids regulate membrane proteins. Biochem Soc Trans 2021; 49:1685-1694. [PMID: 34346484 DOI: 10.1042/bst20201074] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/15/2021] [Accepted: 07/19/2021] [Indexed: 12/17/2022]
Abstract
The study of membrane proteins is undergoing a golden era, and we are gaining unprecedented knowledge on how this key group of proteins works. However, we still have only a basic understanding of how the chemical composition and the physical properties of lipid bilayers control the activity of membrane proteins. Single-molecule (SM) fluorescence methods can resolve sample heterogeneity, allowing to discriminate between the different molecular populations that biological systems often adopt. This short review highlights relevant examples of how SM fluorescence methodologies can illuminate the different ways in which lipids regulate the activity of membrane proteins. These studies are not limited to lipid molecules acting as ligands, but also consider how the physical properties of the bilayer can be determining factors on how membrane proteins function.
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8
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Kim DH, Triet HM, Ryu SH. Regulation of EGFR activation and signaling by lipids on the plasma membrane. Prog Lipid Res 2021; 83:101115. [PMID: 34242725 DOI: 10.1016/j.plipres.2021.101115] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 06/02/2021] [Accepted: 07/01/2021] [Indexed: 12/12/2022]
Abstract
Lipids on the plasma membrane are not only components of the membrane biophysical structures but also regulators of receptor functions. Recently, the critical roles of lipid-protein interactions have been intensively highlighted. Epidermal growth factor receptor (EGFR) is one of the most extensively studied receptors exhibiting various lipid interactions, including interactions with phosphatidylcholine, phosphatidylserine, phosphatidylinositol phosphate, cholesterol, gangliosides, and palmitate. Here, we review recent findings on how direct interaction with these lipids regulates EGFR activation and signaling, providing unprecedented insight into the comprehensive roles of various lipids in the control of EGFR functions. Finally, the current limitations in investigating lipid-protein interactions and novel technologies to potentially overcome these limitations are discussed.
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Affiliation(s)
- Do-Hyeon Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Hong Minh Triet
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Sung Ho Ryu
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea.
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9
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Westerfield JM, Sahoo AR, Alves DS, Grau B, Cameron A, Maxwell M, Schuster JA, Souza PCT, Mingarro I, Buck M, Barrera FN. Conformational Clamping by a Membrane Ligand Activates the EphA2 Receptor. J Mol Biol 2021; 433:167144. [PMID: 34229012 DOI: 10.1016/j.jmb.2021.167144] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 06/03/2021] [Accepted: 06/30/2021] [Indexed: 02/07/2023]
Abstract
The EphA2 receptor is a promising drug target for cancer treatment, since EphA2 activation can inhibit metastasis and tumor progression. It has been recently described that the TYPE7 peptide activates EphA2 using a novel mechanism that involves binding to the single transmembrane domain of the receptor. TYPE7 is a conditional transmembrane (TM) ligand, which only inserts into membranes at neutral pH in the presence of the TM region of EphA2. However, how membrane interactions can activate EphA2 is not known. We systematically altered the sequence of TYPE7 to identify the binding motif used to activate EphA2. With the resulting six peptides, we performed biophysical and cell migration assays that identified a new potent peptide variant. We also performed a mutational screen that determined the helical interface that mediates dimerization of the TM domain of EphA2 in cells. These results, together with molecular dynamic simulations, allowed to elucidate the molecular mechanism that TYPE7 uses to activate EphA2, where the membrane peptide acts as a molecular clamp that wraps around the TM dimer of the receptor. We propose that this binding mode stabilizes the active conformation of EphA2. Our data, additionally, provide clues into the properties that TM ligands need to have in order to achieve activation of membrane receptors.
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Affiliation(s)
- Justin M Westerfield
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, 1311 Cumberland Avenue, Knoxville, TN 37996, USA
| | - Amita R Sahoo
- Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - Daiane S Alves
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, 1311 Cumberland Avenue, Knoxville, TN 37996, USA
| | - Brayan Grau
- Departament de Bioquímica i Biologia Molecular, Institut Universitari de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València, E-46100 Burjassot, Spain
| | - Alayna Cameron
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, 1311 Cumberland Avenue, Knoxville, TN 37996, USA
| | - Mikayla Maxwell
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, 1311 Cumberland Avenue, Knoxville, TN 37996, USA
| | - Jennifer A Schuster
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, 1311 Cumberland Avenue, Knoxville, TN 37996, USA
| | - Paulo C T Souza
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS & University of Lyon, 7 Passage du Vercors, F-69367 Lyon, France
| | - Ismael Mingarro
- Departament de Bioquímica i Biologia Molecular, Institut Universitari de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València, E-46100 Burjassot, Spain
| | - Matthias Buck
- Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - Francisco N Barrera
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, 1311 Cumberland Avenue, Knoxville, TN 37996, USA.
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10
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Mason EO, Goldgur Y, Robev D, Freywald A, Nikolov DB, Himanen JP. Structure of the EphB6 receptor ectodomain. PLoS One 2021; 16:e0247335. [PMID: 33770085 PMCID: PMC7997048 DOI: 10.1371/journal.pone.0247335] [Citation(s) in RCA: 3] [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: 11/24/2020] [Accepted: 02/04/2021] [Indexed: 12/15/2022] Open
Abstract
Eph receptors are the largest group amongst the receptor tyrosine kinases and are divided into two subgroups, A and B, based on ligand binding specificities and sequence conservation. Through ligand-induced and ligand-independent activities, Ephs play central roles in diverse biological processes, including embryo development, regulation of neuronal signaling, immune responses, vasculogenesis, as well as tumor initiation, progression, and metastasis. The Eph extracellular regions (ECDs) are constituted of multiple domains, and previous structural studies of the A class receptors revealed how they interact with ephrin ligands and simultaneously mediate Eph-Eph clustering necessary for biological activity. Specifically, EphA structures highlighted a model, where clustering of ligand-bound receptors relies on two distinct receptor/receptor interfaces. Interestingly, most unliganded A class receptors also form an additional, third interface, between the ligand binding domain (LBD) and the fibronectin III domain (FN3) of neighboring molecules. Structures of B-class Eph ECDs, on the other hand, have never been reported. To further our understanding of Eph receptor function, we crystallized the EphB6-ECD and determined its three-dimensional structure using X-ray crystallography. EphB6 has important functions in both normal physiology and human malignancies and is especially interesting because this atypical receptor innately lacks kinase activity and our understanding of the mechanism of action is still incomplete. Our structural data reveals the overall EphB6-ECD architecture and shows EphB6-LBD/FN3 interactions similar to those observed for the unliganded A class receptors, suggesting that these unusual interactions are of general importance to the Eph group. We also observe unique structural features, which likely reflect the atypical signaling properties of EphB6, namely the need of co-receptor(s) for this kinase-inactive Eph. These findings provide new valuable information on the structural organization and mechanism of action of the B-class Ephs, and specifically EphB6, which in the future will assist in identifying clinically relevant targets for cancer therapy.
