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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 2024:107441. [PMID: 38838777 DOI: 10.1016/j.jbc.2024.107441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [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 associate into 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, 3400 Charles Street, Baltimore, MD 21218
| | - Ece Özdemir
- Department of Materials Science and Engineering, Johns Hopkins University, 3400 Charles Street, Baltimore, MD 21218
| | - William C Wimley
- Tulane University School of Medicine, Department of Biochemistry and Molecular Biology, New Orleans, LA
| | - 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;.
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2
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Singh PK, Rybak JA, Schuck RJ, Barrera FN, Smith AW. Phosphatidylinositol (4,5)-bisphosphate drives the formation of EGFR and EphA2 complexes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.03.592400. [PMID: 38746348 PMCID: PMC11092790 DOI: 10.1101/2024.05.03.592400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Receptor tyrosine kinases (RTKs) regulate many cellular functions and are important targets in pharmaceutical development, particularly in cancer treatment. EGFR and EphA2 are two key RTKs that are associated with oncogenic phenotypes. Several studies have reported functional interplay between these receptors, but the mechanism of interaction is still unresolved. Here we utilize a time-resolved fluorescence spectroscopy called PIE-FCCS to resolve EGFR and EphA2 interactions in live cells. We tested the role of ligands and found that EGF, but not ephrin A1 (EA1), stimulated hetero-multimerization between the receptors. To determine the effect of anionic lipids, we targeted phospholipase C (PLC) activity to alter the abundance of phosphatidylinositol (4,5)-bisphosphate (PIP 2 ). We found that higher PIP 2 levels increased homo-multimerization of both EGFR and EphA2, as well as hetero-multimerization. This study provides a direct characterization of EGFR and EphA2 interactions in live cells and shows that PIP 2 can have a substantial effect on the spatial organization of RTKs.
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3
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Girych M, Kulig W, Enkavi G, Vattulainen I. How Neuromembrane Lipids Modulate Membrane Proteins: Insights from G-Protein-Coupled Receptors (GPCRs) and Receptor Tyrosine Kinases (RTKs). Cold Spring Harb Perspect Biol 2023; 15:a041419. [PMID: 37487628 PMCID: PMC10547395 DOI: 10.1101/cshperspect.a041419] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
Lipids play a diverse and critical role in cellular processes in all tissues. The unique lipid composition of nerve membranes is particularly interesting because it contains, among other things, polyunsaturated lipids, such as docosahexaenoic acid, which the body only gets through the diet. The crucial role of lipids in neurological processes, especially in receptor-mediated cell signaling, is emphasized by the fact that in many neuropathological diseases there are significant deviations in the lipid composition of nerve membranes compared to healthy individuals. The lipid composition of neuromembranes can significantly affect the function of receptors by regulating the physical properties of the membrane or by affecting specific interactions between receptors and lipids. In addition, it is worth noting that the ligand-binding pocket of many receptors is located inside the cell membrane, due to which lipids can even modulate the binding of ligands to their receptors. These mechanisms highlight the importance of lipids in the regulation of membrane receptor activation and function. In this article, we focus on two major protein families: G-protein-coupled receptors (GPCRs) and receptor tyrosine kinases (RTKs) and discuss how lipids affect their function in neuronal membranes, elucidating the basic mechanisms underlying neuronal function and dysfunction.
