1
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Cao X, Huang S, Wagner MM, Cho YT, Chiu DC, Wartchow KM, Lazarian A, McIntire LB, Smolka MB, Baskin JM. A phosphorylation-controlled switch confers cell cycle-dependent protein relocalization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.05.597552. [PMID: 38895347 PMCID: PMC11185714 DOI: 10.1101/2024.06.05.597552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Tools for acute manipulation of protein localization enable elucidation of spatiotemporally defined functions, but their reliance on exogenous triggers can interfere with cell physiology. This limitation is particularly apparent for studying mitosis, whose highly choreographed events are sensitive to perturbations. Here we exploit the serendipitous discovery of a phosphorylation-controlled, cell cycle-dependent localization change of the adaptor protein PLEKHA5 to develop a system for mitosis-specific protein recruitment to the plasma membrane that requires no exogenous stimulus. Mitosis-enabled Anchor-away/Recruiter System (MARS) comprises an engineered, 15-kDa module derived from PLEKHA5 capable of recruiting functional protein cargoes to the plasma membrane during mitosis, either through direct fusion or via GFP-GFP nanobody interaction. Applications of MARS include both knock sideways to rapidly extract proteins from their native localizations during mitosis and conditional recruitment of lipid-metabolizing enzymes for mitosis-selective editing of plasma membrane lipid content, without the need for exogenous triggers or perturbative synchronization methods.
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Affiliation(s)
- Xiaofu Cao
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, United States, 14853
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, United States, 14853
| | - Shiying Huang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, United States, 14853
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, United States, 14853
| | - Mateusz M. Wagner
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, United States, 14853
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States, 14853
| | - Yuan-Ting Cho
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, United States, 14853
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, United States, 14853
| | - Din-Chi Chiu
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, United States, 14853
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, United States, 14853
| | - Krista M. Wartchow
- Department of Radiology, Weill Cornell Medicine, New York, New York, United States, 10065
| | - Artur Lazarian
- Department of Radiology, Weill Cornell Medicine, New York, New York, United States, 10065
| | - Laura Beth McIntire
- Department of Radiology, Weill Cornell Medicine, New York, New York, United States, 10065
| | - Marcus B. Smolka
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, United States, 14853
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States, 14853
| | - Jeremy M. Baskin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, United States, 14853
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, United States, 14853
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2
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Cheng J, Li L, Jin D, Zhang Y, Yu W, Yu J, Zou J, Dai Y, Zhu Y, Liu M, Zhang M, Sun Y, Liu Y, Chen X. A non-metal single atom nanozyme for cutting off the energy and reducing power of tumors. Angew Chem Int Ed Engl 2024; 63:e202319982. [PMID: 38361437 DOI: 10.1002/anie.202319982] [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: 12/24/2023] [Revised: 02/13/2024] [Accepted: 02/15/2024] [Indexed: 02/17/2024]
Abstract
Enzymes are considered safe and effective therapeutic tools for various diseases. With the increasing integration of biomedicine and nanotechnology, artificial nanozymes offer advanced controllability and functionality in medical design. However, several notable gaps, such as catalytic diversity, specificity and biosafety, still exist between nanozymes and their native counterparts. Here we report a non-metal single-selenium (Se)-atom nanozyme (SeSAE), which exhibits potent nicotinamide adenine dinucleotide phosphate (NADPH) oxidase-mimetic activity. This novel single atom nanozyme provides a safe alternative to conventional metal-based catalysts and effectively cuts off the cellular energy and reduction equivalents through its distinctive catalytic function in tumors. In this study, we have demonstrated the substantial efficacy of SeSAE as an antitumor nanomedicine across diverse mouse models without discernible systemic adverse effects. The mechanism of the NADPH oxidase-like activity of the non-metal SeSAE was rationalized by density functional theory calculations. Furthermore, comprehensive elucidation of the biological functions, cell death pathways, and metabolic remodeling effects of the nanozyme was conducted, aiming to provide valuable insights into the development of single atom nanozymes with clinical translation potential.
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Affiliation(s)
- Junjie Cheng
- Department of Chemistry, Key Laboratory of Precision and Intelligent Chemistry, University of Science and Technology of China, Hefei, 230026, China
| | - Li Li
- Hefei National Research Center for Physical Sciences at Microscale, University of Science and Technology of China, Hefei, 230026, China
| | - Duo Jin
- Department of Chemistry, Key Laboratory of Precision and Intelligent Chemistry, University of Science and Technology of China, Hefei, 230026, China
| | - Yajie Zhang
- Central Laboratory, Department of Biobank, Nanjing Hospital of Chinese Medicine Affiliated to Nanjing University of Chinese Medicine, Nanjing, 210022, China
| | - Wenxin Yu
- Department of Chemistry, Key Laboratory of Precision and Intelligent Chemistry, University of Science and Technology of China, Hefei, 230026, China
| | - Jiaji Yu
- Department of Chemistry, Key Laboratory of Precision and Intelligent Chemistry, University of Science and Technology of China, Hefei, 230026, China
| | - Jianhua Zou
- Departments of Diagnostic Radiology, Surgery, Chemical and Biomolecular Engineering, and Biomedical Engineering, Yong Loo Lin School of Medicine and College of Design and Engineering, National University of Singapore, Singapore, 119074, Singapore
- Clinical Imaging Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore
- Nanomedicine Translational Research Program, NUS Center for Nanomedicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
- Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore
| | - Yi Dai
- College of Pharmaceutical Sciences, Anhui Xinhua University, Hefei, 230088, China
| | - Yang Zhu
- Departments of Diagnostic Radiology, Surgery, Chemical and Biomolecular Engineering, and Biomedical Engineering, Yong Loo Lin School of Medicine and College of Design and Engineering, National University of Singapore, Singapore, 119074, Singapore
- Clinical Imaging Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore
- Nanomedicine Translational Research Program, NUS Center for Nanomedicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
- Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore
| | - Manman Liu
- Department of Chemistry, Key Laboratory of Precision and Intelligent Chemistry, University of Science and Technology of China, Hefei, 230026, China
| | - Miya Zhang
- Departments of Diagnostic Radiology, Surgery, Chemical and Biomolecular Engineering, and Biomedical Engineering, Yong Loo Lin School of Medicine and College of Design and Engineering, National University of Singapore, Singapore, 119074, Singapore
- Clinical Imaging Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore
- Nanomedicine Translational Research Program, NUS Center for Nanomedicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
- Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore
| | - Yongfu Sun
- Hefei National Research Center for Physical Sciences at Microscale, University of Science and Technology of China, Hefei, 230026, China
| | - Yangzhong Liu
- Department of Chemistry, Key Laboratory of Precision and Intelligent Chemistry, University of Science and Technology of China, Hefei, 230026, China
| | - Xiaoyuan Chen
- Departments of Diagnostic Radiology, Surgery, Chemical and Biomolecular Engineering, and Biomedical Engineering, Yong Loo Lin School of Medicine and College of Design and Engineering, National University of Singapore, Singapore, 119074, Singapore
- Clinical Imaging Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore
- Nanomedicine Translational Research Program, NUS Center for Nanomedicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
- Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore
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3
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Erazo-Oliveras A, Muñoz-Vega M, Salinas ML, Wang X, Chapkin RS. Dysregulation of cellular membrane homeostasis as a crucial modulator of cancer risk. FEBS J 2024; 291:1299-1352. [PMID: 36282100 PMCID: PMC10126207 DOI: 10.1111/febs.16665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 09/09/2022] [Accepted: 10/24/2022] [Indexed: 11/07/2022]
Abstract
Cellular membranes serve as an epicentre combining extracellular and cytosolic components with membranous effectors, which together support numerous fundamental cellular signalling pathways that mediate biological responses. To execute their functions, membrane proteins, lipids and carbohydrates arrange, in a highly coordinated manner, into well-defined assemblies displaying diverse biological and biophysical characteristics that modulate several signalling events. The loss of membrane homeostasis can trigger oncogenic signalling. More recently, it has been documented that select membrane active dietaries (MADs) can reshape biological membranes and subsequently decrease cancer risk. In this review, we emphasize the significance of membrane domain structure, organization and their signalling functionalities as well as how loss of membrane homeostasis can steer aberrant signalling. Moreover, we describe in detail the complexities associated with the examination of these membrane domains and their association with cancer. Finally, we summarize the current literature on MADs and their effects on cellular membranes, including various mechanisms of dietary chemoprevention/interception and the functional links between nutritional bioactives, membrane homeostasis and cancer biology.
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Affiliation(s)
- Alfredo Erazo-Oliveras
- Program in Integrative Nutrition and Complex Diseases; Texas A&M University; College Station, Texas, 77843; USA
- Department of Nutrition; Texas A&M University; College Station, Texas, 77843; USA
| | - Mónica Muñoz-Vega
- Program in Integrative Nutrition and Complex Diseases; Texas A&M University; College Station, Texas, 77843; USA
- Department of Nutrition; Texas A&M University; College Station, Texas, 77843; USA
| | - Michael L. Salinas
- Program in Integrative Nutrition and Complex Diseases; Texas A&M University; College Station, Texas, 77843; USA
- Department of Nutrition; Texas A&M University; College Station, Texas, 77843; USA
| | - Xiaoli Wang
- Program in Integrative Nutrition and Complex Diseases; Texas A&M University; College Station, Texas, 77843; USA
- Department of Nutrition; Texas A&M University; College Station, Texas, 77843; USA
| | - Robert S. Chapkin
- Program in Integrative Nutrition and Complex Diseases; Texas A&M University; College Station, Texas, 77843; USA
- Department of Nutrition; Texas A&M University; College Station, Texas, 77843; USA
- Center for Environmental Health Research; Texas A&M University; College Station, Texas, 77843; USA
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4
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Zhuang J, Ma Z, Li N, Chen H, Yang L, Lu Y, Guo K, Zhao N, Tang BZ. Molecular Engineering of Plasma Membrane and Mitochondria Dual-Targeted NIR-II AIE Photosensitizer Evoking Synergetic Pyroptosis and Apoptosis. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2309488. [PMID: 37988801 DOI: 10.1002/adma.202309488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 11/17/2023] [Indexed: 11/23/2023]
Abstract
Phototherapy provides a noninvasive and spatiotemporal controllable paradigm to inhibit the evasion of the programmed cell death (PCD) of tumors. However, conventional photosensitizers (PSs) often induce a single PCD process, resulting in insufficient photodamage and severely impeding their application scopes. In this study, molecular engineering is conducted by adjusting electron donors to develop an aggregation-induced NIR-II emissive PS (DPITQ) for plasma membrane and mitochondria dual-targeted tumor therapy by evoking synergetic pyroptosis and apoptosis. DPITQ displays boosted type I and II reactive oxygen species generation as well as a high photothermal conversion efficacy (43%) after laser irradiation of 635 nm. The excellent biocompatibility and appropriate lipophilicity help the DPITQ to specifically anchor in the plasma membrane and mitochondria of cancer cells. Furthermore, the photosensitized DPITQ can disrupt the intact plasma membrane and cause mitochondrial dysfunction, ultimately causing concurrent pyroptosis and apoptosis to suppress cancer cell proliferation even under hypoxia. It is noteworthy that the DPITQ nanoparticles (NPs) present clear NIR-II fluorescence imaging capability on the venous vessels of nude mice. Notably, the DPITQ NPs exert efficient NIR-II fluorescence imaging-guided phototherapy both in multicellular tumor spheroids and in vivo, causing maximum destruction to tumors but minimum adverse effects to normal tissue.