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Affiliation(s)
- Emilia O. Mason
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Yehuda Goldgur
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Dorothea Robev
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Andrew Freywald
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Dimitar B. Nikolov
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
- * E-mail: (DBN); (JPH)
| | - Juha P. Himanen
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
- * E-mail: (DBN); (JPH)
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11
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Stefanski KM, Russell CM, Westerfield JM, Lamichhane R, Barrera FN. PIP 2 promotes conformation-specific dimerization of the EphA2 membrane region. J Biol Chem 2021; 296:100149. [PMID: 33277361 PMCID: PMC7900517 DOI: 10.1074/jbc.ra120.016423] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/18/2020] [Accepted: 12/04/2020] [Indexed: 12/27/2022] Open
Abstract
The impact of the EphA2 receptor on cancer malignancy hinges on the two different ways it can be activated. EphA2 induces antioncogenic signaling after ligand binding, but ligand-independent activation of EphA2 is pro-oncogenic. It is believed that the transmembrane (TM) domain of EphA2 adopts two alternate conformations in the ligand-dependent and the ligand-independent states. However, it is poorly understood how the difference in TM helical crossing angles found in the two conformations impacts the activity and regulation of EphA2. We devised a method that uses hydrophobic matching to stabilize two conformations of a peptide comprising the EphA2 TM domain and a portion of the intracellular juxtamembrane (JM) segment. The two conformations exhibit different TM crossing angles, resembling the ligand-dependent and ligand-independent states. We developed a single-molecule technique using styrene maleic acid lipid particles to measure dimerization in membranes. We observed that the signaling lipid PIP2 promotes TM dimerization, but only in the small crossing angle state, which we propose corresponds to the ligand-independent conformation. In this state the two TMs are almost parallel, and the positively charged JM segments are expected to be close to each other, causing electrostatic repulsion. The mechanism PIP2 uses to promote dimerization might involve alleviating this repulsion due to its high density of negative charges. Our data reveal a conformational coupling between the TM and JM regions and suggest that PIP2 might directly exert a regulatory effect on EphA2 activation in cells that is specific to the ligand-independent conformation of the receptor.
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Affiliation(s)
- Katherine M Stefanski
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, USA
| | - Charles M Russell
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, USA
| | - Justin M Westerfield
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, USA
| | - Rajan Lamichhane
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, USA.
| | - Francisco N Barrera
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, USA.
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12
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Baudet S, Bécret J, Nicol X. Approaches to Manipulate Ephrin-A:EphA Forward Signaling Pathway. Pharmaceuticals (Basel) 2020; 13:ph13070140. [PMID: 32629797 PMCID: PMC7407804 DOI: 10.3390/ph13070140] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 06/19/2020] [Accepted: 06/28/2020] [Indexed: 02/07/2023] Open
Abstract
Erythropoietin-producing hepatocellular carcinoma A (EphA) receptors and their ephrin-A ligands are key players of developmental events shaping the mature organism. Their expression is mostly restricted to stem cell niches in adults but is reactivated in pathological conditions including lesions in the heart, lung, or nervous system. They are also often misregulated in tumors. A wide range of molecular tools enabling the manipulation of the ephrin-A:EphA system are available, ranging from small molecules to peptides and genetically-encoded strategies. Their mechanism is either direct, targeting EphA receptors, or indirect through the modification of intracellular downstream pathways. Approaches enabling manipulation of ephrin-A:EphA forward signaling for the dissection of its signaling cascade, the investigation of its physiological roles or the development of therapeutic strategies are summarized here.
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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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14
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Binamé F, Pham-Van LD, Spenlé C, Jolivel V, Birmpili D, Meyer LA, Jacob L, Meyer L, Mensah-Nyagan AG, Po C, Van der Heyden M, Roussel G, Bagnard D. Disruption of Sema3A/Plexin-A1 inhibitory signalling in oligodendrocytes as a therapeutic strategy to promote remyelination. EMBO Mol Med 2019; 11:e10378. [PMID: 31566924 PMCID: PMC6835579 DOI: 10.15252/emmm.201910378] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 08/23/2019] [Accepted: 09/04/2019] [Indexed: 11/15/2022] Open
Abstract
Current treatments in multiple sclerosis (MS) are modulating the inflammatory component of the disease, but no drugs are currently available to repair lesions. Our study identifies in MS patients the overexpression of Plexin‐A1, the signalling receptor of the oligodendrocyte inhibitor Semaphorin 3A. Using a novel type of peptidic antagonist, we showed the possibility to counteract the Sema3A inhibitory effect on oligodendrocyte migration and differentiation in vitro when antagonizing Plexin‐A1. The use of this compound in vivo demonstrated a myelin protective effect as shown with DTI‐MRI and confirmed at the histological level in the mouse cuprizone model of induced demyelination/remyelination. This effect correlated with locomotor performances fully preserved in chronically treated animals. The administration of the peptide also showed protective effects, leading to a reduced severity of demyelination in the context of experimental autoimmune encephalitis (EAE). Hence, the disruption of the inhibitory microenvironmental molecular barriers allows normal myelinating cells to exert their spontaneous remyelinating capacity. This opens unprecedented therapeutic opportunity for patients suffering a disease for which no curative options are yet available.