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Affiliation(s)
- Mykhailo Girych
- Department of Physics, University of Helsinki, FI-00014 Helsinki, Finland
| | - Waldemar Kulig
- Department of Physics, University of Helsinki, FI-00014 Helsinki, Finland
| | - Giray Enkavi
- Department of Physics, University of Helsinki, FI-00014 Helsinki, Finland
| | - Ilpo Vattulainen
- Department of Physics, University of Helsinki, FI-00014 Helsinki, Finland
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4
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Liu T, Khanal S, Hertslet GD, Lamichhane R. Single-molecule analysis reveals that a glucagon-bound extracellular domain of the glucagon receptor is dynamic. J Biol Chem 2023; 299:105160. [PMID: 37586587 PMCID: PMC10514447 DOI: 10.1016/j.jbc.2023.105160] [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: 02/13/2023] [Revised: 08/07/2023] [Accepted: 08/10/2023] [Indexed: 08/18/2023] Open
Abstract
Dynamic information is vital to understanding the activation mechanism of G protein-coupled receptors (GPCRs). Despite the availability of high-resolution structures of different conformational states, the dynamics of those states at the molecular level are poorly understood. Here, we used total internal reflection fluorescence microscopy to study the extracellular domain (ECD) of the glucagon receptor (GCGR), a class B family GPCR that controls glucose homeostasis. Single-molecule fluorescence resonance energy transfer was used to observe the ECD dynamics of GCGR molecules expressed and purified from mammalian cells. We observed that for apo-GCGR, the ECD is dynamic and spent time predominantly in a closed conformation. In the presence of glucagon, the ECD is wide open and also shows more dynamic behavior than apo-GCGR, a finding that was not previously reported. These results suggest that both apo-GCGR and glucagon-bound GCGRs show reversible opening and closing of the ECD with respect to the seven-transmembrane (7TM) domain. This work demonstrates a molecular approach to visualizing the dynamics of the GCGR ECD and provides a foundation for understanding the conformational changes underlying GPCR activation, which is critical in the development of new therapeutics.
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Affiliation(s)
- Ting Liu
- Department of Biochemistry & Cellular and Molecular Biology, College of Arts & Sciences, University of Tennessee, Knoxville, Tennessee, USA
| | - Susmita Khanal
- Department of Biochemistry & Cellular and Molecular Biology, College of Arts & Sciences, University of Tennessee, Knoxville, Tennessee, USA
| | - Gillian D Hertslet
- Department of Biochemistry & Cellular and Molecular Biology, College of Arts & Sciences, University of Tennessee, Knoxville, Tennessee, USA
| | - Rajan Lamichhane
- Department of Biochemistry & Cellular and Molecular Biology, College of Arts & Sciences, University of Tennessee, Knoxville, Tennessee, USA.
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5
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Real Hernandez LM, Levental I. Lipid packing is disrupted in copolymeric nanodiscs compared with intact membranes. Biophys J 2023; 122:2256-2266. [PMID: 36641625 PMCID: PMC10257115 DOI: 10.1016/j.bpj.2023.01.013] [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] [Received: 08/31/2022] [Revised: 12/02/2022] [Accepted: 01/11/2023] [Indexed: 01/15/2023] Open
Abstract
Discoidal lipid-protein nanoparticles known as nanodiscs are widely used tools in structural and membrane biology. Amphipathic, synthetic copolymers have recently become an attractive alternative to membrane scaffold proteins for the formation of nanodiscs. Such copolymers can directly intercalate into, and form nanodiscs from, intact membranes without detergents. Although these copolymer nanodiscs can extract native membrane lipids, it remains unclear whether native membrane properties are also retained. To determine the extent to which bilayer lipid packing is retained in nanodiscs, we measured the behavior of packing-sensitive fluorescent dyes in various nanodisc preparations compared with intact lipid bilayers. We analyzed styrene-maleic acid (SMA), diisobutylene-maleic acid (DIBMA), and polymethacrylate (PMA) as nanodisc scaffolds at various copolymer-to-lipid ratios and temperatures. Measurements of Laurdan spectral shifts revealed that dimyristoyl-phosphatidylcholine (DMPC) nanodiscs had increased lipid headgroup packing compared with large unilamellar vesicles (LUVs) above the lipid melting temperature for all three copolymers. Similar effects were observed for DMPC nanodiscs stabilized by membrane scaffolding protein MSP1E1. Increased lipid headgroup packing was also observed when comparing nanodiscs with intact membranes composed of binary mixtures of 1-palmitoyl-2-oleoyl-phosphocholine (POPC) and di-palmitoyl-phosphocholine (DPPC), which show fluid-gel-phase coexistence. Similarly, Laurdan reported increased headgroup packing in nanodiscs for biomimetic mixtures containing cholesterol, most notable for relatively disordered membranes. The magnitudes of these ordering effects were not identical for the various copolymers, with SMA being the most and DIBMA being the least perturbing. Finally, nanodiscs derived from mammalian cell membranes showed similarly increased lipid headgroup packing. We conclude that nanodiscs generally do not completely retain the physical properties of intact membranes.