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Affiliation(s)
- Jiabao Zhuang
- Key Laboratory of Applied Surface and Colloid Chemistry of Ministry of Education, Key Laboratory of Macromolecular Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, P. R. China
| | - Zhedong Ma
- Key Laboratory of Applied Surface and Colloid Chemistry of Ministry of Education, Key Laboratory of Macromolecular Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, P. R. China
| | - Nan Li
- Key Laboratory of Applied Surface and Colloid Chemistry of Ministry of Education, Key Laboratory of Macromolecular Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, P. R. China
| | - Huan Chen
- Key Laboratory of Applied Surface and Colloid Chemistry of Ministry of Education, Key Laboratory of Macromolecular Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, P. R. China
| | - Lijin Yang
- Key Laboratory of Applied Surface and Colloid Chemistry of Ministry of Education, Key Laboratory of Macromolecular Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, P. R. China
| | - Ying Lu
- Key Laboratory of Applied Surface and Colloid Chemistry of Ministry of Education, Key Laboratory of Macromolecular Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, P. R. China
| | - Keyi Guo
- Key Laboratory of Applied Surface and Colloid Chemistry of Ministry of Education, Key Laboratory of Macromolecular Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, P. R. China
| | - Na Zhao
- Key Laboratory of Applied Surface and Colloid Chemistry of Ministry of Education, Key Laboratory of Macromolecular Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, P. R. China
| | - Ben Zhong Tang
- School of Science and Engineering, The Chinese University of Hong Kong, Shenzhen (CUHK-Shenzhen), Shenzhen, 518172, P. R. China
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5
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Nakamura A, Goto Y, Sugiyama H, Tsukiji S, Aoki K. Chemogenetic Manipulation of Endogenous Proteins in Fission Yeast Using a Self-Localizing Ligand-Induced Protein Translocation System. ACS Chem Biol 2023; 18:2506-2515. [PMID: 37990966 DOI: 10.1021/acschembio.3c00478] [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: 11/23/2023]
Abstract
Cells sense extracellular stimuli through membrane receptors and process information through an intracellular signaling network. Protein translocation triggers intracellular signaling, and techniques such as chemically induced dimerization (CID) have been used to manipulate signaling pathways by altering the subcellular localization of signaling molecules. However, in the fission yeast Schizosaccharomyces pombe, the commonly used FKBP-FRB system has technical limitations, and therefore, perturbation tools with low cytotoxicity and high temporal resolution are needed. We here applied our recently developed self-localizing ligand-induced protein translocation (SLIPT) system to S. pombe and successfully perturbed several cell cycle-related proteins. The SLIPT system utilizes self-localizing ligands to recruit binding partners to specific subcellular compartments such as the plasma membrane or nucleus. We optimized the self-localizing ligands to maintain the long-term recruitment of target molecules to the plasma membrane. By knocking in genes encoding the binding partners for self-localizing ligands, we observed changes in the localization of several endogenous molecules and found perturbations in the cell cycle and associated phenotypes. This study demonstrates the effectiveness of the SLIPT system as a chemogenetic tool for rapid perturbation of endogenous molecules in S. pombe, providing a valuable approach for studying intracellular signaling and cell cycle regulation with an improved temporal resolution.
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Affiliation(s)
- Akinobu Nakamura
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
| | - Yuhei Goto
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
- Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
| | - Hironori Sugiyama
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
| | - Shinya Tsukiji
- Department of Nanopharmaceutical Sciences, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Kazuhiro Aoki
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
- Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi 444-8787, Japan
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6
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Has C, Das SL. The Functionality of Membrane-Inserting Proteins and Peptides: Curvature Sensing, Generation, and Pore Formation. J Membr Biol 2023; 256:343-372. [PMID: 37650909 DOI: 10.1007/s00232-023-00289-7] [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: 01/17/2023] [Accepted: 08/04/2023] [Indexed: 09/01/2023]
Abstract
Proteins and peptides with hydrophobic and amphiphilic segments are responsible for many biological functions. The sensing and generation of membrane curvature are the functions of several protein domains or motifs. While some specific membrane proteins play an essential role in controlling the curvature of distinct intracellular membranes, others participate in various cellular processes such as clathrin-mediated endocytosis, where several proteins sort themselves at the neck of the membrane bud. A few membrane-inserting proteins form nanopores that permeate selective ions and water to cross the membrane. In addition, many natural and synthetic small peptides and protein toxins disrupt the membrane by inducing nonspecific pores in the membrane. The pore formation causes cell death through the uncontrolled exchange between interior and exterior cellular contents. In this article, we discuss the insertion depth and orientation of protein/peptide helices, and their role as a sensor and inducer of membrane curvature as well as a pore former in the membrane. We anticipate that this extensive review will assist biophysicists to gain insight into curvature sensing, generation, and pore formation by membrane insertion.
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Affiliation(s)
- Chandra Has
- Department of Chemical Engineering, GSFC University, Vadodara, 391750, Gujarat, India.
| | - Sovan Lal Das
- Physical and Chemical Biology Laboratory and Department of Mechanical Engineering, Indian Institute of Technology, Palakkad, 678623, Kerala, India
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7
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Leblanc JA, Sugiyama MG, Antonescu CN, Brown AI. Quantitative modeling of EGF receptor ligand discrimination via internalization proofreading. Phys Biol 2023; 20:056008. [PMID: 37557183 DOI: 10.1088/1478-3975/aceecd] [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: 05/11/2023] [Accepted: 08/09/2023] [Indexed: 08/11/2023]
Abstract
The epidermal growth factor receptor (EGFR) is a central regulator of cell physiology that is stimulated by multiple distinct ligands. Although ligands bind to EGFR while the receptor is exposed on the plasma membrane, EGFR incorporation into endosomes following receptor internalization is an important aspect of EGFR signaling, with EGFR internalization behavior dependent upon the type of ligand bound. We develop quantitative modeling for EGFR recruitment to and internalization from clathrin domains, focusing on how internalization competes with ligand unbinding from EGFR. We develop two model versions: a kinetic model with EGFR behavior described as transitions between discrete states and a spatial model with EGFR diffusion to circular clathrin domains. We find that a combination of spatial and kinetic proofreading leads to enhanced EGFR internalization ratios in comparison to unbinding differences between ligand types. Various stages of the EGFR internalization process, including recruitment to and internalization from clathrin domains, modulate the internalization differences between receptors bound to different ligands. Our results indicate that following ligand binding, EGFR may encounter multiple clathrin domains before successful recruitment and internalization. The quantitative modeling we have developed describes competition between EGFR internalization and ligand unbinding and the resulting proofreading.
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Affiliation(s)
- Jaleesa A Leblanc
- Department of Physics, Toronto Metropolitan University, Toronto, Ontario, Canada
| | - Michael G Sugiyama
- Department of Chemistry and Biology, Toronto Metropolitan University, Toronto, Ontario, Canada
| | - Costin N Antonescu
- Department of Chemistry and Biology, Toronto Metropolitan University, Toronto, Ontario, Canada
| | - Aidan I Brown
- Department of Physics, Toronto Metropolitan University, Toronto, Ontario, Canada
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8
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Saini P, Anugula S, Fong YW. The Role of ATP-Binding Cassette Proteins in Stem Cell Pluripotency. Biomedicines 2023; 11:1868. [PMID: 37509507 PMCID: PMC10377311 DOI: 10.3390/biomedicines11071868] [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: 05/17/2023] [Revised: 06/20/2023] [Accepted: 06/22/2023] [Indexed: 07/30/2023] Open
Abstract
Pluripotent stem cells (PSCs) are highly proliferative cells that can self-renew indefinitely in vitro. Upon receiving appropriate signals, PSCs undergo differentiation and can generate every cell type in the body. These unique properties of PSCs require specific gene expression patterns that define stem cell identity and dynamic regulation of intracellular metabolism to support cell growth and cell fate transitions. PSCs are prone to DNA damage due to elevated replicative and transcriptional stress. Therefore, mechanisms to prevent deleterious mutations in PSCs that compromise stem cell function or increase the risk of tumor formation from becoming amplified and propagated to progenitor cells are essential for embryonic development and for using PSCs including induced PSCs (iPSCs) as a cell source for regenerative medicine. In this review, we discuss the role of the ATP-binding cassette (ABC) superfamily in maintaining PSC homeostasis, and propose how their activities can influence cellular signaling and stem cell fate decisions. Finally, we highlight recent discoveries that not all ABC family members perform only canonical metabolite and peptide transport functions in PSCs; rather, they can participate in diverse cellular processes from genome surveillance to gene transcription and mRNA translation, which are likely to maintain the pristine state of PSCs.
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Affiliation(s)
- Prince Saini
- Brigham Regenerative Medicine Center, Brigham and Women’s Hospital, Boston, MA 02115, USA; (P.S.); (S.A.)
- Department of Medicine, Cardiovascular Medicine Division, Harvard Medical School, Boston, MA 02115, USA
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Sharath Anugula
- Brigham Regenerative Medicine Center, Brigham and Women’s Hospital, Boston, MA 02115, USA; (P.S.); (S.A.)
- Department of Medicine, Cardiovascular Medicine Division, Harvard Medical School, Boston, MA 02115, USA
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Yick W. Fong
- Brigham Regenerative Medicine Center, Brigham and Women’s Hospital, Boston, MA 02115, USA; (P.S.); (S.A.)
- Department of Medicine, Cardiovascular Medicine Division, Harvard Medical School, Boston, MA 02115, USA
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA
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9
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Izbicka E, Streeper RT. Mitigation of Insulin Resistance by Natural Products from a New Class of Molecules, Membrane-Active Immunomodulators. Pharmaceuticals (Basel) 2023; 16:913. [PMID: 37513825 PMCID: PMC10386479 DOI: 10.3390/ph16070913] [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: 04/10/2023] [Revised: 06/14/2023] [Accepted: 06/15/2023] [Indexed: 07/30/2023] Open
Abstract
Insulin resistance (IR), accompanied by an impaired cellular glucose uptake, characterizes diverse pathologies that include, but are not limited to, metabolic disease, prediabetes and type 2 diabetes. Chronic inflammation associated with deranged cellular signaling is thought to contribute to IR. The key molecular players in IR are plasma membrane proteins, including the insulin receptor and glucose transporter 4. Certain natural products, such as lipids, phenols, terpenes, antibiotics and alkaloids have beneficial effects on IR, yet their mode of action remains obscured. We hypothesized that these products belong to a novel class of bioactive molecules that we have named membrane-active immunomodulators (MAIMs). A representative MAIM, the naturally occurring medium chain fatty acid ester diethyl azelate (DEA), has been shown to increase the fluidity of cell plasma membranes with subsequent downstream effects on cellular signaling. DEA has also been shown to improve markers of IR, including blood glucose, insulin and lipid levels, in humans. The literature supports the notion that DEA and other natural MAIMs share similar mechanisms of action in improving IR. These findings shed a new light on the mechanism of IR mitigation using natural products, and may facilitate the discovery of other compounds with similar activities.