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Affiliation(s)
- Fabien Binamé
- INSERM U1119 Biopathology of Myelin, Neuroprotection, Therapeutic Strategy, Labex Medalis, Fédération de Médecine Translationnelle de Strasbourg, Strasbourg University, Strasbourg, France
| | - Lucas D Pham-Van
- INSERM U1119 Biopathology of Myelin, Neuroprotection, Therapeutic Strategy, Labex Medalis, Fédération de Médecine Translationnelle de Strasbourg, Strasbourg University, Strasbourg, France
| | - Caroline Spenlé
- INSERM U1119 Biopathology of Myelin, Neuroprotection, Therapeutic Strategy, Labex Medalis, Fédération de Médecine Translationnelle de Strasbourg, Strasbourg University, Strasbourg, France
| | - Valérie Jolivel
- INSERM U1119 Biopathology of Myelin, Neuroprotection, Therapeutic Strategy, Labex Medalis, Fédération de Médecine Translationnelle de Strasbourg, Strasbourg University, Strasbourg, France
| | - Dafni Birmpili
- INSERM U1119 Biopathology of Myelin, Neuroprotection, Therapeutic Strategy, Labex Medalis, Fédération de Médecine Translationnelle de Strasbourg, Strasbourg University, Strasbourg, France
| | - Lionel A Meyer
- INSERM U1119 Biopathology of Myelin, Neuroprotection, Therapeutic Strategy, Labex Medalis, Fédération de Médecine Translationnelle de Strasbourg, Strasbourg University, Strasbourg, France
| | - Laurent Jacob
- INSERM U1119 Biopathology of Myelin, Neuroprotection, Therapeutic Strategy, Labex Medalis, Fédération de Médecine Translationnelle de Strasbourg, Strasbourg University, Strasbourg, France
| | - Laurence Meyer
- INSERM U1119 Biopathology of Myelin, Neuroprotection, Therapeutic Strategy, Labex Medalis, Fédération de Médecine Translationnelle de Strasbourg, Strasbourg University, Strasbourg, France
| | - Ayikoé G Mensah-Nyagan
- INSERM U1119 Biopathology of Myelin, Neuroprotection, Therapeutic Strategy, Labex Medalis, Fédération de Médecine Translationnelle de Strasbourg, Strasbourg University, Strasbourg, France
| | - Chrystelle Po
- Institut de Physique Biologique, Faculté de Médecine, Strasbourg University, Strasbourg, France
| | - Michaël Van der Heyden
- INSERM U1119 Biopathology of Myelin, Neuroprotection, Therapeutic Strategy, Labex Medalis, Fédération de Médecine Translationnelle de Strasbourg, Strasbourg University, Strasbourg, France
| | - Guy Roussel
- INSERM U1119 Biopathology of Myelin, Neuroprotection, Therapeutic Strategy, Labex Medalis, Fédération de Médecine Translationnelle de Strasbourg, Strasbourg University, Strasbourg, France
| | - Dominique Bagnard
- INSERM U1119 Biopathology of Myelin, Neuroprotection, Therapeutic Strategy, Labex Medalis, Fédération de Médecine Translationnelle de Strasbourg, Strasbourg University, Strasbourg, France
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15
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Sheng Y, Wei J, Zhang Y, Gao X, Wang Z, Yang J, Yan S, Zhu Y, Zhang Z, Xu D, Wang C, Zheng Y, Dong Q, Qin L. Mutated EPHA2 is a target for combating lymphatic metastasis in intrahepatic cholangiocarcinoma. Int J Cancer 2019; 144:2440-2452. [PMID: 30412282 DOI: 10.1002/ijc.31979] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Revised: 10/22/2018] [Accepted: 11/02/2018] [Indexed: 12/13/2022]
Abstract
Exploring the genetic aberrations favoring metastasis is important for understanding and developing novel strategies to combat cancer metastasis. It remains lack of effective treatment for the dismal prognosis of intrahepatic cholangiocarcinoma (ICC). Here, we aimed to study genetic alternations during lymph node metastasis of ICC and investigate potential mechanisms and clinical strategy focused on mutations. We performed whole-exome sequencing and transcriptome sequencing on samples from 30 ICC patients, including lymph node metastases from five of the patients. We identified the alterations of genetic pattern related to lymph node metastases of ICC. EPHA2, a member of the tyrosine kinase family, was found to be frequently mutated in ICC. Correlation analysis indicated that EPHA2 mutations were closely associated with lymph node metastasis of ICC. In vitro and in vivo experiments revealed that EPHA2 mutations could lead to ligand independent phosphorylation of Ser897, and promote lymphatic metastasis of ICC, in which NOTCH1 signaling pathway played an important role. In both in vitro assays and patient-derived xenografts, an inhibitor of Ser897 phosphorylation effectively suppressed the metastasis of ICC with mutated EPHA2. Our findings demonstrated that EPHA2 mutants may be an attractive therapeutic target for lymphatic metastasis of ICC.
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Affiliation(s)
- Yuanyuan Sheng
- Department of General Surgery, Huashan Hospital and Cancer Metastasis Institute and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Jinwang Wei
- Department of General Surgery, Huashan Hospital and Cancer Metastasis Institute and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Yu Zhang
- Department of General Surgery, Huashan Hospital and Cancer Metastasis Institute and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Xiaomei Gao
- Department of General Surgery, Huashan Hospital and Cancer Metastasis Institute and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Zheng Wang
- Department of General Surgery, Huashan Hospital and Cancer Metastasis Institute and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Jing Yang
- Department of General Surgery, Huashan Hospital and Cancer Metastasis Institute and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Shican Yan
- Department of General Surgery, Huashan Hospital and Cancer Metastasis Institute and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Ying Zhu
- Department of General Surgery, Huashan Hospital and Cancer Metastasis Institute and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Ze Zhang
- Department of General Surgery, Huashan Hospital and Cancer Metastasis Institute and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Da Xu
- Department of General Surgery, Huashan Hospital and Cancer Metastasis Institute and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Chaoqun Wang
- Department of General Surgery, Huashan Hospital and Cancer Metastasis Institute and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Yan Zheng
- Department of General Surgery, Huashan Hospital and Cancer Metastasis Institute and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Qiongzhu Dong
- Department of General Surgery, Huashan Hospital and Cancer Metastasis Institute and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Lunxiu Qin
- Department of General Surgery, Huashan Hospital and Cancer Metastasis Institute and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
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16
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Alves DS, Westerfield JM, Shi X, Nguyen VP, Stefanski KM, Booth KR, Kim S, Morrell-Falvey J, Wang BC, Abel SM, Smith AW, Barrera FN. A novel pH-dependent membrane peptide that binds to EphA2 and inhibits cell migration. eLife 2018; 7:36645. [PMID: 30222105 PMCID: PMC6192698 DOI: 10.7554/elife.36645] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 09/16/2018] [Indexed: 12/19/2022] Open
Abstract
Misregulation of the signaling axis formed by the receptor tyrosine kinase (RTK) EphA2 and its ligand, ephrinA1, causes aberrant cell-cell contacts that contribute to metastasis. Solid tumors are characterized by an acidic extracellular medium. We intend to take advantage of this tumor feature to design new molecules that specifically target tumors. We created a novel pH-dependent transmembrane peptide, TYPE7, by altering the sequence of the transmembrane domain of EphA2. TYPE7 is highly soluble and interacts with the surface of lipid membranes at neutral pH, while acidity triggers transmembrane insertion. TYPE7 binds to endogenous EphA2 and reduces Akt phosphorylation and cell migration as effectively as ephrinA1. Interestingly, we found large differences in juxtamembrane tyrosine phosphorylation and the extent of EphA2 clustering when comparing TYPE7 with activation by ephrinA1. This work shows that it is possible to design new pH-triggered membrane peptides to activate RTK and gain insights on its activation mechanism.