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Affiliation(s)
- Luis M Real Hernandez
- Department of Molecular Physiology and Biological Physics, Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, Virginia
| | - Ilya Levental
- Department of Molecular Physiology and Biological Physics, Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, Virginia.
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6
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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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7
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Sokolova A, Galic M. Modulation of self-organizing circuits at deforming membranes by intracellular and extracellular factors. Biol Chem 2023; 404:417-425. [PMID: 36626681 DOI: 10.1515/hsz-2022-0290] [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: 09/26/2022] [Accepted: 12/16/2022] [Indexed: 01/12/2023]
Abstract
Mechanical forces exerted to the plasma membrane induce cell shape changes. These transient shape changes trigger, among others, enrichment of curvature-sensitive molecules at deforming membrane sites. Strikingly, some curvature-sensing molecules not only detect membrane deformation but can also alter the amplitude of forces that caused to shape changes in the first place. This dual ability of sensing and inducing membrane deformation leads to the formation of curvature-dependent self-organizing signaling circuits. How these cell-autonomous circuits are affected by auxiliary parameters from inside and outside of the cell has remained largely elusive. Here, we explore how such factors modulate self-organization at the micro-scale and its emerging properties at the macroscale.
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Affiliation(s)
- Anastasiia Sokolova
- Institute of Medical Physics and Biophysics, University of Münster, Robert-Koch-Straße 31, 48149 Münster, Germany.,CiM-IMRPS Graduate Program, Schlossplatz 5, 48149 Münster, Germany
| | - Milos Galic
- Institute of Medical Physics and Biophysics, University of Münster, Robert-Koch-Straße 31, 48149 Münster, Germany.,'Cells in Motion' Interfaculty Centre, University of Münster, Röntgenstraße 16, 48149 Münster, Germany
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8
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Russell CM, Schaefer KG, Dixson A, Gray ALH, Pyron RJ, Alves DS, Moore N, Conley EA, Schuck RJ, White TA, Do TD, King GM, Barrera FN. The Candida albicans virulence factor candidalysin polymerizes in solution to form membrane pores and damage epithelial cells. eLife 2022; 11:e75490. [PMID: 36173096 PMCID: PMC9522247 DOI: 10.7554/elife.75490] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 08/15/2022] [Indexed: 11/28/2022] Open
Abstract
Candida albicans causes severe invasive candidiasis. C. albicans infection requires the virulence factor candidalysin (CL) which damages target cell membranes. However, the mechanism that CL uses to permeabilize membranes is unclear. We reveal that CL forms membrane pores using a unique mechanism. Unexpectedly, CL readily assembled into polymers in solution. We propose that the basic structural unit in polymer formation is a CL oligomer, which is sequentially added into a string configuration that can close into a loop. CL loops appear to spontaneously insert into the membrane to become pores. A CL mutation (G4W) inhibited the formation of polymers in solution and prevented pore formation in synthetic lipid systems. Epithelial cell studies showed that G4W CL failed to activate the danger response pathway, a hallmark of the pathogenic effect of CL. These results indicate that CL polymerization in solution is a necessary step for the damage of cellular membranes. Analysis of CL pores by atomic force microscopy revealed co-existence of simple depressions and more complex pores, which are likely formed by CL assembled in an alternate oligomer orientation. We propose that this structural rearrangement represents a maturation mechanism that stabilizes pore formation to achieve more robust cellular damage. To summarize, CL uses a previously unknown mechanism to damage membranes, whereby pre-assembly of CL loops in solution leads to formation of membrane pores. Our investigation not only unravels a new paradigm for the formation of membrane pores, but additionally identifies CL polymerization as a novel therapeutic target to treat candidiasis.