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10
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Liu J, Li RS, Zhang L, Wang J, Dong Q, Xu Z, Kang Y, Xue P. Enzyme-Activatable Polypeptide for Plasma Membrane Disruption and Antitumor Immunity Elicitation. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2206912. [PMID: 36932931 DOI: 10.1002/smll.202206912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 03/01/2023] [Indexed: 06/15/2023]
Abstract
Enzyme-instructed self-assembly of bioactive molecules into nanobundles inside cells is conceived to potentially disrupt plasma membrane and subcellular structure. Herein, an alkaline phosphatase (ALP)-activatable hybrid of ICG-CF4 KYp is facilely synthesized by conjugating photosensitizer indocyanine green (ICG) with CF4 KYp peptide via classical Michael addition reaction. ALP-induced dephosphorylation of ICG-CF4 KYp enables its transformation from small-molecule precursor into rigid nanofibrils, and such fibrillation in situ causes severe mechanical disruption of cytomembrane. Besides, ICG-mediated photosensitization causes additional oxidative damage of plasma membrane by lipid peroxidation. Hollow MnO2 nanospheres devote to deliver ICG-CF4 KYp into tumorous tissue through tumor-specific acidity/glutathione-triggered degradation of MnO2 , which is monitored by fluorescent probing and magnetic resonance imaging. The burst release of damage-associated molecular patterns and other tumor antigens during therapy effectively triggers immunogenetic cell death and improves immune stimulatory, as demonstrated by the promotion of dendritic cell maturation and CD8+ lymphocyte infiltration, as well as constraint of regulatory T cell population. Taken together, such cytomembrane injury strategy based on peptide fibrillation in situ holds high clinical promise for lesion-specific elimination of primary, abscopal, and metastatic tumors, which may enlighten more bioinspired nanoplatforms for anticancer theranostics.
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Affiliation(s)
- Jiahui Liu
- School of Materials and Energy, Southwest University, Chongqing, 400715, China
| | - Rong Sheng Li
- National Demonstration Center for Experimental Chemistry and Chemical Engineering Education, School of Chemical Science and Engineering, Yunnan University, Kunming, 650091, China
| | - Lei Zhang
- Cancer Center, Medical Research Institute, Southwest University, Chongqing, 400716, China
| | - Jie Wang
- Cancer Center, Medical Research Institute, Southwest University, Chongqing, 400716, China
| | - Qi Dong
- School of Materials and Energy, Southwest University, Chongqing, 400715, China
| | - Zhigang Xu
- School of Materials and Energy, Southwest University, Chongqing, 400715, China
| | - Yuejun Kang
- School of Materials and Energy, Southwest University, Chongqing, 400715, China
| | - Peng Xue
- School of Materials and Energy, Southwest University, Chongqing, 400715, China
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11
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Tuomivaara ST, Teo CF, Jan YN, Jan LY, Wiita AP. SLAPSHOT reveals rapid dynamics of extracellularly exposed proteome in response to calcium-activated plasma membrane phospholipid scrambling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.26.534250. [PMID: 36993417 PMCID: PMC10055316 DOI: 10.1101/2023.03.26.534250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
To facilitate our understanding of the often rapid and nuanced dynamics of extracellularly exposed proteomes during signaling events, it is important to devise robust workflows affording fast time resolution without biases and confounding factors. Here, we present Surface-exposed protein Labeling using PeroxidaSe, H2O2, and Tyramide-derivative (SLAPSHOT), to label extracellularly exposed proteins in a rapid, sensitive, and specific manner, while preserving cellular integrity. This experimentally simple and flexible method utilizes recombinant soluble APEX2 peroxidase that is applied to cells, thus circumventing biological perturbations, tedious engineering of tools and cells, and labeling biases. APEX2 neither requires metal cations for activity nor contains disulfide bonds, conferring versatility for a wide spectrum of experimental setups. We applied SLAPSHOT followed by quantitative mass spectrometry-based proteomics analysis to examine the immediate and extensive cell surface expansion and ensuing restorative membrane shedding upon the activation of Scott syndrome-linked TMEM16F, a ubiquitously expressed calcium-dependent phospholipid scramblase and ion channel. Time-course data ranging from one to thirty minutes of calcium stimulation using wild-type and TMEM16F deficient cells revealed intricate co-regulation of known protein families, including those in the integrin and ICAM families. Crucially, we identified proteins that are known to reside in intracellular organelles, including ER, as occupants of the freshly deposited membrane, and mitovesicles as an abundant component and contributor to the extracellularly exposed proteome. Our study not only provides the first accounts of the immediate consequences of calcium signaling on the extracellularly exposed proteome, but also presents a blueprint for the application of SLAPSHOT as a general approach for monitoring extracellularly exposed protein dynamics.
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Affiliation(s)
- Sami T. Tuomivaara
- Department of Laboratory Medicine, University of California, San Francisco, CA
| | - Chin Fen Teo
- Howard Hughes Medical Institute, University of California, San Francisco, CA
| | - Yuh Nung Jan
- Howard Hughes Medical Institute, University of California, San Francisco, CA
- Department of Physiology, University of California, San Francisco, CA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA
| | - Lily Y. Jan
- Howard Hughes Medical Institute, University of California, San Francisco, CA
- Department of Physiology, University of California, San Francisco, CA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA
| | - Arun P. Wiita
- Department of Laboratory Medicine, University of California, San Francisco, CA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA
- Chan Zuckerberg Biohub, San Francisco, CA
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12
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Sotodosos-Alonso L, Pulgarín-Alfaro M, Del Pozo MA. Caveolae Mechanotransduction at the Interface between Cytoskeleton and Extracellular Matrix. Cells 2023; 12:cells12060942. [PMID: 36980283 PMCID: PMC10047380 DOI: 10.3390/cells12060942] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/08/2023] [Accepted: 03/10/2023] [Indexed: 03/30/2023] Open
Abstract
The plasma membrane (PM) is subjected to multiple mechanical forces, and it must adapt and respond to them. PM invaginations named caveolae, with a specific protein and lipid composition, play a crucial role in this mechanosensing and mechanotransduction process. They respond to PM tension changes by flattening, contributing to the buffering of high-range increases in mechanical tension, while novel structures termed dolines, sharing Caveolin1 as the main component, gradually respond to low and medium forces. Caveolae are associated with different types of cytoskeletal filaments, which regulate membrane tension and also initiate multiple mechanotransduction pathways. Caveolar components sense the mechanical properties of the substrate and orchestrate responses that modify the extracellular matrix (ECM) according to these stimuli. They perform this function through both physical remodeling of ECM, where the actin cytoskeleton is a central player, and via the chemical alteration of the ECM composition by exosome deposition. Here, we review mechanotransduction regulation mediated by caveolae and caveolar components, focusing on how mechanical cues are transmitted through the cellular cytoskeleton and how caveolae respond and remodel the ECM.
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Affiliation(s)
- Laura Sotodosos-Alonso
- Mechanoadaptation and Caveolae Biology Laboratory, Novel Mechanisms of Atherosclerosis Program, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Marta Pulgarín-Alfaro
- Mechanoadaptation and Caveolae Biology Laboratory, Novel Mechanisms of Atherosclerosis Program, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Miguel A Del Pozo
- Mechanoadaptation and Caveolae Biology Laboratory, Novel Mechanisms of Atherosclerosis Program, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
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13
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Abstract
The biophysical response of the human body to electric current is widely appreciated as a barometer of fluid distribution and cell function. From distinct raw bioelectrical impedance (BIA) variables assessed in the field of body composition, phase angle (PhA) has been repeatedly indicated as a functional marker of the cell's health and mass. Although resistance training (RT) programs have demonstrated to be effective to improve PhA, with varying degrees of change depending on other raw BIA variables, there is still limited research explaining the biological mechanisms behind these changes. Here, we aim to provide the rationale for the responsiveness of PhA determinants to RT, as well as to summarize all available evidence addressing the effect of varied RT programs on PhA of different age groups. Available data led us to conclude that RT modulates the cell volume by increasing the levels of intracellular glycogen and water, thus triggering structural and functional changes in different cell organelles. These alterations lead, respectively, to shifts in the resistive path of the electric current (resistance, R) and capacitive properties of the human body (reactance, Xc), which ultimately impact PhA, considering that it is the angular transformation of the ratio between Xc and R. Evidence drawn from experimental research suggests that RT is highly effective for enhancing PhA, especially when adopting high-intensity, volume, and duration RT programs combining other types of exercise. Still, additional research exploring the effects of RT on whole-body and regional BIA variables of alternative population groups is recommended for further knowledge development.
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Affiliation(s)
- Luís B Sardinha
- Exercise and Health Laboratory, Faculdade de Motricidade Humana, CIPER, Universidade de Lisboa, , Cruz Quebrada, Portugal.
| | - Gil B Rosa
- Exercise and Health Laboratory, Faculdade de Motricidade Humana, CIPER, Universidade de Lisboa, , Cruz Quebrada, Portugal
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14
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Badu-Nkansah KA, Sernas D, Natwick DE, Collins SR. Modeling Subcellular Protein Recruitment Dynamics for Synthetic Biology. Methods Mol Biol 2023; 2553:189-207. [PMID: 36227545 DOI: 10.1007/978-1-0716-2617-7_10] [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] [Indexed: 06/16/2023]
Abstract
Compartmentalized protein recruitment is a fundamental feature of signal transduction. Accordingly, the cell cortex is a primary site of signaling supported by the recruitment of protein regulators to the plasma membrane. Recent emergence of optogenetic strategies designed to control localized protein recruitment has offered valuable toolsets for investigating spatiotemporal dynamics of associated signaling mechanisms. However, determining proper recruitment parameters is important for optimizing synthetic control. In this chapter, we describe a stepwise process for building linear differential equation models that characterize the kinetics and spatial distribution of optogenetic protein recruitment to the plasma membrane. Specifically, we outline how to construct (1) ordinary differential equations that capture the kinetics, efficiency, and magnitude of recruitment and (2) partial differential equations that model spatial recruitment dynamics and diffusion. Additionally, we explore how these models can be used to evaluate the overall system performance and determine how component parameters can be tuned to optimize synthetic recruitment.
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Affiliation(s)
- Kwabena A Badu-Nkansah
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Diana Sernas
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Dean E Natwick
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Sean R Collins
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, USA.