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Affiliation(s)
- Daiane S Alves
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, United States
| | - Justin M Westerfield
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, United States
| | - Xiaojun Shi
- Department of Chemistry, University of Akron, Akron, United States.,Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, United States.,Pharmacology, Case Western Reserve University, Cleveland, United States.,Rammelkamp Center for Research, MetroHealth Medical Center, Cleveland, United States
| | - Vanessa P Nguyen
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, United States
| | - Katherine M Stefanski
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, United States
| | - Kristen R Booth
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, United States
| | - Soyeon Kim
- Department of Chemistry, University of Akron, Akron, United States
| | - Jennifer Morrell-Falvey
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, United States.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, United States
| | - Bing-Cheng Wang
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, United States.,Pharmacology, Case Western Reserve University, Cleveland, United States.,Rammelkamp Center for Research, MetroHealth Medical Center, Cleveland, United States
| | - Steven M Abel
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, United States.,National Institute for Mathematical and Biological Synthesis, University of Tennessee, Knoxville, United States
| | - Adam W Smith
- Department of Chemistry, University of Akron, Akron, United States
| | - Francisco N Barrera
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, United States
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17
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Ventrella R, Kaplan N, Hoover P, Perez White BE, Lavker RM, Getsios S. EphA2 Transmembrane Domain Is Uniquely Required for Keratinocyte Migration by Regulating Ephrin-A1 Levels. J Invest Dermatol 2018; 138:2133-2143. [PMID: 29705292 DOI: 10.1016/j.jid.2018.04.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Revised: 04/11/2018] [Accepted: 04/12/2018] [Indexed: 12/19/2022]
Abstract
EphA2 receptor tyrosine kinase is activated by ephrin-A1 ligand, which harbors a glycosylphosphatidylinositol anchor that enhances lipid raft localization. Although EphA2 and ephrin-A1 modulate keratinocyte migration and differentiation, the ability of this cell-cell communication complex to localize to different membrane regions in keratinocytes remains unknown. Using a combination of biochemical and imaging approaches, we provide evidence that ephrin-A1 and a ligand-activated form of EphA2 partition outside of lipid raft domains in response to calcium-mediated cell-cell contact stabilization in normal human epidermal keratinocytes. EphA2 transmembrane domain swapping with a shorter and molecularly distinct transmembrane domain of EphA1 resulted in decreased localization of this receptor tyrosine kinase at cell-cell junctions and increased expression of ephrin-A1, which is a negative regulator of keratinocyte migration. Accordingly, altered EphA2 membrane distribution at cell-cell contacts limited the ability of keratinocytes to seal linear scratch wounds in vitro in an ephrin-A1-dependent manner. Collectively, these studies highlight a key role for the EphA2 transmembrane domain in receptor-ligand membrane distribution at cell-cell contacts that modulates ephrin-A1 levels to allow for efficient keratinocyte migration with relevance for cutaneous wound healing.
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Affiliation(s)
- Rosa Ventrella
- Department of Dermatology, 303 East Chicago Avenue, Ward 9, Northwestern University, Chicago, Illinois, USA
| | - Nihal Kaplan
- Department of Dermatology, 303 East Chicago Avenue, Ward 9, Northwestern University, Chicago, Illinois, USA
| | - Paul Hoover
- Department of Dermatology, 303 East Chicago Avenue, Ward 9, Northwestern University, Chicago, Illinois, USA
| | - Bethany E Perez White
- Department of Dermatology, 303 East Chicago Avenue, Ward 9, Northwestern University, Chicago, Illinois, USA
| | - Robert M Lavker
- Department of Dermatology, 303 East Chicago Avenue, Ward 9, Northwestern University, Chicago, Illinois, USA
| | - Spiro Getsios
- Department of Dermatology, 303 East Chicago Avenue, Ward 9, Northwestern University, Chicago, Illinois, USA.
