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Takayama M, Maeda S, Watanabe D, Takebayashi K, Hiroshima M, Ueda M. Cholesterol suppresses spontaneous activation of EGFR-mediated signal transduction. Biochem Biophys Res Commun 2024; 704:149673. [PMID: 38401305 DOI: 10.1016/j.bbrc.2024.149673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 01/30/2024] [Accepted: 02/11/2024] [Indexed: 02/26/2024]
Abstract
Epidermal growth factor receptor (EGFR)-mediated signal transduction controls cell growth and proliferation. The signaling pathway is regulated so that it is activated only by external EGF stimuli, but the mechanisms that prevent EGF-independent spontaneous activation of EGFR-mediated signaling are unknown. Here we report cholesterol depletion activates EGFR-mediated signaling without EGF. We applied automated single-molecule imaging to EGFR and characterized the lateral diffusion and cluster formation on cholesterol-depleted and cholesterol-supplemented membranes. In cells in which cholesterol was depleted by methyl-β-cyclodextrin (MβCD) treatment, EGFR exhibited a reduction in lateral diffusion, an acceleration of cluster formation, and autophosphorylation without EGF. Concurrently, extracellular signal-regulated kinase (ERK), which is regulated by EGFR-mediated signaling, exhibited phosphorylation and nuclear translocation without EGF. These cholesterol depletion-induced changes were similar, albeit less efficient, to those that occurred with EGF stimulation in normal cells without MβCD, indicating the spontaneous activation of EGFR signaling. The exogenous supplementation of cholesterol suppressed the MβCD-induced spontaneous activation of EGFR and ERK nuclear translocation. Single-molecule imaging of EGFR in a large number of cells revealed cell-to-cell heterogeneity, with a sub-population showing a high ability for spontaneous activation. These results provide evidence that EGFR-mediated signaling is properly regulated by cholesterol metabolism to prevent uncontrolled spontaneous activation.
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Affiliation(s)
- Miri Takayama
- Laboratory of Single Molecular Biology, Graduate School of Science and Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan; Laboratory for Cell Signaling Dynamics, BDR (Biosystems and Dynamics Research Center), RIKEN, Suita, Osaka, 565-0874, Japan
| | - Sakura Maeda
- Laboratory of Single Molecular Biology, Graduate School of Science and Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan; Laboratory for Cell Signaling Dynamics, BDR (Biosystems and Dynamics Research Center), RIKEN, Suita, Osaka, 565-0874, Japan
| | - Daisuke Watanabe
- Laboratory of Single Molecular Biology, Graduate School of Science and Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan; Laboratory for Cell Signaling Dynamics, BDR (Biosystems and Dynamics Research Center), RIKEN, Suita, Osaka, 565-0874, Japan
| | - Kazutoshi Takebayashi
- Laboratory of Single Molecular Biology, Graduate School of Science and Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan; Laboratory for Cell Signaling Dynamics, BDR (Biosystems and Dynamics Research Center), RIKEN, Suita, Osaka, 565-0874, Japan
| | - Michio Hiroshima
- Laboratory of Single Molecular Biology, Graduate School of Science and Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan; Laboratory for Cell Signaling Dynamics, BDR (Biosystems and Dynamics Research Center), RIKEN, Suita, Osaka, 565-0874, Japan.
| | - Masahiro Ueda
- Laboratory of Single Molecular Biology, Graduate School of Science and Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan; Laboratory for Cell Signaling Dynamics, BDR (Biosystems and Dynamics Research Center), RIKEN, Suita, Osaka, 565-0874, Japan.
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Tu G, Fu T, Zheng G, Xu B, Gou R, Luo D, Wang P, Xue W. Computational Chemistry in Structure-Based Solute Carrier Transporter Drug Design: Recent Advances and Future Perspectives. J Chem Inf Model 2024; 64:1433-1455. [PMID: 38294194 DOI: 10.1021/acs.jcim.3c01736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Solute carrier transporters (SLCs) are a class of important transmembrane proteins that are involved in the transportation of diverse solute ions and small molecules into cells. There are approximately 450 SLCs within the human body, and more than a quarter of them are emerging as attractive therapeutic targets for multiple complex diseases, e.g., depression, cancer, and diabetes. However, only 44 unique transporters (∼9.8% of the SLC superfamily) with 3D structures and specific binding sites have been reported. To design innovative and effective drugs targeting diverse SLCs, there are a number of obstacles that need to be overcome. However, computational chemistry, including physics-based molecular modeling and machine learning- and deep learning-based artificial intelligence (AI), provides an alternative and complementary way to the classical drug discovery approach. Here, we present a comprehensive overview on recent advances and existing challenges of the computational techniques in structure-based drug design of SLCs from three main aspects: (i) characterizing multiple conformations of the proteins during the functional process of transportation, (ii) identifying druggability sites especially the cryptic allosteric ones on the transporters for substrates and drugs binding, and (iii) discovering diverse small molecules or synthetic protein binders targeting the binding sites. This work is expected to provide guidelines for a deep understanding of the structure and function of the SLC superfamily to facilitate rational design of novel modulators of the transporters with the aid of state-of-the-art computational chemistry technologies including artificial intelligence.