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15
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Xiao Y, Chen M, Zheng N, Xu Z, Zhang J, Hu X, Li L, Gu R, Du X, Wang J. Transcriptome Analysis Identifies Novel Genes Associated with Low-Temperature Seed Germination in Sweet Corn. PLANTS (BASEL, SWITZERLAND) 2022; 12:159. [PMID: 36616288 PMCID: PMC9824086 DOI: 10.3390/plants12010159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 12/21/2022] [Accepted: 12/21/2022] [Indexed: 06/17/2023]
Abstract
Typically, sweet corn, particularly sh2 sweet corn, has low seed vigor owing to its high sugar and low starch content, which is a major problem in sweet corn production, particularly at low temperatures. There is considerable variation in the germination rates among sweet corn varieties under low-temperature conditions, and the underlying mechanisms behind this phenomenon remain unclear. In this study, we screened two inbred sweet corn lines (tolerant line L282 and sensitive line L693) differing in their low-temperature germination rates; while no difference was observed in their germination rates at normal temperatures. To identify the specifically induced genes influencing the germination capacity of sweet corn at low temperatures, a transcriptome analysis of the two lines was conducted at both normal and low temperatures. Compared to the lines at a normal temperature, 3926 and 1404 differently expressed genes (DEGs) were identified from L282 and L693, respectively, under low-temperature conditions. Of them, 830 DEGs were common DEGs (cDEGs) that were identified from both L282 and L693, which were majorly enriched in terms of microtubule-based processes, histone H3-K9 modification, single-organism cellular processes, and carbohydrate metabolic processes. In addition, 3096 special DEGs (sDEGs), with 2199 upregulated and 897 downregulated, were detected in the tolerant line L282, but not in the sensitive line L693. These sDEGs were primarily related to plasma membranes and oxygen-containing compounds. Furthermore, electric conductivity measurements demonstrated that the membrane of L282 experienced less damage, which is consistent with its strong tolerance at low temperatures. These results expand our understanding of the complex mechanisms involved in the cold germination of sweet corn and provide a set of candidate genes for further genetic analysis.
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Affiliation(s)
- Yingni Xiao
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Mei Chen
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Nannan Zheng
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Zhuoyi Xu
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Jie Zhang
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Xinmin Hu
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Li Li
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Riliang Gu
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Xuemei Du
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Jianhua Wang
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
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16
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Dutta P, Roy P, Sengupta N. Effects of External Perturbations on Protein Systems: A Microscopic View. ACS OMEGA 2022; 7:44556-44572. [PMID: 36530249 PMCID: PMC9753117 DOI: 10.1021/acsomega.2c06199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
Protein folding can be viewed as the origami engineering of biology resulting from the long process of evolution. Even decades after its recognition, research efforts worldwide focus on demystifying molecular factors that underlie protein structure-function relationships; this is particularly relevant in the era of proteopathic disease. A complex co-occurrence of different physicochemical factors such as temperature, pressure, solvent, cosolvent, macromolecular crowding, confinement, and mutations that represent realistic biological environments are known to modulate the folding process and protein stability in unique ways. In the current review, we have contextually summarized the substantial efforts in unveiling individual effects of these perturbative factors, with major attention toward bottom-up approaches. Moreover, we briefly present some of the biotechnological applications of the insights derived from these studies over various applications including pharmaceuticals, biofuels, cryopreservation, and novel materials. Finally, we conclude by summarizing the challenges in studying the combined effects of multifactorial perturbations in protein folding and refer to complementary advances in experiment and computational techniques that lend insights to the emergent challenges.
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Affiliation(s)
- Pallab Dutta
- Department
of Biological Sciences, Indian Institute
of Science Education and Research (IISER) Kolkata, Mohanpur741246, India
| | - Priti Roy
- Department
of Biological Sciences, Indian Institute
of Science Education and Research (IISER) Kolkata, Mohanpur741246, India
- Department
of Chemistry, Oklahoma State University, Stillwater, Oklahoma74078, United States
| | - Neelanjana Sengupta
- Department
of Biological Sciences, Indian Institute
of Science Education and Research (IISER) Kolkata, Mohanpur741246, India
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17
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Liu J, Li M, Zuo X. DNA Nanotechnology-Empowered Live Cell Measurements. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2204711. [PMID: 36124715 DOI: 10.1002/smll.202204711] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/30/2022] [Indexed: 06/15/2023]
Abstract
The systematic analysis and precise manipulation of a variety of biomolecules should lead to unprecedented findings in fundamental biology. However, conventional technology cannot meet the current requirements. Despite this, there has been progress as DNA nanotechnology has evolved to generate DNA nanostructures and circuits over the past four decades. Many potential applications of DNA nanotechnology for live cell measurements have begun to emerge owing to the biocompatibility, nanometer addressability, and stimulus responsiveness of DNA. In this review, the DNA nanotechnology-empowered live cell measurements which are currently available are summarized. The stability of the DNA nanostructures, in a cellular microenvironment, which is crucial for accomplishing precise live cell measurements, is first summarized. Thereafter, measurements in the extracellular and intracellular microenvironment, in live cells, are introduced. Finally, the challenges that are innate to, and the further developments that are possible in this nascent field are discussed.
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Affiliation(s)
- Jiangbo Liu
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Min Li
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
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18
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Liu Y, Zheng X, Guan D, Jiang X, Hu G. Heterogeneous Nanostructures Cause Anomalous Diffusion in Lipid Monolayers. ACS NANO 2022; 16:16054-16066. [PMID: 36149751 DOI: 10.1021/acsnano.2c04089] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The diffusion and mobility in biomembranes are crucial for various cell functions; however, the mechanisms involved in such processes remain ambiguous due to the complex membrane structures. Herein, we investigate how the heterogeneous nanostructures cause anomalous diffusion in dipalmitoylphosphatidylcholine (DPPC) monolayers. By identifying the existence of condensed nanodomains and clarifying their impact, our findings renew the understanding of the hydrodynamic description and the statistical feature of the diffusion in the monolayers. We find a universal characteristic of the multistage mean square displacement (MSD) with an intermediate crossover, signifying two membrane viscosities at different scales: the short-time scale describes the local fluidity and is independent of the nominal DPPC density, and the long-time scale represents the global continuous phase taking into account nanodomains and increases with DPPC density. The constant short-time viscosity reflects a dynamic equilibrium between the continuous fluid phase and the condensed nanodomains in the molecular scale. Notably, we observe an "anomalous yet Brownian" phenomenon exhibiting an unusual double-peaked displacement probability distribution (DPD), which is attributed to the net dipolar repulsive force from the heterogeneous nanodomains around the microdomains. The findings provide physical insights into the transport of membrane inclusions that underpin various biological functions and drug deliveries.
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Affiliation(s)
- Yang Liu
- State Key Laboratory of Nonlinear Mechanics (LNM), Beijing Key Laboratory of Engineered Construction and Mechanobiology, Institute of Mechanics, Chinese Academy of Sciences, Beijing 100190, People's Republic of China
- Frontier Scientific Research Centre for Fluidized Mining of Deep Underground Resources, China University of Mining & Technology, Xuzhou 221116, People's Republic of China
| | - Xu Zheng
- State Key Laboratory of Nonlinear Mechanics (LNM), Beijing Key Laboratory of Engineered Construction and Mechanobiology, Institute of Mechanics, Chinese Academy of Sciences, Beijing 100190, People's Republic of China
| | - Dongshi Guan
- State Key Laboratory of Nonlinear Mechanics (LNM), Beijing Key Laboratory of Engineered Construction and Mechanobiology, Institute of Mechanics, Chinese Academy of Sciences, Beijing 100190, People's Republic of China
| | - Xikai Jiang
- State Key Laboratory of Nonlinear Mechanics (LNM), Beijing Key Laboratory of Engineered Construction and Mechanobiology, Institute of Mechanics, Chinese Academy of Sciences, Beijing 100190, People's Republic of China
| | - Guoqing Hu
- Department of Engineering Mechanics, State Key Laboratory of Fluid Power and Mechatronic Systems, Zhejiang University, Hangzhou 310027, People's Republic of China
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19
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Samakovli D, Roka L, Plitsi PK, Drakakaki G, Haralampidis K, Stravopodis DJ, Hatzopoulos P, Milioni D. BRI1 and BAK1 Canonical Distribution in Plasma Membrane Is HSP90 Dependent. Cells 2022; 11:3341. [PMID: 36359737 PMCID: PMC9656807 DOI: 10.3390/cells11213341] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 10/16/2022] [Accepted: 10/18/2022] [Indexed: 10/22/2023] Open
Abstract
The activation of BRASSINOSTEROID INSENSITIVE1 (BRI1) and its association with the BRI1 ASSOCIATED RECEPTOR KINASE1 (BAK1) are key steps for the initiation of the BR signaling cascade mediating hypocotyl elongation. Heat shock protein 90 (HSP90) is crucial in the regulation of signaling processes and the activation of hormonal receptors. We report that HSP90 is required for the maintenance of the BRI1 receptor at the plasma membrane (PM) and its association with the BAK1 co-receptor during BL-ligand stimulation. HSP90 mediates BR perception and signal transduction through physical interactions with BRI1 and BAK1, while chaperone depletion resulted in lower levels of BRI1 and BAK1 receptors at the PM and affected the spatial partitioning and organization of BRI1/BAK1 heterocomplexes at the PM. The BRI1/BAK1 interaction relies on the HSP90-dependent activation of the kinase domain of BRI1 which leads to the confinement of the spatial dynamics of the membrane resident BRI1 and the attenuation of the downstream signaling. This is evident by the impaired activation and transcriptional activity of BRI1 EMS SUPPRESSOR 1 (BES1) upon HSP90 depletion. Our findings provide conclusive evidence that further expands the commitment of HSP90 in BR signaling through the HSP90-mediated activation of BRI1 in the control of the BR signaling cascade in plants.
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Affiliation(s)
- Despina Samakovli
- Biotechnology Department, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
| | - Loukia Roka
- Biotechnology Department, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
| | | | - Georgia Drakakaki
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Kosmas Haralampidis
- Biology Department, National and Kapodistrian University of Athens, 15701 Athens, Greece
| | | | - Polydefkis Hatzopoulos
- Biotechnology Department, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
| | - Dimitra Milioni
- Biotechnology Department, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
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20
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Canales Coutiño B, Mayor R. Neural crest mechanosensors: Seeing old proteins in a new light. Dev Cell 2022; 57:1792-1801. [PMID: 35901790 DOI: 10.1016/j.devcel.2022.07.005] [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: 03/31/2022] [Revised: 05/26/2022] [Accepted: 07/05/2022] [Indexed: 11/25/2022]
Abstract
Mechanical forces exerted on neural crest cells control their collective migration and differentiation. This perspective discusses our current understanding of neural crest mechanotransduction during cell migration and differentiation. Additionally, we describe proteins that have mechanosensitive functions in other systems, such as mechanosensitive G-protein-coupled receptors, mechanosensitive ion channels, cell-cell adhesion, and cell-matrix-interacting proteins, and highlight that these same proteins have in the past been studied in neural crest development from a purely signaling point of view. We propose that future studies elucidate the mechanosensitive functions these receptors may play in neural crest development and integrate this with their known molecular role.
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Affiliation(s)
- Brenda Canales Coutiño
- Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Roberto Mayor
- Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, UK.