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18
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Bocharov EV. Alternative dimerization of receptor tyrosine kinases with signal transduction through a cellular membrane. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2017. [DOI: 10.1134/s1068162017050041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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19
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Conformational transitions and interactions underlying the function of membrane embedded receptor protein kinases. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:1417-1429. [DOI: 10.1016/j.bbamem.2017.01.025] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 01/06/2017] [Accepted: 01/09/2017] [Indexed: 01/08/2023]
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20
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Bocharov EV, Bragin PE, Pavlov KV, Bocharova OV, Mineev KS, Polyansky AA, Volynsky PE, Efremov RG, Arseniev AS. The Conformation of the Epidermal Growth Factor Receptor Transmembrane Domain Dimer Dynamically Adapts to the Local Membrane Environment. Biochemistry 2017; 56:1697-1705. [DOI: 10.1021/acs.biochem.6b01085] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Eduard V. Bocharov
- Department of Structural Biology, Shemyakin−Ovchinnikov Institute of Bioorganic Chemistry RAS, str. Miklukho-Maklaya 16/10, Moscow 117997, Russian Federation
| | - Pavel E. Bragin
- Department of Structural Biology, Shemyakin−Ovchinnikov Institute of Bioorganic Chemistry RAS, str. Miklukho-Maklaya 16/10, Moscow 117997, Russian Federation
| | - Konstantin V. Pavlov
- Department of Structural Biology, Shemyakin−Ovchinnikov Institute of Bioorganic Chemistry RAS, str. Miklukho-Maklaya 16/10, Moscow 117997, Russian Federation
| | - Olga V. Bocharova
- Department of Structural Biology, Shemyakin−Ovchinnikov Institute of Bioorganic Chemistry RAS, str. Miklukho-Maklaya 16/10, Moscow 117997, Russian Federation
| | - Konstantin S. Mineev
- Department of Structural Biology, Shemyakin−Ovchinnikov Institute of Bioorganic Chemistry RAS, str. Miklukho-Maklaya 16/10, Moscow 117997, Russian Federation
| | - Anton A. Polyansky
- Department of Structural Biology, Shemyakin−Ovchinnikov Institute of Bioorganic Chemistry RAS, str. Miklukho-Maklaya 16/10, Moscow 117997, Russian Federation
- Department of Structural and Computational
Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna
Biocenter 5, Vienna AT-1030, Austria
| | - Pavel E. Volynsky
- Department of Structural Biology, Shemyakin−Ovchinnikov Institute of Bioorganic Chemistry RAS, str. Miklukho-Maklaya 16/10, Moscow 117997, Russian Federation
| | - Roman G. Efremov
- Department of Structural Biology, Shemyakin−Ovchinnikov Institute of Bioorganic Chemistry RAS, str. Miklukho-Maklaya 16/10, Moscow 117997, Russian Federation
- Higher School of Economics, Myasnitskaya ul. 20, Moscow 101000, Russian Federation
| | - Alexander S. Arseniev
- Department of Structural Biology, Shemyakin−Ovchinnikov Institute of Bioorganic Chemistry RAS, str. Miklukho-Maklaya 16/10, Moscow 117997, Russian Federation
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21
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Bethke E, Pinchuk B, Renn C, Witt L, Schlosser J, Peifer C. From Type I to Type II: Design, Synthesis, and Characterization of Potent Pyrazin-2-ones as DFG-Out Inhibitors of PDGFRβ. ChemMedChem 2016; 11:2664-2674. [PMID: 27885822 DOI: 10.1002/cmdc.201600494] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 10/30/2016] [Indexed: 11/09/2022]
Abstract
Reversible protein kinase inhibitors that bind in the ATP cleft can be classified as type I or type II binders. Of these, type I inhibitors address the active form, whereas type II inhibitors typically lock the kinase in an inactive form. At the molecular level, the conformation of the flexible activation loop holding the key DFG motif controls access to the ATP site, thereby determining an active or inactive kinase state. Accordingly, type I and type II kinase inhibitors bind to so-called DFG-in or DFG-out conformations, respectively. Based on our former study on highly selective platelet-derived growth factor receptor β (PDGFRβ) pyrazin-2-one type I inhibitors, we expanded this scaffold toward the deep pocket, yielding the highly potent and effective type II inhibitor 5 (4-[(4-methylpiperazin-1-yl)methyl]-N-[3-[[6-oxo-5-(3,4,5-trimethoxyphenyl)-1H-pyrazin-3-yl]methyl]phenyl]benzamide). In vitro characterization, including selectivity panel data from activity-based assays (300 kinases) and affinity-based assays (97 kinases) of these PDGFRβ type I (1; 5-(4-hydroxy-3-methoxy-phenyl)-3-(3,4,5-trimethoxyphenyl)-1H-pyrazin-2-one) and II (5) inhibitors showing the same pyrazin-2-one chemotype are compared. Implications are discussed regarding the data for selectivity and efficacy of type I and type II ligands.
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Affiliation(s)
- Eugen Bethke
- Christian Albrechts University of Kiel, Institute of Pharmacy, Gutenbergstr. 76, 24118, Kiel, Germany
| | - Boris Pinchuk
- Christian Albrechts University of Kiel, Institute of Pharmacy, Gutenbergstr. 76, 24118, Kiel, Germany
| | - Christian Renn
- Christian Albrechts University of Kiel, Institute of Pharmacy, Gutenbergstr. 76, 24118, Kiel, Germany
| | - Lydia Witt
- Christian Albrechts University of Kiel, Institute of Pharmacy, Gutenbergstr. 76, 24118, Kiel, Germany
| | - Joachim Schlosser
- Christian Albrechts University of Kiel, Institute of Pharmacy, Gutenbergstr. 76, 24118, Kiel, Germany
| | - Christian Peifer
- Christian Albrechts University of Kiel, Institute of Pharmacy, Gutenbergstr. 76, 24118, Kiel, Germany
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22
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Bocharov EV, Mineev KS, Pavlov KV, Akimov SA, Kuznetsov AS, Efremov RG, Arseniev AS. Helix-helix interactions in membrane domains of bitopic proteins: Specificity and role of lipid environment. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1859:561-576. [PMID: 27884807 DOI: 10.1016/j.bbamem.2016.10.024] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 09/18/2016] [Accepted: 10/20/2016] [Indexed: 12/23/2022]
Abstract
Interaction between transmembrane helices often determines biological activity of membrane proteins. Bitopic proteins, a broad subclass of membrane proteins, form dimers containing two membrane-spanning helices. Some aspects of their structure-function relationship cannot be fully understood without considering the protein-lipid interaction, which can determine the protein conformational ensemble. Experimental and computer modeling data concerning transmembrane parts of bitopic proteins are reviewed in the present paper. They highlight the importance of lipid-protein interactions and resolve certain paradoxes in the behavior of such proteins. Besides, some properties of membrane organization provided a clue to understanding of allosteric interactions between distant parts of proteins. Interactions of these kinds appear to underlie a signaling mechanism, which could be widely employed in the functioning of many membrane proteins. Treatment of membrane proteins as parts of integrated fine-tuned proteolipid system promises new insights into biological function mechanisms and approaches to drug design. This article is part of a Special Issue entitled: Lipid order/lipid defects and lipid-control of protein activity edited by Dirk Schneider.