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Affiliation(s)
- Charles M Russell
- Department of Biochemistry & Cellular and Molecular Biology, University of TennesseeKnoxvilleUnited States
| | - Katherine G Schaefer
- Department of Physics and Astronomy, University of MissouriColumbiaUnited States
| | - Andrew Dixson
- Department of Biochemistry & Cellular and Molecular Biology, University of TennesseeKnoxvilleUnited States
| | - Amber LH Gray
- Department of Chemistry, University of TennesseeKnoxvilleUnited States
| | - Robert J Pyron
- Department of Biochemistry & Cellular and Molecular Biology, University of TennesseeKnoxvilleUnited States
| | - Daiane S Alves
- Department of Biochemistry & Cellular and Molecular Biology, University of TennesseeKnoxvilleUnited States
| | - Nicholas Moore
- Department of Biochemistry & Cellular and Molecular Biology, University of TennesseeKnoxvilleUnited States
| | - Elizabeth A Conley
- Department of Physics and Astronomy, University of MissouriColumbiaUnited States
| | - Ryan J Schuck
- Department of Biochemistry & Cellular and Molecular Biology, University of TennesseeKnoxvilleUnited States
| | - Tommi A White
- Department of Biochemistry, University of MissouriColumbiaUnited States
- Electron Microscopy Core, University of MissouriColumbiaUnited States
| | - Thanh D Do
- Department of Chemistry, University of TennesseeKnoxvilleUnited States
| | - Gavin M King
- Department of Physics and Astronomy, University of MissouriColumbiaUnited States
- Department of Biochemistry, University of MissouriColumbiaUnited States
| | - Francisco N Barrera
- Department of Biochemistry & Cellular and Molecular Biology, University of TennesseeKnoxvilleUnited States
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9
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Xiong L, Liu Y, Zhao H, Wang Y, Sun Y, Wang A, Zhang L, Zhang Y. The Mechanism of Chaiyin Particles in the Treatment of COVID-19 Based on Network Pharmacology and Experimental Verification. Nat Prod Commun 2022. [DOI: 10.1177/1934578x221114853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Objective: To explore the potential active components of Chaiyin particles (CYPs) in the treatment of coronavirus disease 2019 (COVID-19) and their mechanism of action using network pharmacology and molecular docking technology. Methods: Based on the components of CYPs, we obtained potential targets of the interaction between CYPs and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The potential targets were analyzed by protein–protein interaction, gene ontology, and Kyoto Encyclopedia of Genes and Genomes pathway analyses. The key active components of CYPs were subjected to molecular docking with 3-chymotrypsin-like protease, angiotensin-converting enzyme II (ACE2), RNA-dependent RNA polymerase, and papain-like protease. The components that may bind to the key target proteins of SARS-CoV-2 were screened to obtain the potential active components, targets and pathways for CYP treatment of COVID-19. The above-described network analysis results were then verified experimentally. Results: CYPs may prevent and treat COVID-19 by inhibiting the release of inflammatory factors such as IL-6 and TNF-α; participating in the AGE-Rage signaling pathway, the HIF-1 signaling pathway, and other anti-inflammatory, antiviral, and immune regulatory signaling pathways; and blocking ACE2 via fortunellin and baicalin. Conclusion: This work illustrated that CYPs mainly play an anti-inflammatory and immunomodulatory role in COVID-19 prevention and treatment. The potential active components and molecular mechanism of CYPs can provide theoretical support and a pharmacological basis for further development and utilization of CYPs in the prevention and treatment of COVID-19. These results provide important insights into future studies of Traditional Chinese medicines (TCMs) modernization and prevention.