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21
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Zhao H, Li N, Ma C, Wei Z, Zeng Q, Zhang K, Zhao N, Tang BZ. An AIE probe for long-term plasma membrane imaging and membrane-targeted photodynamic therapy. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.07.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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22
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Multiscale Dynamics of Lipid Vesicles in Polymeric Microenvironment. MEMBRANES 2022; 12:membranes12070640. [PMID: 35877843 PMCID: PMC9318666 DOI: 10.3390/membranes12070640] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/15/2022] [Accepted: 06/18/2022] [Indexed: 02/06/2023]
Abstract
Understanding dynamic and complex interaction of biological membranes with extracellular matrices plays a crucial role in controlling a variety of cell behavior and functions, from cell adhesion and growth to signaling and differentiation. Tremendous interest in tissue engineering has made it possible to design polymeric scaffolds mimicking the topology and mechanical properties of the native extracellular microenvironment; however, a fundamental question remains unanswered: that is, how the viscoelastic extracellular environment modifies the hierarchical dynamics of lipid membranes. In this work, we used aqueous solutions of poly(ethylene glycol) (PEG) with different molecular weights to mimic the viscous medium of cells and nearly monodisperse unilamellar DMPC/DMPG liposomes as a membrane model. Using small-angle X-ray scattering (SAXS), dynamic light scattering, temperature-modulated differential scanning calorimetry, bulk rheology, and fluorescence lifetime spectroscopy, we investigated the structural phase map and multiscale dynamics of the liposome–polymer mixtures. The results suggest an unprecedented dynamic coupling between polymer chains and phospholipid bilayers at different length/time scales. The microviscosity of the lipid bilayers is directly influenced by the relaxation of the whole chain, resulting in accelerated dynamics of lipids within the bilayers in the case of short chains compared to the polymer-free liposome case. At the macroscopic level, the gel-to-fluid transition of the bilayers results in a remarkable thermal-stiffening behavior of polymer–liposome solutions that can be modified by the concentration of the liposomes and the polymer chain length.
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23
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Li T, Li J, Wang H, Zhao J, Yan M, He H, Yu S. Exosomes: Potential Biomarkers and Functions in Head and Neck Squamous Cell Carcinoma. Front Mol Biosci 2022; 9:881794. [PMID: 35775082 PMCID: PMC9237451 DOI: 10.3389/fmolb.2022.881794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 05/30/2022] [Indexed: 12/24/2022] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC), originating from the mucosal epithelial cells of the oral cavity, pharynx, and larynx, is a lethal malignancy of the head and neck. Patients with advanced and recurrent HNSCC have poor outcomes due to limited therapeutic options. Exosomes have active roles in the pathophysiology of tumors and are suggested as a potential therapeutic target of HNSCC. Exosomes in HNSCC have been intensively studied for disease activity, tumor staging, immunosuppression, and therapeutic monitoring. In this review, the biological mechanisms and the recent clinical application of exosomes are highlighted to reveal the potential of exosomes as biomarkers and therapeutic targets for HNSCC.
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Affiliation(s)
- Ting Li
- Department of Head and Neck Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Juan Li
- Department of Pathology, Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Haitao Wang
- Thoracic Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Jiayu Zhao
- Department of Head and Neck Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Mingze Yan
- Department of Head and Neck Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Hongjiang He
- Department of Head and Neck Surgery, Harbin Medical University Cancer Hospital, Harbin, China
- *Correspondence: Hongjiang He, ; Shan Yu,
| | - Shan Yu
- Department of Pathology, Second Affiliated Hospital of Harbin Medical University, Harbin, China
- *Correspondence: Hongjiang He, ; Shan Yu,
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24
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Dadhich R, Kapoor S. Lipidomic and Membrane Mechanical Signatures in Triple-Negative Breast Cancer: Scope for Membrane-Based Theranostics. Mol Cell Biochem 2022; 477:2507-2528. [PMID: 35595957 DOI: 10.1007/s11010-022-04459-4] [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: 09/28/2021] [Accepted: 04/28/2022] [Indexed: 10/18/2022]
Abstract
Triple-negative breast cancer (TNBC) is a highly aggressive form of breast cancer associated with poor prognosis, higher grade, and a high rate of metastatic occurrence. Limited therapeutic interventions and the compounding issue of drug resistance in triple-negative breast cancer warrants the discovery of novel therapeutic targets and diagnostic modules. To this view, in addition to proteins, lipids also regulate cellular functions via the formation of membranes that modulate membrane protein function, diffusion, and their localization; thus, orchestrating signaling hot spots enriched in specific lipids/proteins on cell membranes. Lipid deregulation in cancer leads to reprogramming of the membrane dynamics and functions impacting cell proliferation, metabolism, and metastasis, providing exciting starting points for developing lipid-based approaches for treating TNBC. In this review, we provide a detailed account of specific lipidic changes in breast cancer, link the altered lipidome with membrane structure and mechanical properties, and describe how these are linked to subsequent downstream functions implicit in cancer progression, metastasis, and chemoresistance. At the fundamental level, we discuss how the lipid-centric findings in TNBC are providing cues for developing lipid-inspired theranostic strategies while bridging existing gaps in our understanding of the functional involvement of lipid membranes in cancer.
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Affiliation(s)
- Ruchika Dadhich
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, 400076, India
| | - Shobhna Kapoor
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, 400076, India. .,Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, 739-8528, Japan.
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25
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Abstract
Lipid-DNA conjugates have emerged as highly useful tools to modify the cell membranes. These conjugates generally consist of a lipid anchor for membrane modification and a functional DNA nanostructure for membrane analysis or regulation. There are several unique properties of these lipid-DNA conjugates, especially including their programmability, fast and efficient membrane insertion, and precise sequence-specific assembly. These unique properties have enabled a broad range of biophysical applications on live cell membranes. In this review, we will mainly focus on recent tremendous progress, especially during the past three years, in regulating the biophysical features of these lipid-DNA conjugates and their key applications in studying cell membrane biophysics. Some insights into the current challenges and future directions of this interdisciplinary field have also been provided.
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Insights into Membrane Curvature Sensing and Membrane Remodeling by Intrinsically Disordered Proteins and Protein Regions. J Membr Biol 2022; 255:237-259. [PMID: 35451616 PMCID: PMC9028910 DOI: 10.1007/s00232-022-00237-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 03/29/2022] [Indexed: 12/15/2022]
Abstract
Cellular membranes are highly dynamic in shape. They can rapidly and precisely regulate their shape to perform various cellular functions. The protein’s ability to sense membrane curvature is essential in various biological events such as cell signaling and membrane trafficking. As they are bound, these curvature-sensing proteins may also change the local membrane shape by one or more curvature driving mechanisms. Established curvature-sensing/driving mechanisms rely on proteins with specific structural features such as amphipathic helices and intrinsically curved shapes. However, the recent discovery and characterization of many proteins have shattered the protein structure–function paradigm, believing that the protein functions require a unique structural feature. Typically, such structure-independent functions are carried either entirely by intrinsically disordered proteins or hybrid proteins containing disordered regions and structured domains. It is becoming more apparent that disordered proteins and regions can be potent sensors/inducers of membrane curvatures. In this article, we outline the basic features of disordered proteins and regions, the motifs in such proteins that encode the function, membrane remodeling by disordered proteins and regions, and assays that may be employed to investigate curvature sensing and generation by ordered/disordered proteins.
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27
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Lanphere C, Ciccone J, Dorey A, Hagleitner-Ertuğrul N, Knyazev D, Haider S, Howorka S. Triggered Assembly of a DNA-Based Membrane Channel. J Am Chem Soc 2022; 144:4333-4344. [PMID: 35253434 PMCID: PMC8931747 DOI: 10.1021/jacs.1c06598] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Indexed: 01/01/2023]
Abstract
Chemistry is in a powerful position to synthetically replicate biomolecular structures. Adding functional complexity is key to increase the biomimetics' value for science and technology yet is difficult to achieve with poorly controlled building materials. Here, we use defined DNA blocks to rationally design a triggerable synthetic nanopore that integrates multiple functions of biological membrane proteins. Soluble triggers bind via molecular recognition to the nanopore components changing their structure and membrane position, which controls the assembly into a defined channel for efficient transmembrane cargo transport. Using ensemble, single-molecule, and simulation analysis, our activatable pore provides insight into the kinetics and structural dynamics of DNA assembly at the membrane interface. The triggered channel advances functional DNA nanotechnology and synthetic biology and will guide the design of controlled nanodevices for sensing, cell biological research, and drug delivery.
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Affiliation(s)
- Conor Lanphere
- Department
of Chemistry, Institute of Structural Molecular Biology, University College London, London WC1H 0AJ, United Kingdom
| | - Jonah Ciccone
- Department
of Chemistry, Institute of Structural Molecular Biology, University College London, London WC1H 0AJ, United Kingdom
| | - Adam Dorey
- Department
of Chemistry, Institute of Structural Molecular Biology, University College London, London WC1H 0AJ, United Kingdom
| | | | - Denis Knyazev
- Institute
of Applied Experimental Biophysics, Johannes
Kepler University, 4040 Linz, Austria
| | - Shozeb Haider
- Department
of Pharmaceutical and Biological Chemistry, University College London School of Pharmacy, London WC1N 1AX, United Kingdom
| | - Stefan Howorka
- Department
of Chemistry, Institute of Structural Molecular Biology, University College London, London WC1H 0AJ, United Kingdom
- Institute
of Applied Experimental Biophysics, Johannes
Kepler University, 4040 Linz, Austria
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28
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Sotolongo Bellón J, Birkholz O, Richter CP, Eull F, Kenneweg H, Wilmes S, Rothbauer U, You C, Walter MR, Kurre R, Piehler J. Four-color single-molecule imaging with engineered tags resolves the molecular architecture of signaling complexes in the plasma membrane. CELL REPORTS METHODS 2022; 2:100165. [PMID: 35474965 PMCID: PMC9017138 DOI: 10.1016/j.crmeth.2022.100165] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 11/19/2021] [Accepted: 01/13/2022] [Indexed: 12/22/2022]
Abstract
Localization and tracking of individual receptors by single-molecule imaging opens unique possibilities to unravel the assembly and dynamics of signaling complexes in the plasma membrane. We present a comprehensive workflow for imaging and analyzing receptor diffusion and interaction in live cells at single molecule level with up to four colors. Two engineered, monomeric GFP variants, which are orthogonally recognized by anti-GFP nanobodies, are employed for efficient and selective labeling of target proteins in the plasma membrane with photostable fluorescence dyes. This labeling technique enables us to quantitatively resolve the stoichiometry and dynamics of the interferon-γ (IFNγ) receptor signaling complex in the plasma membrane of living cells by multicolor single-molecule imaging. Based on versatile spatial and spatiotemporal correlation analyses, we identify ligand-induced receptor homo- and heterodimerization. Multicolor single-molecule co-tracking and quantitative single-molecule Förster resonance energy transfer moreover reveals transient assembly of IFNγ receptor heterotetramers and confirms its structural architecture.