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Affiliation(s)
- Eduard V Bocharov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya ul. 16/10, Moscow, 117997, Russian Federation; National Research Centre "Kurchatov Institute", Akad. Kurchatova pl. 1, Moscow, 123182, Russian Federation.
| | - Konstantin S Mineev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya ul. 16/10, Moscow, 117997, Russian Federation
| | - Konstantin V Pavlov
- Frumkin Institute of Physical Chemistry and Electrochemistry RAS, Leninskiy prospect 31/5, Moscow, 119071, Russian Federation
| | - Sergey A Akimov
- Frumkin Institute of Physical Chemistry and Electrochemistry RAS, Leninskiy prospect 31/5, Moscow, 119071, Russian Federation; National University of Science and Technology "MISiS", Leninskiy prospect 4, Moscow, 119049, Russian Federation
| | - Andrey S Kuznetsov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya ul. 16/10, Moscow, 117997, Russian Federation
| | - Roman G Efremov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya ul. 16/10, Moscow, 117997, Russian Federation; Higher School of Economics, Myasnitskaya ul. 20, Moscow, 101000, Russian Federation
| | - Alexander S Arseniev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya ul. 16/10, Moscow, 117997, Russian Federation.
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23
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Singh DR, Pasquale EB, Hristova K. A small peptide promotes EphA2 kinase-dependent signaling by stabilizing EphA2 dimers. Biochim Biophys Acta Gen Subj 2016; 1860:1922-8. [PMID: 27281300 DOI: 10.1016/j.bbagen.2016.06.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 05/31/2016] [Accepted: 06/03/2016] [Indexed: 12/01/2022]
Abstract
BACKGROUND The EphA2 receptor tyrosine kinase is known to promote cancer cell malignancy in the absence of activation by ephrin ligands. This behavior depends on high EphA2 phosphorylation on Ser897 and low tyrosine phosphorylation, resulting in increased cell migration and invasiveness. We have previously shown that EphA2 forms dimers in the absence of ephrin ligand binding, and that dimerization of unliganded EphA2 can decrease EphA2 Ser897 phosphorylation. We have also identified a small peptide called YSA, which binds EphA2 and competes with the naturally occurring ephrin ligands. METHODS Here, we investigate the effect of YSA on EphA2 dimer stability and EphA2 function using quantitative FRET techniques, Western blotting, and cell motility assays. RESULTS We find that the YSA peptide stabilizes the EphA2 dimer, increases EphA2 Tyr phosphorylation, and decreases both Ser897 phosphorylation and cell migration. CONCLUSIONS The experiments demonstrate that the small peptide ligand YSA reduces EphA2 Ser897 pro-tumorigenic signaling by stabilizing the EphA2 dimer. GENERAL SIGNIFICANCE This work is a proof-of-principle demonstration that EphA2 homointeractions in the plasma membrane can be pharmacologically modulated to decrease the pro-tumorigenic signaling of the receptor.
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Affiliation(s)
- Deo R Singh
- Department of Materials Science and Engineering, Johns Hopkins University, 3400 Charles Street, Baltimore, MD 21218, United States
| | - Elena B Pasquale
- Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Road, La Jolla, San Diego, CA 92037, United States
| | - Kalina Hristova
- Department of Materials Science and Engineering, Johns Hopkins University, 3400 Charles Street, Baltimore, MD 21218, United States.
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Bocharov EV, Lesovoy DM, Pavlov KV, Pustovalova YE, Bocharova OV, Arseniev AS. Alternative packing of EGFR transmembrane domain suggests that protein-lipid interactions underlie signal conduction across membrane. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:1254-61. [PMID: 26903218 DOI: 10.1016/j.bbamem.2016.02.023] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 02/15/2016] [Accepted: 02/17/2016] [Indexed: 10/22/2022]
Abstract
The human epidermal growth factor receptor (EGFR) of HER/ErbB receptor tyrosine kinase family mediates a broad spectrum of cellular responses transducing biochemical signals via lateral dimerization in plasma membrane, while inactive receptors can exist in both monomeric and dimeric forms. Recently, the dimeric conformation of the helical single-span transmembrane domains of HER/ErbB employing the relatively polar N-terminal motifs in a fashion permitting proper kinase activation was experimentally determined. Here we describe the EGFR transmembrane domain dimerization via an alternative weakly polar C-terminal motif A(661)xxxG(665) presumably corresponding to the inactive receptor state. During association, the EGFR transmembrane helices undergo a structural adjustment with adaptation of inter-molecular polar and hydrophobic interactions depending upon the surrounding membrane properties that directly affect the transmembrane helix packing. This might imply that signal transduction through membrane and allosteric regulation are inclusively mediated by coupled protein-protein and protein-lipid interactions, elucidating paradoxically loose linkage between ligand binding and kinase activation.
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Affiliation(s)
- Eduard V Bocharov
- Department of Structural Biology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, str. Miklukho-Maklaya 16/10, Moscow, 117997, Russian Federation.
| | - Dmitry M Lesovoy
- Department of Structural Biology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, str. Miklukho-Maklaya 16/10, Moscow, 117997, Russian Federation
| | - Konstantin V Pavlov
- Department of Structural Biology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, str. Miklukho-Maklaya 16/10, Moscow, 117997, Russian Federation
| | - Yulia E Pustovalova
- Department of Structural Biology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, str. Miklukho-Maklaya 16/10, Moscow, 117997, Russian Federation
| | - Olga V Bocharova
- Department of Structural Biology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, str. Miklukho-Maklaya 16/10, Moscow, 117997, Russian Federation
| | - Alexander S Arseniev
- Department of Structural Biology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, str. Miklukho-Maklaya 16/10, Moscow, 117997, Russian Federation
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25
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Bragin PE, Mineev KS, Bocharova OV, Volynsky PE, Bocharov EV, Arseniev AS. HER2 Transmembrane Domain Dimerization Coupled with Self-Association of Membrane-Embedded Cytoplasmic Juxtamembrane Regions. J Mol Biol 2015; 428:52-61. [PMID: 26585403 DOI: 10.1016/j.jmb.2015.11.007] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Revised: 10/23/2015] [Accepted: 11/10/2015] [Indexed: 01/05/2023]
Abstract
Receptor tyrosine kinases of the human epidermal growth factor receptor (HER or ErbB) family transduce biochemical signals across plasma membrane, playing a significant role in vital cellular processes and in various cancers. Inactive HER/ErbB receptors exist in equilibrium between the monomeric and unspecified pre-dimerized states. After ligand binding, the receptors are involved in strong lateral dimerization with proper assembly of their extracellular ligand-binding, single-span transmembrane, and cytoplasmic kinase domains. The dimeric conformation of the HER2 transmembrane domain that is believed to support the cytoplasmic kinase domain configuration corresponding to the receptor active state was previously described in lipid bicelles. Here we used high-resolution NMR spectroscopy in another membrane-mimicking micellar environment and identified an alternative HER2 transmembrane domain dimerization coupled with self-association of membrane-embedded cytoplasmic juxtamembrane region. Such a dimerization mode appears to be capable of effectively inhibiting the receptor kinase activity. This finding refines the molecular mechanism regarding the signal propagation steps from the extracellular to cytoplasmic domains of HER/ErbB receptors.