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Affiliation(s)
- Lewen Xiong
- Key Laboratory of Traditional Chinese Medicine Resources in Universities of Shandong Province, School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Yan Liu
- Key Laboratory of Traditional Chinese Medicine Resources in Universities of Shandong Province, School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Hongwei Zhao
- Key Laboratory of Traditional Chinese Medicine Resources in Universities of Shandong Province, School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Yang Wang
- Key Laboratory of Traditional Chinese Medicine Resources in Universities of Shandong Province, School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Ying Sun
- Lunan Pharmaceutical Group Co., Ltd., Linyi, China
| | - Aiyuan Wang
- Key Laboratory of Traditional Chinese Medicine Resources in Universities of Shandong Province, School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Longfei Zhang
- Key Laboratory of Traditional Chinese Medicine Resources in Universities of Shandong Province, School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Yongqing Zhang
- Key Laboratory of Traditional Chinese Medicine Resources in Universities of Shandong Province, School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
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10
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Wei S, Thakur N, Ray AP, Jin B, Obeng S, McCurdy CR, McMahon LR, Gutiérrez-de-Terán H, Eddy MT, Lamichhane R. Slow conformational dynamics of the human A 2A adenosine receptor are temporally ordered. Structure 2022; 30:329-337.e5. [PMID: 34895472 PMCID: PMC8897252 DOI: 10.1016/j.str.2021.11.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 09/26/2021] [Accepted: 11/17/2021] [Indexed: 01/12/2023]
Abstract
A more complete depiction of protein energy landscapes includes the identification of different function-related conformational states and the determination of the pathways connecting them. We used total internal reflection fluorescence (TIRF) imaging to investigate the conformational dynamics of the human A2A adenosine receptor (A2AAR), a class A G protein-coupled receptor (GPCR), at the single-molecule level. Slow, reversible conformational exchange was observed among three different fluorescence emission states populated for agonist-bound A2AAR. Transitions among these states predominantly occurred in a specific order, and exchange between inactive and active-like conformations proceeded through an intermediate state. Models derived from molecular dynamics simulations with available A2AAR structures rationalized the relative fluorescence emission intensities for the highest and lowest emission states but not the transition state. This suggests that the functionally critical intermediate state required to achieve activation is not currently visualized among available A2AAR structures.
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Affiliation(s)
- Shushu Wei
- Department of Biochemistry & Cellular and Molecular Biology, College of Arts and Sciences, University of Tennessee, 1311 Cumberland Avenue, Knoxville, TN 37932, USA
| | - Naveen Thakur
- Department of Chemistry, College of Liberal Arts and Sciences, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
| | - Arka P Ray
- Department of Chemistry, College of Liberal Arts and Sciences, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
| | - Beining Jin
- Department of Chemistry, College of Liberal Arts and Sciences, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
| | - Samuel Obeng
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA; Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA
| | - Christopher R McCurdy
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA; Translational Drug Development Core, Clinical and Translational Sciences Institute, University of Florida, Gainesville, FL 32610, USA
| | - Lance R McMahon
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA
| | - Hugo Gutiérrez-de-Terán
- Department of Cell and Molecular Biology, Uppsala University, B.M.C., Box 596, Uppsala 751 24, Sweden
| | - Matthew T Eddy
- Department of Chemistry, College of Liberal Arts and Sciences, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA.
| | - Rajan Lamichhane
- Department of Biochemistry & Cellular and Molecular Biology, College of Arts and Sciences, University of Tennessee, 1311 Cumberland Avenue, Knoxville, TN 37932, USA.