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Affiliation(s)
- Gao Tu
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Tingting Fu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | | | - Binbin Xu
- Chengdu Sintanovo Biotechnology Co., Ltd., Chengdu 610200, China
| | - Rongpei Gou
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Ding Luo
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Panpan Wang
- College of Chemistry and Pharmaceutical Engineering, Huanghuai University, Zhumadian 463000, China
| | - Weiwei Xue
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
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Liu X, Jiang Y, Cui Y, Yuan J, Fang X. Deep learning in single-molecule imaging and analysis: recent advances and prospects. Chem Sci 2022; 13:11964-11980. [PMID: 36349113 PMCID: PMC9600384 DOI: 10.1039/d2sc02443h] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 09/19/2022] [Indexed: 09/19/2023] Open
Abstract
Single-molecule microscopy is advantageous in characterizing heterogeneous dynamics at the molecular level. However, there are several challenges that currently hinder the wide application of single molecule imaging in bio-chemical studies, including how to perform single-molecule measurements efficiently with minimal run-to-run variations, how to analyze weak single-molecule signals efficiently and accurately without the influence of human bias, and how to extract complete information about dynamics of interest from single-molecule data. As a new class of computer algorithms that simulate the human brain to extract data features, deep learning networks excel in task parallelism and model generalization, and are well-suited for handling nonlinear functions and extracting weak features, which provide a promising approach for single-molecule experiment automation and data processing. In this perspective, we will highlight recent advances in the application of deep learning to single-molecule studies, discuss how deep learning has been used to address the challenges in the field as well as the pitfalls of existing applications, and outline the directions for future development.
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Affiliation(s)
- Xiaolong Liu
- Key Laboratory of Molecular Nanostructure and Nanotechnology, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 P. R. China
| | - Yifei Jiang
- Institute of Basic Medicine and Cancer, Chinese Academy of Sciences Hangzhou 310022 Zhejiang China
| | - Yutong Cui
- Key Laboratory of Molecular Nanostructure and Nanotechnology, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 P. R. China
| | - Jinghe Yuan
- Key Laboratory of Molecular Nanostructure and Nanotechnology, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences Beijing 100190 China
| | - Xiaohong Fang
- Key Laboratory of Molecular Nanostructure and Nanotechnology, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 P. R. China
- Institute of Basic Medicine and Cancer, Chinese Academy of Sciences Hangzhou 310022 Zhejiang China
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Three live-imaging techniques for comprehensively understanding the initial trigger for insulin-responsive intracellular GLUT4 trafficking. iScience 2022; 25:104164. [PMID: 35434546 PMCID: PMC9010770 DOI: 10.1016/j.isci.2022.104164] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 11/16/2021] [Accepted: 03/24/2022] [Indexed: 01/31/2023] Open
Abstract
Quantitative features of GLUT4 glucose transporter's behavior deep inside cells remain largely unknown. Our previous analyses with live-cell imaging of intracellular GLUT4 trafficking demonstrated two crucial early events responsible for triggering insulin-responsive translocation processes, namely, heterotypic fusion and liberation. To quantify the regulation, interrelationships, and dynamics of the initial events more accurately and comprehensively, we herein applied three analyses, each based on our distinct dual-color live-cell imaging approaches. With these approaches, heterotypic fusion was found to be the first trigger for insulin-responsive GLUT4 redistributions, preceding liberation, and to be critically regulated by Akt substrate of 160 kDa (AS160) and actin dynamics. In addition, demonstrating the subcellular regional dependence of GLUT4 dynamics revealed that liberated GLUT4 molecules are promptly incorporated into the trafficking itinerary of transferrin receptors. Our approaches highlight the physiological significance of endosomal "GLUT4 molecule trafficking" rather than "GLUT4 vesicle delivery" to the plasma membrane in response to insulin.