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Affiliation(s)
- Pavel E Bragin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya Street, Moscow 117997, Russian Federation; Lomonosov Moscow State University, Leninskie Gory, 1, Moscow 119991, Russian Federation
| | - Konstantin S Mineev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya Street, Moscow 117997, Russian Federation
| | - Olga V Bocharova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya Street, Moscow 117997, Russian Federation
| | - Pavel E Volynsky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya Street, Moscow 117997, Russian Federation
| | - Eduard V Bocharov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya Street, Moscow 117997, Russian Federation.
| | - Alexander S Arseniev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya Street, Moscow 117997, Russian Federation; Moscow Institute of Physics and Technology, Institutsky Per., 9, Dolgoprudnyi 141700, Russian Federation
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26
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Abstract
Transmembrane (TM) helices of integral membrane proteins can facilitate strong and specific noncovalent protein-protein interactions. Mutagenesis and structural analyses have revealed numerous examples in which the interaction between TM helices of single-pass membrane proteins is dependent on a GxxxG or (small)xxx(small) motif. It is therefore tempting to use the presence of these simple motifs as an indicator of TM helix interactions. In this Current Topic review, we point out that these motifs are quite common, with more than 50% of single-pass TM domains containing a (small)xxx(small) motif. However, the actual interaction strength of motif-containing helices depends strongly on sequence context and membrane properties. In addition, recent studies have revealed several GxxxG-containing TM domains that interact via alternative interfaces involving hydrophobic, polar, aromatic, or even ionizable residues that do not form recognizable motifs. In multipass membrane proteins, GxxxG motifs can be important for protein folding, and not just oligomerization. Our current knowledge thus suggests that the presence of a GxxxG motif alone is a weak predictor of protein dimerization in the membrane.
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Affiliation(s)
- Mark G Teese
- Lehrstuhl für Chemie der Biopolymere, Technische Universität München , 85354 Freising, Germany.,Center for Integrated Protein Science Munich (CIPSM) , 81377 Munich, Germany
| | - Dieter Langosch
- Lehrstuhl für Chemie der Biopolymere, Technische Universität München , 85354 Freising, Germany.,Center for Integrated Protein Science Munich (CIPSM) , 81377 Munich, Germany
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27
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Abstract
Epithelial cells are tightly coupled together through specialized intercellular junctions, including adherens junctions, desmosomes, tight junctions, and gap junctions. A growing body of evidence suggests epithelial cells also directly exchange information at cell-cell contacts via the Eph family of receptor tyrosine kinases and their membrane-associated ephrin ligands. Ligand-dependent and -independent signaling via Eph receptors as well as reverse signaling through ephrins impact epithelial tissue homeostasis by organizing stem cell compartments and regulating cell proliferation, migration, adhesion, differentiation, and survival. This review focuses on breast, gut, and skin epithelia as representative examples for how Eph receptors and ephrins modulate diverse epithelial cell responses in a context-dependent manner. Abnormal Eph receptor and ephrin signaling is implicated in a variety of epithelial diseases raising the intriguing possibility that this cell-cell communication pathway can be therapeutically harnessed to normalize epithelial function in pathological settings like cancer or chronic inflammation.
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Key Words
- ADAM, a disintegrin and metalloprotease
- Apc, adenomatous polyposis coli
- Breast
- ER, estrogen receptor
- Eph receptor
- Eph, erythropoietin-producing hepatocellular
- Erk, extracellular signal-regulated kinase
- GEF, guanine nucleotide exchange factor
- GPI, glycosylphosphatidylinositol
- HER2, human epidermal growth factor receptor 2
- HGF, hepatocyte growth factor
- IBD, inflammatory bowel disease
- KLF, Krüppel-like factor
- MAPK, mitogen-activated protein kinase
- MMTV-LTR, mouse mammary tumor virus-long terminal repeat
- MT1-MMP, membrane-type 1 matrix metalloproteinase
- PDZ, postsynaptic density protein 95, discs large 1, and zonula occludens-1
- PTP, protein tyrosine phosphatase
- RTK, receptor tyrosine kinase
- SH2, Src homology 2
- SHIP2, SH2 inositol phosphatase 2
- SLAP, Src-like adaptor protein
- TCF, T-cell specific transcription factor
- TEB, terminal end bud
- TNFα, tumor necrosis factor α.
- cell-cell
- ephrin
- epithelial
- intestine
- receptor tyrosine kinase
- skin
- stem cell
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28
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Maruyama IN. Activation of transmembrane cell-surface receptors via a common mechanism? The "rotation model". Bioessays 2015; 37:959-67. [PMID: 26241732 PMCID: PMC5054922 DOI: 10.1002/bies.201500041] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
It has long been thought that transmembrane cell-surface receptors, such as receptor tyrosine kinases and cytokine receptors, among others, are activated by ligand binding through ligand-induced dimerization of the receptors. However, there is growing evidence that prior to ligand binding, various transmembrane receptors have a preformed, yet inactive, dimeric structure on the cell surface. Various studies also demonstrate that during transmembrane signaling, ligand binding to the extracellular domain of receptor dimers induces a rotation of transmembrane domains, followed by rearrangement and/or activation of intracellular domains. The paper here describes transmembrane cell-surface receptors that are known or proposed to exist in dimeric form prior to ligand binding, and discusses how these preformed dimers are activated by ligand binding.
