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Dong L, Fan Z, Fang B, Zhao X, Yao H, Cai G, Yang S, Zhang G, Cheng X, Feng Y, Mi S, Sun W. Oriented cellulose hydrogel: Directed tissue regeneration for reducing corneal leukoplakia and managing fungal corneal ulcers. Bioact Mater 2024; 41:15-29. [PMID: 39101028 PMCID: PMC11292264 DOI: 10.1016/j.bioactmat.2024.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 06/18/2024] [Accepted: 07/04/2024] [Indexed: 08/06/2024] Open
Abstract
Fungal corneal ulcer is one of the leading causes of corneal blindness in developing countries. Corneal scars such as leukoplakia are formed due to inflammation, oxidative stress and non-directed repair, which seriously affect the patients' subsequent visual and life quality. In this study, drawing inspiration from the oriented structure of collagen fibers within the corneal stroma, we first proposed the directional arrangement of CuTA-CMHT hydrogel system at micro and macro scales based on the 3D printing extrusion method combined with secondary patterning. It played an antifungal role and induced oriented repair in therapy of fungal corneal ulcer. The results showed that it effectively inhibited Candida albicans, Aspergillus Niger, Fusarium sapropelum, which mainly affects TNF, NF-kappa B, and HIF-1 signaling pathways, achieving effective antifungal functions. More importantly, the fibroblasts interacted with extracellular matrix (ECM) of corneal stroma through formation of focal adhesions, promoted the proliferation and directional migration of cells in vitro, induced the directional alignment of collagen fibers and corneal stromal orthogonally oriented repair in vivo. This process is mainly associated with MYLK, MYL9, and ITGA3 molecules. Furthermore, the downregulation the growth factors TGF-β and PDGF-β inhibits myofibroblast development and reduces scar-type ECM production, thereby reducing corneal leukoplakia. It also activates the PI3K-AKT signaling pathway, promoting corneal healing. In conclusion, the oriented CuTA-CMHT hydrogel system mimics the orthogonal arrangement of collagen fibers, inhibits inflammation, eliminates reactive oxygen species, and reduces corneal leukoplakia, which is of great significance in the treatment of fungal corneal ulcer and is expected to write a new chapter in corneal tissue engineering.
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Affiliation(s)
- Lina Dong
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
- Department of Burns, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang, China
| | - Zixin Fan
- Shenzhen Eye Hospital, Jinan University, Shenzhen Eye Institute, Shenzhen, Guangdong, 518040, China
| | - Bixing Fang
- Department of Otolaryngology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang, China
| | - Xiaoyu Zhao
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Hongyi Yao
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Gangpei Cai
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Shuo Yang
- Shenzhen Eye Hospital, Jinan University, Shenzhen Eye Institute, Shenzhen, Guangdong, 518040, China
| | - Guoming Zhang
- Shenzhen Eye Hospital, Jinan University, Shenzhen Eye Institute, Shenzhen, Guangdong, 518040, China
| | - Xiaoqi Cheng
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Yun Feng
- Department of Ophthalmology, Peking University Third Hospital, Beijing, 100191, China
| | - Shengli Mi
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Wei Sun
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
- Department of Mechanical Engineering, Biomanufacturing Center, Tsinghua University, Beijing, China
- Department of Mechanical Engineering, Drexel University, Philadelphia, PA, USA
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2
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Liu X, Wang C, Huang Y, Lv Q, Yu C, Ying J, Duan L, Guo Y, Huang G, Shen W, Jiang M, Mao W, Zuo Z, Zhao A. Abnormal Cellular Populations Shape Thymic Epithelial Tumor Heterogeneity and Anti-Tumor by Blocking Metabolic Interactions in Organoids. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2406653. [PMID: 39258580 DOI: 10.1002/advs.202406653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2024] [Revised: 08/08/2024] [Indexed: 09/12/2024]
Abstract
A variety of abnormal epithelial cells and immature and mature immune cells in thymic epithelial tumors (TETs) affect histopathological features, the degree of malignancy, and the response to treatment. Here, gene expression, trajectory inference, and T cell antigen receptor (TCR)-based lineage tracking are profiled in TETs at single-cell resolution. An original subpopulation of KRT14+ progenitor cells with a spindle cell phenotype is shown. An abnormal infiltration of immature T cells with a TCR hyper-rearrangement state is revealed, due to the lack of CCL21+ medullary epithelial cells. For thymic carcinoma, the novel biomarkers of MSLN, CCL20, and SLC1A5 are identified and observed an elevated expression of LAG3 and HAVCR2 in malignant tumorn-infiltrating mature T cells. These common features based on the single-cell populations may inform pathological reclassification of TETs. Meanwhile, it is found that macrophages (MACs) attract thymic tumor cells through the LGALS9-SLC1A5 axis, providing them with glutamine to elicit metabolic reprogramming. This MAC-based metabolic pattern can promote malignancy progression. Additionally, an interactive immune environment in TETs is identified that correlates with the infiltration of abnormal FOXI1+ CFTR- ionocytes. Collectively, the data broaden the knowledge of TET cellular ecosystems, providing a basis for tackling histopathological diagnosis and related treatment.