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Vermeulen I, Isin EM, Barton P, Cillero-Pastor B, Heeren RM. Multimodal molecular imaging in drug discovery and development. Drug Discov Today 2022; 27:2086-2099. [DOI: 10.1016/j.drudis.2022.04.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 03/03/2022] [Accepted: 04/08/2022] [Indexed: 02/06/2023]
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Laasfeld T, Ehrminger R, Tahk MJ, Veiksina S, Kõlvart KR, Min M, Kopanchuk S, Rinken A. Budded baculoviruses as a receptor display system to quantify ligand binding with TIRF microscopy. NANOSCALE 2021; 13:2436-2447. [PMID: 33464268 DOI: 10.1039/d0nr06737g] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Studying mechanisms of receptor-ligand interactions has remained challenging due to several limitations of different measurement methods. Here we present a total internal reflection fluorescence microscopy-based method that maintains the right balance between retaining the receptors in the natural lipid environment, sufficient throughput for ligand screening, high sensitivity, and offering more detailed view into the ligand-binding process. The novel method combines G protein-coupled receptor display in budded baculovirus particles and the immobilization of the particles to a functionalized coverslip. We adapted and validated the functionalized coverslip preparation process to achieve selective immobilization of budded baculovirus particles. The selectivity of budded baculovirus immobilization was validated with budded baculovirus particles displaying either Frizzled 6 receptors labeled with mCherry or neuropeptide Y Y1 receptors. To scale the system for ligand binding assays, we developed both open-source multiwell systems and image analysis software SPOTNIC for flexible assay design. The neuropeptide Y Y1 receptor was used for further receptor-ligand binding studies with high-affinity TAMRA labeled fluorescent ligand UR-MC026. The affinities of the fluorescent ligand and four unlabeled ligands (BIBO3304, UR-MK299, PYY, pNPY) were obtained with the developed method and followed a similar trend with both the parallel measurements with fluorescence anisotropy method and the data published earlier. The novel method could be extended for various advanced assays utilizing multidimensional detection modes, integrating super-resolution methods for single molecule detection and microfluidic devices for kinetic measurements.
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Affiliation(s)
- Tõnis Laasfeld
- University of Tartu, Institute of Chemistry, Ravila 14a, 50411, Tartu, Estonia.
| | - Robin Ehrminger
- University of Tartu, Institute of Chemistry, Ravila 14a, 50411, Tartu, Estonia. and Tallinn University of Technology, Thomas Johann Seebeck Department of Electronics, Ehitajate Tee 5, 19086, Tallinn, Estonia
| | - Maris-Johanna Tahk
- University of Tartu, Institute of Chemistry, Ravila 14a, 50411, Tartu, Estonia.
| | - Santa Veiksina
- University of Tartu, Institute of Chemistry, Ravila 14a, 50411, Tartu, Estonia.
| | - Karl Rene Kõlvart
- University of Tartu, Institute of Chemistry, Ravila 14a, 50411, Tartu, Estonia.
| | - Mart Min
- Tallinn University of Technology, Thomas Johann Seebeck Department of Electronics, Ehitajate Tee 5, 19086, Tallinn, Estonia
| | - Sergei Kopanchuk
- University of Tartu, Institute of Chemistry, Ravila 14a, 50411, Tartu, Estonia.
| | - Ago Rinken
- University of Tartu, Institute of Chemistry, Ravila 14a, 50411, Tartu, Estonia.
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Yanagawa M, Sako Y. Workflows of the Single-Molecule Imaging Analysis in Living Cells: Tutorial Guidance to the Measurement of the Drug Effects on a GPCR. Methods Mol Biol 2021; 2274:391-441. [PMID: 34050488 DOI: 10.1007/978-1-0716-1258-3_32] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Single-molecule imaging (SMI) is a powerful method to measure the dynamics of membrane proteins on the cell membrane. The single-molecule tracking (SMT) analysis provides information about the diffusion dynamics, the oligomer size distribution, and the particle density change. The affinity and on/off-rate of a protein-protein interaction can be estimated from the dual-color SMI analysis. However, it is difficult for trainees to determine quantitative information from the SMI movies. The present protocol guides the detailed workflows to measure the drug-activated dynamics of a G protein-coupled receptor (GPCR) and metabotropic glutamate receptor 3 (mGluR3), by using the total internal reflection fluorescence microscopy (TIRFM). This tutorial guidance comprises an open-source software, named smDynamicsAnalyzer, with which one can easily analyze the SMT dataset by just following the workflows after building a designated folder structure ( https://github.com/masataka-yanagawa/IgorPro8-smDynamicsAnalyzer ).
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Affiliation(s)
- Masataka Yanagawa
- Cellular Informatics Laboratory, RIKEN Cluster for Pioneering Research, Saitama, Japan.
| | - Yasushi Sako
- Cellular Informatics Laboratory, RIKEN Cluster for Pioneering Research, Saitama, Japan
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