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11
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It Takes More than Two to Tango: Complex, Hierarchal, and Membrane-Modulated Interactions in the Regulation of Receptor Tyrosine Kinases. Cancers (Basel) 2022; 14:cancers14040944. [PMID: 35205690 PMCID: PMC8869822 DOI: 10.3390/cancers14040944] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 02/09/2022] [Accepted: 02/12/2022] [Indexed: 12/18/2022] Open
Abstract
The search for an understanding of how cell fate and motility are regulated is not a purely scientific undertaking, but it can also lead to rationally designed therapies against cancer. The discovery of tyrosine kinases about half a century ago, the subsequent characterization of certain transmembrane receptors harboring tyrosine kinase activity, and their connection to the development of human cancer ushered in a new age with the hope of finding a treatment for malignant diseases in the foreseeable future. However, painstaking efforts were required to uncover the principles of how these receptors with intrinsic tyrosine kinase activity are regulated. Developments in molecular and structural biology and biophysical approaches paved the way towards better understanding of these pathways. Discoveries in the past twenty years first resulted in the formulation of textbook dogmas, such as dimerization-driven receptor association, which were followed by fine-tuning the model. In this review, the role of molecular interactions taking place during the activation of receptor tyrosine kinases, with special attention to the epidermal growth factor receptor family, will be discussed. The fact that these receptors are anchored in the membrane provides ample opportunities for modulatory lipid-protein interactions that will be considered in detail in the second part of the manuscript. Although qualitative and quantitative alterations in lipids in cancer are not sufficient in their own right to drive the malignant transformation, they both contribute to tumor formation and also provide ways to treat cancer. The review will be concluded with a summary of these medical aspects of lipid-protein interactions.
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12
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Kratochvil HT, Newberry RW, Mensa B, Mravic M, DeGrado WF. Spiers Memorial Lecture: Analysis and de novo design of membrane-interactive peptides. Faraday Discuss 2021; 232:9-48. [PMID: 34693965 PMCID: PMC8979563 DOI: 10.1039/d1fd00061f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Membrane-peptide interactions play critical roles in many cellular and organismic functions, including protection from infection, remodeling of membranes, signaling, and ion transport. Peptides interact with membranes in a variety of ways: some associate with membrane surfaces in either intrinsically disordered conformations or well-defined secondary structures. Peptides with sufficient hydrophobicity can also insert vertically as transmembrane monomers, and many associate further into membrane-spanning helical bundles. Indeed, some peptides progress through each of these stages in the process of forming oligomeric bundles. In each case, the structure of the peptide and the membrane represent a delicate balance between peptide-membrane and peptide-peptide interactions. We will review this literature from the perspective of several biologically important systems, including antimicrobial peptides and their mimics, α-synuclein, receptor tyrosine kinases, and ion channels. We also discuss the use of de novo design to construct models to test our understanding of the underlying principles and to provide useful leads for pharmaceutical intervention of diseases.
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Affiliation(s)
- Huong T Kratochvil
- Department of Pharmaceutical Chemistry, University of California - San Francisco, San Francisco, CA 94158, USA.
| | - Robert W Newberry
- Department of Pharmaceutical Chemistry, University of California - San Francisco, San Francisco, CA 94158, USA.
| | - Bruk Mensa
- Department of Pharmaceutical Chemistry, University of California - San Francisco, San Francisco, CA 94158, USA.
| | - Marco Mravic
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - William F DeGrado
- Department of Pharmaceutical Chemistry, University of California - San Francisco, San Francisco, CA 94158, USA.
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13
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Sahoo AR, Buck M. Structural and Functional Insights into the Transmembrane Domain Association of Eph Receptors. Int J Mol Sci 2021; 22:ijms22168593. [PMID: 34445298 PMCID: PMC8395321 DOI: 10.3390/ijms22168593] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/02/2021] [Accepted: 08/06/2021] [Indexed: 12/04/2022] Open
Abstract
Eph receptors are the largest family of receptor tyrosine kinases and by interactions with ephrin ligands mediate a myriad of processes from embryonic development to adult tissue homeostasis. The interaction of Eph receptors, especially at their transmembrane (TM) domains is key to understanding their mechanism of signal transduction across cellular membranes. We review the structural and functional aspects of EphA1/A2 association and the techniques used to investigate their TM domains: NMR, molecular modelling/dynamics simulations and fluorescence. We also introduce transmembrane peptides, which can be used to alter Eph receptor signaling and we provide a perspective for future studies.