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Affiliation(s)
- Ichiro N Maruyama
- Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
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29
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Sun F, Xu L, Chen P, Wei P, Qu J, Chen J, Luo SZ. Insights into the Packing Switching of the EphA2 Transmembrane Domain by Molecular Dynamic Simulations. J Phys Chem B 2015; 119:7816-24. [PMID: 26022644 DOI: 10.1021/acs.jpcb.5b01116] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Receptor tyrosine kinases play an important role in mediating cell migration and adhesion associated with various biology processes. With a single-span transmembrane domain (TMD), the activities of the receptors are regulated by the definite packing configurations of the TMDs. For the EphA2 receptor, increasing studies have been conducted to investigate the packing domains that induce its switching TMD dimerization. However, the inherent transformation mechanisms including the interrelations among the involved packing domains remain unclear. Herein, we applied multiple simulation methods to explore the underlying packing mechanisms within the EphA2 TMD dimer. Our results demonstrated that the G(540)xxxG(544) contributed to the formation of the right-handed configuration while the heptad repeat L(535)xxxG(539)xxA(542)xxxV(546)xxL(549)xxxG(553) motif together with the FFxH(559) region mediated the parallel mode. Furthermore, the FF(557) residues packing mutually as rigid riveting structures were found comparable to the heptad repeat motif in maintaining the parallel configuration. In addition, the H(559) residue associated definitely with the lower bilayer leaflet, which was proved to stabilize the parallel mode significantly. The simulations provide a full range of insights into the essential packing motifs or residues involved in the switching TMD dimer configurations, which can enrich our comprehension toward the EphA2 receptor.
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Affiliation(s)
- Fude Sun
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Lida Xu
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Peng Chen
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Peng Wei
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Jing Qu
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Jialin Chen
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Shi-Zhong Luo
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
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31
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Chavent M, Chetwynd AP, Stansfeld PJ, Sansom MSP. Dimerization of the EphA1 receptor tyrosine kinase transmembrane domain: Insights into the mechanism of receptor activation. Biochemistry 2014; 53:6641-52. [PMID: 25286141 PMCID: PMC4298228 DOI: 10.1021/bi500800x] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
EphA1
is a receptor tyrosine kinase (RTK) that plays a key role
in developmental processes, including guidance of the migration of
axons and cells in the nervous system. EphA1, in common with other
RTKs, contains an N-terminal extracellular domain, a single transmembrane
(TM) α-helix, and a C-terminal intracellular kinase domain.
The TM helix forms a dimer, as seen in recent NMR studies. We have
modeled the EphA1 TM dimer using a multiscale approach combining coarse-grain
(CG) and atomistic molecular dynamics (MD) simulations. The one-dimensional
potential of mean force (PMF) for this system, based on interhelix
separation, has been calculated using CG MD simulations. This provides
a view of the free energy landscape for helix–helix interactions
of the TM dimer in a lipid bilayer. The resulting PMF profiles suggest
two states, consistent with a rotation-coupled activation mechanism.
The more stable state corresponds to a right-handed helix dimer interacting
via an N-terminal glycine zipper motif, consistent with a recent NMR
structure (2K1K). A second metastable state corresponds to a structure in which
the glycine zipper motif is not involved. Analysis of unrestrained
CG MD simulations based on representative models from the PMF calculations
or on the NMR structure reveals possible pathways of interconversion
between these two states, involving helix rotations about their long
axes. This suggests that the interaction of TM helices in EphA1 dimers
may be intrinsically dynamic. This provides a potential mechanism
for signaling whereby extracellular events drive a shift in the repopulation
of the underlying TM helix dimer energy landscape.
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Affiliation(s)
- Matthieu Chavent
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, United Kingdom
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32
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Sawma P, Roth L, Blanchard C, Bagnard D, Crémel G, Bouveret E, Duneau JP, Sturgis JN, Hubert P. Evidence for new homotypic and heterotypic interactions between transmembrane helices of proteins involved in receptor tyrosine kinase and neuropilin signaling. J Mol Biol 2014; 426:4099-4111. [PMID: 25315821 DOI: 10.1016/j.jmb.2014.10.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 09/26/2014] [Accepted: 10/08/2014] [Indexed: 12/31/2022]
Abstract
Signaling in eukaryotic cells frequently relies on dynamic interactions of single-pass membrane receptors involving their transmembrane (TM) domains. To search for new such interactions, we have developed a bacterial two-hybrid system to screen for both homotypic and heterotypic interactions between TM helices. We have explored the dimerization of TM domains from 16 proteins involved in both receptor tyrosine kinase and neuropilin signaling. This study has revealed several new interactions. We found that the TM domain of Mucin-4, a putative intramembrane ligand for erbB2, dimerizes not only with erbB2 but also with all four members of the erbB family. In the Neuropilin/Plexin family of receptors, we showed that the TM domains of Neuropilins 1 and 2 dimerize with themselves and also with Plexin-A1, Plexin-B1, and L1CAM, but we were unable to observe interactions with several other TM domains notably those of members of the VEGF receptor family. The potentially important Neuropilin 1/Plexin-A1 interaction was confirmed using a surface plasmon resonance assay. This work shows that TM domain interactions can be highly specific. Exploring further the propensities of TM helix-helix association in cell membrane should have important practical implications related to our understanding of the structure-function of bitopic proteins' assembly and subsequent function, especially in the regulation of signal transduction.
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Affiliation(s)
- Paul Sawma
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, UMR 7255, Centre National de la Recherche Scientifique and Aix-Marseille University, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
| | - Lise Roth
- INSERM U 1109 and University of Strasbourg, 3 Avenue Molière, 67200 Strasbourg, France
| | - Cécile Blanchard
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, UMR 7255, Centre National de la Recherche Scientifique and Aix-Marseille University, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
| | - Dominique Bagnard
- INSERM U 1109 and University of Strasbourg, 3 Avenue Molière, 67200 Strasbourg, France
| | - Gérard Crémel
- INSERM U 1109 and University of Strasbourg, 3 Avenue Molière, 67200 Strasbourg, France
| | - Emmanuelle Bouveret
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, UMR 7255, Centre National de la Recherche Scientifique and Aix-Marseille University, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
| | - Jean-Pierre Duneau
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, UMR 7255, Centre National de la Recherche Scientifique and Aix-Marseille University, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
| | - James N Sturgis
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, UMR 7255, Centre National de la Recherche Scientifique and Aix-Marseille University, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
| | - Pierre Hubert
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, UMR 7255, Centre National de la Recherche Scientifique and Aix-Marseille University, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France.
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