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Affiliation(s)
- Junel Sotolongo Bellón
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, Osnabrück, Germany
| | - Oliver Birkholz
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, Osnabrück, Germany
| | - Christian P. Richter
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, Osnabrück, Germany
| | - Florian Eull
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, Osnabrück, Germany
| | - Hella Kenneweg
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, Osnabrück, Germany
| | - Stephan Wilmes
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, Osnabrück, Germany
- Division of Cell Signalling and Immunology, University of Dundee, School of Life Sciences, Dundee, UK
| | - Ulrich Rothbauer
- Pharmaceutical Biotechnology, Eberhard-Karls-University, Tübingen, Germany
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Changjiang You
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, Osnabrück, Germany
| | - Mark R. Walter
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Rainer Kurre
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, Osnabrück, Germany
| | - Jacob Piehler
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, Osnabrück, Germany
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Asymmetrical DNA Engineering of Cell Membrane via Membrane Fusion. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2022. [DOI: 10.1016/j.cjac.2022.100053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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30
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DNA-Based Molecular Engineering of the Cell Membrane. MEMBRANES 2022; 12:membranes12020111. [PMID: 35207033 PMCID: PMC8876765 DOI: 10.3390/membranes12020111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 12/28/2021] [Accepted: 12/29/2021] [Indexed: 01/27/2023]
Abstract
The cell membrane serves as a barrier and gatekeeper to regulate the cellular transportation of substances and information. It plays a significant role in protecting the cell from the extracellular environment, maintaining intracellular homeostasis, and regulating cellular function and behaviors. The capability to engineer the cell membrane with functional modules that enable dynamic monitoring and manipulating the cell-surface microenvironment would be critical for studying molecular mechanisms underlying various biological processes. To meet this goal, DNA, with intrinsic advantages of high versatility, programmability, and biocompatibility, has gained intense attention as a molecular tool for cell-surface engineering. The past three decades have witnessed the rapid advances of diverse nucleic acid materials, including functional nucleic acids (FNAs), dynamic DNA circuits, and exquisite DNA nanostructures. In this mini review, we have summarized the recent progress of DNA technology for cell membrane engineering, particularly focused on their applications for molecular sensing and imaging, precise cell identification, receptor activity regulation, and artificial membrane structures. Furthermore, we discussed the challenge and outlook on using nucleic acid materials in this specific research area.
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31
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Lin M, Chen Y, Zhao S, Tang R, Nie Z, Xing H. A Biomimetic Approach for Spatially Controlled Cell Membrane Engineering Using Fusogenic Spherical Nucleic Acid. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202111647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Minjie Lin
- Institute of Chemical Biology and Nanomedicine State Key Laboratory of Chemo/Biosensing and Chemometrics Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology College of Chemistry and Chemical Engineering Hunan University Changsha 410082 China
| | - Yuanyuan Chen
- Institute of Chemical Biology and Nanomedicine State Key Laboratory of Chemo/Biosensing and Chemometrics Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology College of Chemistry and Chemical Engineering Hunan University Changsha 410082 China
| | - Sisi Zhao
- Institute of Chemical Biology and Nanomedicine College of Biology Hunan University Changsha 410082 China
| | - Rui Tang
- Institute of Chemical Biology and Nanomedicine State Key Laboratory of Chemo/Biosensing and Chemometrics Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology College of Chemistry and Chemical Engineering Hunan University Changsha 410082 China
| | - Zhou Nie
- Institute of Chemical Biology and Nanomedicine State Key Laboratory of Chemo/Biosensing and Chemometrics Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology College of Chemistry and Chemical Engineering Hunan University Changsha 410082 China
| | - Hang Xing
- Institute of Chemical Biology and Nanomedicine State Key Laboratory of Chemo/Biosensing and Chemometrics Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology College of Chemistry and Chemical Engineering Hunan University Changsha 410082 China
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32
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Bar-Sinai S, Belausov E, Dwivedi V, Sadot E. Collisions of Cortical Microtubules with Membrane Associated Myosin VIII Tail. Cells 2022; 11:cells11010145. [PMID: 35011707 PMCID: PMC8750215 DOI: 10.3390/cells11010145] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 12/26/2021] [Accepted: 12/29/2021] [Indexed: 02/04/2023] Open
Abstract
The distribution of myosin VIII ATM1 tail in association with the plasma membrane is often observed in coordination with that of cortical microtubules (MTs). The prevailing hypothesis is that coordination between the organization of cortical MTs and proteins in the membrane results from the inhibition of free lateral diffusion of the proteins by barriers formed by MTs. Since the positioning of myosin VIII tail in the membrane is relatively stable, we ask: can it affect the organization of MTs? Myosin VIII ATM1 tail co-localized with remorin 6.6, the position of which in the plasma membrane is also relatively stable. Overexpression of myosin VIII ATM1 tail led to a larger fraction of MTs with a lower rate of orientation dispersion. In addition, collisions between MTs and cortical structures labeled by ATM1 tail or remorin 6.6 were observed. Collisions between EB1 labeled MTs and ATM1 tail clusters led to four possible outcomes: 1—Passage of MTs through the cluster; 2—Decreased elongation rate; 3—Disengagement from the membrane followed by a change in direction; and 4—retraction. EB1 tracks became straighter in the presence of ATM1 tail. Taken together, collisions of MTs with ATM1 tail labeled structures can contribute to their coordinated organization.
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33
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Palmere RD, Case DA, Nieuwkoop AJ. Simulations of Kindlin-2 PIP binding domains reveal protonation-dependent membrane binding modes. Biophys J 2021; 120:5504-5512. [PMID: 34813727 DOI: 10.1016/j.bpj.2021.11.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 09/15/2021] [Accepted: 11/17/2021] [Indexed: 11/19/2022] Open
Abstract
Kindlin-2, a member of the Kindlin family of peripheral membrane proteins, is important for integrin activation and stabilization of epidermal growth factor receptor. It associates with the cytoplasmic face of the plasma membrane via dedicated phosphatidylinositol phosphate binding domains located in the N-terminal F0 and Pleckstrin Homology domains. These domains have binding affinity for phosphatidylinositol 4,5-bisphosphate and, to a greater degree, phosphatidylinositol 3,4,5-trisphosphate. The biological significance of the differential binding of these phosphatidylinositol phosphates to Kindlin-2 and the mechanism by which they activate Kindlin-2 are not well understood. Recently, ssNMR identified the predominant protonation states of phosphatidylinositol 4,5-bisphosphate and phosphatidylinositol 3,4,5-trisphosphate near physiological pH in the presence of anionic lipids. Here, we perform atomistic simulation of the bound state of the Pleckstrin Homology and F0 domains of Kindlin-2 at membranes containing phosphatidylinositol 4,5-bisphosphate/phosphatidylinositol 3,4,5-trisphosphate with differing protonation states. This computational approach demonstrates that these two phosphatidylinositol phosphates differently modulate Kindlin-2 subdomain binding in a protonation-state-dependent manner. We speculate these variations in binding mode provide a mechanism for intracellular pH and Ca2+ influx to control the membrane binding behavior and activity of Kindlin-2.
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Affiliation(s)
- Robert D Palmere
- Department of Chemistry and Chemical Biology, School of Arts and Sciences, Rutgers University, Piscataway, New Jersey
| | - David A Case
- Department of Chemistry and Chemical Biology, School of Arts and Sciences, Rutgers University, Piscataway, New Jersey
| | - Andrew J Nieuwkoop
- Department of Chemistry and Chemical Biology, School of Arts and Sciences, Rutgers University, Piscataway, New Jersey.
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34
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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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35
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Pathak BK, Dey S, Mozumder S, Sengupta J. The role of membranes in function and dysfunction of intrinsically disordered amyloidogenic proteins. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2021; 128:397-434. [PMID: 35034725 DOI: 10.1016/bs.apcsb.2021.08.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Membrane-protein interactions play a major role in human physiology as well as in diseases pathology. Interaction of a protein with the membrane was previously thought to be dependent on well-defined three-dimensional structure of the protein. In recent decades, however, it has become evident that a large fraction of the proteome, particularly in eukaryotes, stays disordered in solution and these proteins are termed as intrinsically disordered proteins (IDPs). Also, a vast majority of human proteomes have been reported to contain substantially long disordered regions, called intrinsically disordered regions (IDRs), in addition to the structurally ordered regions. IDPs exist in an ensemble of conformations and the conformational flexibility enables IDPs to achieve functional diversity. IDPs (and IDRs) are found to be important players in cell signaling, where biological membranes act as anchors for signaling cascades. Therefore, IDPs modulate the membrane architectures, at the same time membrane composition also affects the binding of IDPs. Because of intrinsic disorders, misfolding of IDPs often leads to formation of oligomers, protofibrils and mature fibrils through progressive self-association. Accumulation of amyloid-like aggregates of some of the IDPs is a known causative agent for numerous diseases. In this chapter we highlight recent advances in understanding membrane interactions of some of the intrinsically disordered proteins involved in the pathogenesis of human diseases.
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Affiliation(s)
- Bani Kumar Pathak
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Jadavpur, Kolkata, India
| | - Sandip Dey
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Jadavpur, Kolkata, India
| | - Sukanya Mozumder
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Jadavpur, Kolkata, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Jayati Sengupta
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Jadavpur, Kolkata, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.
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36
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Lin M, Chen Y, Zhao S, Tang R, Nie Z, Xing H. A Biomimetic Approach for Spatially Controlled Cell Membrane Engineering Using Fusogenic Spherical Nucleic Acid. Angew Chem Int Ed Engl 2021; 61:e202111647. [PMID: 34637590 DOI: 10.1002/anie.202111647] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Indexed: 11/06/2022]
Abstract
Engineering of the cell plasma membrane using functional DNA is important for studying and controlling cellular behaviors. However, most efforts to apply artificial DNA interactions on cells are limited to external membrane surface due to the lack of suitable synthetic tools to engineer the intracellular side, which impedes many applications in cell biology. Inspired by the natural extracellular vesicle-cell fusion process, we have developed a fusogenic spherical nucleic acid construct to realize robust DNA functionalization on both external and internal cell surfaces via liposome fusion-based transport (LiFT) strategy, which enables applications including the construction of heterotypic cell assembly for programmed signaling pathway and detection of intracellular metabolites. This approach can engineer cell membranes in a highly efficient and spatially controlled manner, allowing one to build anisotropic membrane structures with two orthogonal DNA functionalities.
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Affiliation(s)
- Minjie Lin
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Yuanyuan Chen
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Sisi Zhao
- Institute of Chemical Biology and Nanomedicine, College of Biology, Hunan University, Changsha, 410082, China
| | - Rui Tang
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Zhou Nie
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
| | - Hang Xing
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China
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37
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Huang J, Co HKC, Lee Y, Wu C, Chen S. Multistability maintains redox homeostasis in human cells. Mol Syst Biol 2021; 17:e10480. [PMID: 34612597 PMCID: PMC8493564 DOI: 10.15252/msb.202110480] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 09/11/2021] [Accepted: 09/14/2021] [Indexed: 01/22/2023] Open
Abstract
Cells metabolize nutrients through a complex metabolic and signaling network that governs redox homeostasis. At the core of this, redox regulatory network is a mutually inhibitory relationship between reduced glutathione and reactive oxygen species (ROS)-two opposing metabolites that are linked to upstream nutrient metabolic pathways (glucose, cysteine, and glutamine) and downstream feedback loops of signaling pathways (calcium and NADPH oxidase). We developed a nutrient-redox model of human cells to understand system-level properties of this network. Combining in silico modeling and ROS measurements in individual cells, we show that ROS dynamics follow a switch-like, all-or-none response upon glucose deprivation at a threshold that is approximately two orders of magnitude lower than its physiological concentration. We also confirm that this ROS switch can be irreversible and exhibits hysteresis, a hallmark of bistability. Our findings evidence that bistability modulates redox homeostasis in human cells and provide a general framework for quantitative investigations of redox regulation in humans.