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Affiliation(s)
- Amita R. Sahoo
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA;
| | - Matthias Buck
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA;
- Department of Neurosciences, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- Department of Pharmacology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- Case Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- Correspondence:
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14
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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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15
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Overduin M, Trieber C, Prosser RS, Picard LP, Sheff JG. Structures and Dynamics of Native-State Transmembrane Protein Targets and Bound Lipids. MEMBRANES 2021; 11:451. [PMID: 34204456 PMCID: PMC8235241 DOI: 10.3390/membranes11060451] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 06/08/2021] [Accepted: 06/15/2021] [Indexed: 02/06/2023]
Abstract
Membrane proteins work within asymmetric bilayers of lipid molecules that are critical for their biological structures, dynamics and interactions. These properties are lost when detergents dislodge lipids, ligands and subunits, but are maintained in native nanodiscs formed using styrene maleic acid (SMA) and diisobutylene maleic acid (DIBMA) copolymers. These amphipathic polymers allow extraction of multicomponent complexes of post-translationally modified membrane-bound proteins directly from organ homogenates or membranes from diverse types of cells and organelles. Here, we review the structures and mechanisms of transmembrane targets and their interactions with lipids including phosphoinositides (PIs), as resolved using nanodisc systems and methods including cryo-electron microscopy (cryo-EM) and X-ray diffraction (XRD). We focus on therapeutic targets including several G protein-coupled receptors (GPCRs), as well as ion channels and transporters that are driving the development of next-generation native nanodiscs. The design of new synthetic polymers and complementary biophysical tools bodes well for the future of drug discovery and structural biology of native membrane:protein assemblies (memteins).
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Affiliation(s)
- Michael Overduin
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada;
| | - Catharine Trieber
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada;
| | - R. Scott Prosser
- Department of Chemistry, University of Toronto, UTM, Mississauga, ON L5L 1C6, Canada; (R.S.P.); (L.-P.P.)
| | - Louis-Philippe Picard
- Department of Chemistry, University of Toronto, UTM, Mississauga, ON L5L 1C6, Canada; (R.S.P.); (L.-P.P.)
| | - Joey G. Sheff
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON K1A 0R6, Canada;
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16
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Biological insights from SMA-extracted proteins. Biochem Soc Trans 2021; 49:1349-1359. [PMID: 34110372 PMCID: PMC8286838 DOI: 10.1042/bst20201067] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 05/12/2021] [Accepted: 05/17/2021] [Indexed: 02/08/2023]
Abstract
In the twelve years since styrene maleic acid (SMA) was first used to extract and purify a membrane protein within a native lipid bilayer, this technological breakthrough has provided insight into the structural and functional details of protein–lipid interactions. Most recently, advances in cryo-EM have demonstrated that SMA-extracted membrane proteins are a rich-source of structural data. For example, it has been possible to resolve the details of annular lipids and protein–protein interactions within complexes, the nature of lipids within central cavities and binding pockets, regions involved in stabilising multimers, details of terminal residues that would otherwise remain unresolved and the identification of physiologically relevant states. Functionally, SMA extraction has allowed the analysis of membrane proteins that are unstable in detergents, the characterization of an ultrafast component in the kinetics of electron transfer that was not possible in detergent-solubilised samples and quantitative, real-time measurement of binding assays with low concentrations of purified protein. While the use of SMA comes with limitations such as its sensitivity to low pH and divalent cations, its major advantage is maintenance of a protein's lipid bilayer. This has enabled researchers to view and assay proteins in an environment close to their native ones, leading to new structural and mechanistic insights.
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