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Affiliation(s)
- Jo‐Hsi Huang
- Department of Chemical and Systems BiologyStanford University School of MedicineStanfordCAUSA
| | - Hannah KC Co
- Institute of Molecular BiologyAcademia SinicaTaipeiTaiwan
- Molecular and Cell BiologyTaiwan International Graduate ProgramAcademia Sinica and Graduate Institute of Life ScienceNational Defense Medical CenterTaipeiTaiwan
| | - Yi‐Chen Lee
- Institute of Molecular BiologyAcademia SinicaTaipeiTaiwan
| | - Chia‐Chou Wu
- Institute of Molecular BiologyAcademia SinicaTaipeiTaiwan
| | - Sheng‐hong Chen
- Institute of Molecular BiologyAcademia SinicaTaipeiTaiwan
- Molecular and Cell BiologyTaiwan International Graduate ProgramAcademia Sinica and Graduate Institute of Life ScienceNational Defense Medical CenterTaipeiTaiwan
- Genome and Systems Biology Degree ProgramAcademia Sinica and National Taiwan UniversityTaipeiTaiwan
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38
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Császár N, Bókkon I. Gut serotonin as a general membrane permeability regulator. Curr Neuropharmacol 2021; 20:269-271. [PMID: 34548000 PMCID: PMC9413787 DOI: 10.2174/1570159x19666210921100542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/15/2021] [Accepted: 08/15/2021] [Indexed: 11/26/2022] Open
Affiliation(s)
- Császár N
- Psychosomatic Outpatient Clinics, Budapest. Hungary
| | - Bókkon I
- Psychosomatic Outpatient Clinics, Budapest. Hungary
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39
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Reinkemeier CD, Lemke EA. Dual film-like organelles enable spatial separation of orthogonal eukaryotic translation. Cell 2021; 184:4886-4903.e21. [PMID: 34433013 PMCID: PMC8480389 DOI: 10.1016/j.cell.2021.08.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 05/03/2021] [Accepted: 08/02/2021] [Indexed: 11/18/2022]
Abstract
Engineering new functionality into living eukaryotic systems by enzyme evolution or de novo protein design is a formidable challenge. Cells do not rely exclusively on DNA-based evolution to generate new functionality but often utilize membrane encapsulation or formation of membraneless organelles to separate distinct molecular processes that execute complex operations. Applying this principle and the concept of two-dimensional phase separation, we develop film-like synthetic organelles that support protein translation on the surfaces of various cellular membranes. These sub-resolution synthetic films provide a path to make functionally distinct enzymes within the same cell. We use these film-like organelles to equip eukaryotic cells with dual orthogonal expanded genetic codes that enable the specific reprogramming of distinct translational machineries with single-residue precision. The ability to spatially tune the output of translation within tens of nanometers is not only important for synthetic biology but has implications for understanding the function of membrane-associated protein condensation in cells. 2D phase separation was utilized to design orthogonal enzymes Film-like organelles maintained distinct suppressor tRNA microenvironments Dual film-like synthetic organelles enabled orthogonal translation in eukaryotes Cells were equipped with two expanded genetic codes in addition to the canonical one
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Affiliation(s)
- Christopher D Reinkemeier
- Biocentre, Departments of Biology and Chemistry, Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128 Mainz, Germany; Institute of Molecular Biology gGmbH, Ackermannweg 4, 55128 Mainz, Germany; Structural and Computational Biology Unit and Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Edward A Lemke
- Biocentre, Departments of Biology and Chemistry, Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128 Mainz, Germany; Institute of Molecular Biology gGmbH, Ackermannweg 4, 55128 Mainz, Germany; Structural and Computational Biology Unit and Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
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40
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Smith P, Lorenz CD. LiPyphilic: A Python Toolkit for the Analysis of Lipid Membrane Simulations. J Chem Theory Comput 2021; 17:5907-5919. [PMID: 34450002 DOI: 10.1021/acs.jctc.1c00447] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular dynamics simulations are now widely used to study emergent phenomena in lipid membranes with complex compositions. Here, we present LiPyphilic-a fast, fully tested, and easy-to-install Python package for analyzing such simulations. Analysis tools in LiPyphilic include the identification of cholesterol flip-flop events, the classification of local lipid environments, and the degree of interleaflet registration. LiPyphilic is both force field- and resolution-agnostic, and by using the powerful atom selection language of MDAnalysis, it can handle membranes with highly complex compositions. LiPyphilic also offers two on-the-fly trajectory transformations to (i) fix membranes split across periodic boundaries and (ii) perform nojump coordinate unwrapping. Our implementation of nojump unwrapping accounts for fluctuations in the box volume under the NPT ensemble-an issue that most current implementations have overlooked. The full documentation of LiPyphilic, including installation instructions and links to interactive online tutorials, is available at https://lipyphilic.readthedocs.io/en/latest.
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Affiliation(s)
- Paul Smith
- Department of Physics, King's College London, London WC2R 2LS, U.K
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41
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Optimal ligand discrimination by asymmetric dimerization and turnover of interferon receptors. Proc Natl Acad Sci U S A 2021; 118:2103939118. [PMID: 34507994 DOI: 10.1073/pnas.2103939118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/11/2021] [Indexed: 11/18/2022] Open
Abstract
In multicellular organisms, antiviral defense mechanisms evoke a reliable collective immune response despite the noisy nature of biochemical communication between tissue cells. A molecular hub of this response, the interferon I receptor (IFNAR), discriminates between ligand types by their affinity regardless of concentration. To understand how ligand type can be decoded robustly by a single receptor, we frame ligand discrimination as an information-theoretic problem and systematically compare the major classes of receptor architectures: allosteric, homodimerizing, and heterodimerizing. We demonstrate that asymmetric heterodimers achieve the best discrimination power over the entire physiological range of local ligand concentrations. This design enables sensing of ligand presence and type, and it buffers against moderate concentration fluctuations. In addition, receptor turnover, which drives the receptor system out of thermodynamic equilibrium, allows alignment of activation points for ligands of different affinities and thereby makes ligand discrimination practically independent of concentration. IFNAR exhibits this optimal architecture, and our findings thus suggest that this specialized receptor can robustly decode digital messages carried by its different ligands.
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42
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Habif M, Corbat AA, Silberberg M, Grecco HE. CASPAM: A Triple-Modality Biosensor for Multiplexed Imaging of Caspase Network Activity. ACS Sens 2021; 6:2642-2653. [PMID: 34191492 DOI: 10.1021/acssensors.1c00554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Understanding signal propagation across biological networks requires to simultaneously monitor the dynamics of several nodes to uncover correlations masked by inherent intercellular variability. To monitor the enzymatic activity of more than two components over short time scales has proven challenging. Exploiting the narrow spectral width of homo-FRET-based biosensors, up to three activities can be imaged through fluorescence polarization anisotropy microscopy. We introduce Caspase Activity Sensor by Polarization Anisotropy Multiplexing (CASPAM) a single-plasmid triple-modality reporter of key nodes of the apoptotic network. Apoptosis provides an ideal molecular framework to study interactions between its three composing pathways (intrinsic, extrinsic, and effector). We characterized the biosensor performance and demonstrated the advantages that equimolar expression has in both simplifying experimental procedure and reducing observable variation, thus enabling robust data-driven modeling. Tools like CASPAM become essential to analyze molecular pathways where multiple nodes need to be simultaneously monitored.
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Affiliation(s)
- Martín Habif
- Department of Physics, FCEN, University of Buenos Aires and IFIBA, CONICET, Buenos Aires C1428EHA, Argentina
| | - Agustín A. Corbat
- Department of Physics, FCEN, University of Buenos Aires and IFIBA, CONICET, Buenos Aires C1428EHA, Argentina
| | - Mauro Silberberg
- Department of Physics, FCEN, University of Buenos Aires and IFIBA, CONICET, Buenos Aires C1428EHA, Argentina
| | - Hernán E. Grecco
- Department of Physics, FCEN, University of Buenos Aires and IFIBA, CONICET, Buenos Aires C1428EHA, Argentina
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund 44227, Germany
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43
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Savenko M, Rivel T, Yesylevskyy S, Ramseyer C. Influence of Substrate Hydrophilicity on Structural Properties of Supported Lipid Systems on Graphene, Graphene Oxides, and Silica. J Phys Chem B 2021; 125:8060-8074. [PMID: 34284579 DOI: 10.1021/acs.jpcb.1c04615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pristine graphene, a range of graphene oxides, and silica substrates were used to investigate the effect of surface hydrophilicity on supported lipid bilayers by means of all-atom molecular dynamics simulations. Supported 1,2-dioleoyl-sn-glycero-3-phosphocholine lipid bilayers were found in close-contact conformations with hydrophilic substrates with as low as 5% oxidation level, while self-assembled monolayers occur on pure hydrophobic graphene only. Lipids and water at the surface undergo large redistribution to maintain the stability of the supported bilayers. Deposition of bicelles on increasingly hydrophilic substrates shows the continuous process of reshaping of the supported system and makes intermediate stages between self-assembled monolayers and supported bilayers. The bilayer thickness changes with hydrophilicity in a complex manner, while the number of water molecules per lipid in the hydration layer increases together with hydrophilicity.
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Affiliation(s)
- Mariia Savenko
- Laboratoire Chrono Environnement UMR CNRS 6249, Université de Bourgogne Franche-Comté, 16 route de Gray, 25030 Besançon Cedex, France
| | - Timothée Rivel
- Laboratoire Chrono Environnement UMR CNRS 6249, Université de Bourgogne Franche-Comté, 16 route de Gray, 25030 Besançon Cedex, France.,CEITEC - Central European Institute of Technology, Masaryk University, Kamenice, CZ-62500 Brno, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice, CZ-62500 Brno, Czech Republic
| | - Semen Yesylevskyy
- Laboratoire Chrono Environnement UMR CNRS 6249, Université de Bourgogne Franche-Comté, 16 route de Gray, 25030 Besançon Cedex, France.,Department of Physics of Biological Systems, Institute of Physics of the National Academy of Sciences of Ukraine, Prospect Nauky 46, 03028 Kyiv, Ukraine
| | - Christophe Ramseyer
- Laboratoire Chrono Environnement UMR CNRS 6249, Université de Bourgogne Franche-Comté, 16 route de Gray, 25030 Besançon Cedex, France
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44
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Natwick DE, Collins SR. Optimized iLID Membrane Anchors for Local Optogenetic Protein Recruitment. ACS Synth Biol 2021; 10:1009-1023. [PMID: 33843200 DOI: 10.1021/acssynbio.0c00511] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Optogenetic protein dimerization systems are powerful tools to investigate the biochemical networks that cells use to make decisions and coordinate their activities. These tools, including the improved Light-Inducible Dimer (iLID) system, offer the ability to selectively recruit components to subcellular locations, such as micron-scale regions of the plasma membrane. In this way, the role of individual proteins within signaling networks can be examined with high spatiotemporal resolution. Currently, consistent recruitment is limited by heterogeneous optogenetic component expression, and spatial precision is diminished by protein diffusion, especially over long time scales. Here, we address these challenges within the iLID system with alternative membrane anchoring domains and fusion configurations. Using live cell imaging and mathematical modeling, we demonstrate that the anchoring strategy affects both component expression and diffusion, which in turn impact recruitment strength, kinetics, and spatial dynamics. Compared to the commonly used C-terminal iLID fusion, fusion proteins with large N-terminal anchors show stronger local recruitment, slower diffusion of recruited components, efficient recruitment over wider gene expression ranges, and improved spatial control over signaling outputs. We also define guidelines for component expression regimes for optimal recruitment for both cell-wide and subcellular recruitment strategies. Our findings highlight key sources of imprecision within light-inducible dimer systems and provide tools that allow greater control of subcellular protein localization across diverse cell biological applications.
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Affiliation(s)
- Dean E. Natwick
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, California 95616, United States
| | - Sean R. Collins
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, California 95616, United States
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45
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Brüggemann Y, Karajannis LS, Stanoev A, Stallaert W, Bastiaens PIH. Growth factor-dependent ErbB vesicular dynamics couple receptor signaling to spatially and functionally distinct Erk pools. Sci Signal 2021; 14:14/683/eabd9943. [PMID: 34006609 DOI: 10.1126/scisignal.abd9943] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Growth factor-dependent vesicular dynamics allow cells to regulate the spatial distribution of growth factor receptors and thereby their coupling to downstream signaling effectors that guide cellular responses. We found that the ErbB ligands epidermal growth factor (EGF) and heregulin (HRG) generated distinct spatiotemporal patterns of cognate receptor activities to activate distinct subcellular pools of the extracellular signal-regulated kinase (Erk). Sustained plasma membrane activity of the receptor tyrosine kinases ErbB2/ErbB3 signaled to Erk complexed with the scaffold protein KSR to promote promigratory EphA2 phosphorylation and cellular motility upon HRG stimulation. In contrast, receptor-saturating EGF stimuli caused proliferation-inducing transient activation of cytoplasmic Erk due to the rapid internalization of EGF receptors (EGFR or ErbB1) toward endosomes. Paradoxically, promigratory signaling mediated by Erk complexed to KSR was sustained at low EGF concentrations by vesicular recycling that maintained steady-state amounts of active, phosphorylated EGFR at the plasma membrane. Thus, the effect of ligand identity and concentration on determining ErbB vesicular dynamics constitutes a mechanism by which cells can transduce growth factor composition through spatially distinct Erk pools to enable functionally diverse cellular responses.
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Affiliation(s)
- Yannick Brüggemann
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str.11, 44227 Dortmund, Germany.,Faculty of Chemistry and Chemical Biology, TU Dortmund, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
| | - Lisa S Karajannis
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str.11, 44227 Dortmund, Germany
| | - Angel Stanoev
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str.11, 44227 Dortmund, Germany
| | - Wayne Stallaert
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str.11, 44227 Dortmund, Germany
| | - Philippe I H Bastiaens
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str.11, 44227 Dortmund, Germany. .,Faculty of Chemistry and Chemical Biology, TU Dortmund, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
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46
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Abstract
Preclinical evidence has highlighted the importance of the μ-opioid peptide (MOP) receptor on primary afferents for both the analgesic actions of MOP receptor agonists, as well as the development of tolerance, if not opioid-induced hyperalgesia. There is also growing interest in targeting other opioid peptide receptor subtypes (δ-opioid peptide [DOP], κ-opioid peptide [KOP], and nociceptin/orphanin-FQ opioid peptide [NOP]) on primary afferents, as alternatives to MOP receptors, which may not be associated with as many deleterious side effects. Nevertheless, results from several recent studies of human sensory neurons indicate that although there are many similarities between rodent and human sensory neurons, there may also be important differences. Thus, the purpose of this study was to assess the distribution of opioid receptor subtypes among human sensory neurons. A combination of pharmacology, patch-clamp electrophysiology, Ca imaging, and single-cell semiquantitative polymerase chain reaction was used. Our results suggest that functional MOP-like receptors are present in approximately 50% of human dorsal root ganglion neurons. δ-opioid peptide-like receptors were detected in a subpopulation largely overlapping that with MOP-like receptors. Furthermore, KOP-like and NOP-like receptors are detected in a large proportion (44% and 40%, respectively) of human dorsal root ganglion neurons with KOP receptors also overlapping with MOP receptors at a high rate (83%). Our data confirm that all 4 opioid receptor subtypes are present and functional in human sensory neurons, where the overlap of DOP, KOP, and NOP receptors with MOP receptors suggests that activation of these other opioid receptor subtypes may also have analgesic efficacy.
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47
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El-Beyrouthy J, Freeman E. Characterizing the Structure and Interactions of Model Lipid Membranes Using Electrophysiology. MEMBRANES 2021; 11:319. [PMID: 33925756 PMCID: PMC8145864 DOI: 10.3390/membranes11050319] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 04/22/2021] [Accepted: 04/25/2021] [Indexed: 11/16/2022]
Abstract
The cell membrane is a protective barrier whose configuration determines the exchange both between intracellular and extracellular regions and within the cell itself. Consequently, characterizing membrane properties and interactions is essential for advancements in topics such as limiting nanoparticle cytotoxicity. Characterization is often accomplished by recreating model membranes that approximate the structure of cellular membranes in a controlled environment, formed using self-assembly principles. The selected method for membrane creation influences the properties of the membrane assembly, including their response to electric fields used for characterizing transmembrane exchanges. When these self-assembled model membranes are combined with electrophysiology, it is possible to exploit their non-physiological mechanics to enable additional measurements of membrane interactions and phenomena. This review describes several common model membranes including liposomes, pore-spanning membranes, solid supported membranes, and emulsion-based membranes, emphasizing their varying structure due to the selected mode of production. Next, electrophysiology techniques that exploit these structures are discussed, including conductance measurements, electrowetting and electrocompression analysis, and electroimpedance spectroscopy. The focus of this review is linking each membrane assembly technique to the properties of the resulting membrane, discussing how these properties enable alternative electrophysiological approaches to measuring membrane characteristics and interactions.
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Affiliation(s)
| | - Eric Freeman
- School of Environmental, Civil, Agricultural and Mechanical Engineering, College of Engineering, University of Georgia, Athens, GA 30602, USA;
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48
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Kundu R, Chandra A, Datta A. Fluorescent Chemical Tools for Tracking Anionic Phospholipids. Isr J Chem 2021. [DOI: 10.1002/ijch.202100003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Rajasree Kundu
- Department of Chemical Sciences Tata Institute of Fundamental Research 1 Homi Bhabha Road, Colaba Mumbai 400005 India
| | - Amitava Chandra
- Department of Chemical Sciences Tata Institute of Fundamental Research 1 Homi Bhabha Road, Colaba Mumbai 400005 India
| | - Ankona Datta
- Department of Chemical Sciences Tata Institute of Fundamental Research 1 Homi Bhabha Road, Colaba Mumbai 400005 India
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49
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Kumar SA, Albrecht T, Kauzál O, Tomášek O. No Evidence for Trade-Offs Between Lifespan, Fecundity, and Basal Metabolic Rate Mediated by Liver Fatty Acid Composition in Birds. Front Cell Dev Biol 2021; 9:638501. [PMID: 33869185 PMCID: PMC8045231 DOI: 10.3389/fcell.2021.638501] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 02/23/2021] [Indexed: 01/03/2023] Open
Abstract
The fatty acid composition of biological membranes has been hypothesised to be a key molecular adaptation associated with the evolution of metabolic rates, ageing, and life span – the basis of the membrane pacemaker hypothesis (MPH). MPH proposes that highly unsaturated membranes enhance cellular metabolic processes while being more prone to oxidative damage, thereby increasing the rates of metabolism and ageing. MPH could, therefore, provide a mechanistic explanation for trade-offs between longevity, fecundity, and metabolic rates, predicting that short-lived species with fast metabolic rates and higher fecundity would have greater levels of membrane unsaturation. However, previous comparative studies testing MPH provide mixed evidence regarding the direction of covariation between fatty acid unsaturation and life span or metabolic rate. Moreover, some empirical studies suggest that an n-3/n-6 PUFA ratio or the fatty acid chain length, rather than the overall unsaturation, could be the key traits coevolving with life span. In this study, we tested the coevolution of liver fatty acid composition with maximum life span, annual fecundity, and basal metabolic rate (BMR), using a recently published data set comprising liver fatty acid composition of 106 avian species. While statistically controlling for the confounding effects of body mass and phylogeny, we found no support for long life span evolving with low fatty acid unsaturation and only very weak support for fatty acid unsaturation acting as a pacemaker of BMR. Moreover, our analysis provided no evidence for the previously reported links between life span and n-3 PUFA/total PUFA or MUFA proportion. Our results rather suggest that long life span evolves with long-chain fatty acids irrespective of their degree of unsaturation as life span was positively associated with at least one long-chain fatty acid of each type (i.e., SFA, MUFA, n-6 PUFA, and n-3 PUFA). Importantly, maximum life span, annual fecundity, and BMR were associated with different fatty acids or fatty acid indices, indicating that longevity, fecundity, and BMR coevolve with different aspects of fatty acid composition. Therefore, in addition to posing significant challenges to MPH, our results imply that fatty acid composition does not pose an evolutionary constraint underpinning life-history trade-offs at the molecular level.
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Affiliation(s)
- Sampath A Kumar
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czechia.,Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Tomáš Albrecht
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czechia.,Department of Zoology, Faculty of Science, Charles University, Prague, Czechia
| | - Ondřej Kauzál
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czechia.,Department of Ecology, Faculty of Science, Charles University, Prague, Czechia
| | - Oldřich Tomášek
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czechia.,Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czechia
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50
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Phagocytosis of microparticles increases responsiveness of macrophage-like cell lines U937 and THP-1 to bacterial lipopolysaccharide and lipopeptide. Sci Rep 2021; 11:6782. [PMID: 33762618 PMCID: PMC7990916 DOI: 10.1038/s41598-021-86202-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 03/12/2021] [Indexed: 11/08/2022] Open
Abstract
Following bacterial infection, macrophages produce pro-inflammatory cytokines in response to bacterial cell components, including lipopolysaccharide (LPS) and lipopeptide, and simultaneously phagocytize and digest the invading bacteria. To study the effects of phagocytosis on pro-inflammatory responses, we determined if phagocytosis of polystyrene latex beads with ~ 1 µm diameter increases pro-inflammatory cytokine expression by human macrophage-like U937 and THP-1 cells stimulated with LPS. Treating macrophage-like cells with beads coated with IgG to facilitate Fcγ receptor-mediated phagocytosis increased LPS-induced expression of pro-inflammatory cytokines, including tumor necrosis factor-alpha, interleukin-1 beta, and interleukin-6. Treatment with beads coated with poly-L-lysine to facilitate Fcγ receptor-independent phagocytosis also increased LPS-induced cytokine expression. Our results indicate that LPS-induced pro-inflammatory responses are enhanced by bead phagocytosis regardless of the uptake mechanism. Additionally, phagocytosis enhanced LPS-induced NF-κB activation, suggesting that Toll-like receptor (TLR) 4 signaling is enhanced by phagocytosis. Furthermore, bead phagocytosis enhanced pro-inflammatory responses in U937 cells stimulated with lipopeptide, a ligand for the TLR2/TLR6 heterodimeric receptor. In conclusion, microparticle phagocytosis by macrophage-like U937 and THP-1 cells enhances the innate immune response induced by bacterial components.
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