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Affiliation(s)
- Xuefei Liu
- Zhejiang Cancer Institute, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen, 518055, China
- Shenzhen Institute of Pediatrics, Shenzhen Children's Hospital, Shenzhen, 518026, China
| | - Changchun Wang
- Department of Thoracic Oncology, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China
| | - Yueyu Huang
- Zhejiang Cancer Institute, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China
| | - Qiaoli Lv
- Thoracic Oncology Laboratory, Jiangxi Cancer Hospital, Nanchang Medical College, Nanchang, Jiangxi, 330029, China
| | - Chang Yu
- Department of Pathology, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China
| | - Jianghua Ying
- Department of Ultrasound, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China
| | - Lianhui Duan
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yangzhong Guo
- Thoracic Oncology Laboratory, Jiangxi Cancer Hospital, Nanchang Medical College, Nanchang, Jiangxi, 330029, China
| | - Guanyin Huang
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Wenhui Shen
- Zhejiang Cancer Institute, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China
| | - Ming Jiang
- Center for Genetic Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310011, China
- Zhejiang Provincial Key Laboratory of Genetic & Developmental Disorders, Hangzhou, Zhejiang, 310011, China
| | - Weimin Mao
- Thoracic Oncology Laboratory, Jiangxi Cancer Hospital, Nanchang Medical College, Nanchang, Jiangxi, 330029, China
- Zhejiang Provincial Key Laboratory of Diagnosis and Treatment of Thoracic Cancer, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China
| | - Zhixiang Zuo
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510308, China
| | - An Zhao
- Zhejiang Cancer Institute, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China
- Thoracic Oncology Laboratory, Jiangxi Cancer Hospital, Nanchang Medical College, Nanchang, Jiangxi, 330029, China
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3
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Pacheco-García JL, Cano-Muñoz M, Loginov DS, Vankova P, Man P, Pey AL. Phosphorylation of cytosolic hPGK1 affects protein stability and ligand binding: implications for its subcellular targeting in cancer. FEBS J 2024. [PMID: 39240559 DOI: 10.1111/febs.17262] [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: 10/27/2023] [Revised: 04/24/2024] [Accepted: 08/21/2024] [Indexed: 09/07/2024]
Abstract
Human phosphoglycerate kinase 1(hPGK1) is a key glycolytic enzyme that regulates the balance between ADP and ATP concentrations inside the cell. Phosphorylation of hPGK1 at S203 and S256 has been associated with enzyme import from the cytosol to the mitochondria and the nucleus respectively. These changes in subcellular locations drive tumorigenesis and are likely associated with site-specific changes in protein stability. In this work, we investigate the effects of site-specific phosphorylation on thermal and kinetic stability and protein structural dynamics by hydrogen-deuterium exchange (HDX) and molecular dynamics (MD) simulations. We also investigate the binding of 3-phosphoglycerate and Mg-ADP using these approaches. We show that the phosphomimetic mutation S256D reduces hPGK1 kinetic stability by 50-fold, with no effect of the mutation S203D. Calorimetric studies of ligand binding show a large decrease in affinity for Mg-ADP in the S256D variant, whereas Mg-ADP binding to the WT and S203D can be accurately investigated using protein kinetic stability and binding thermodynamic models. HDX and MD simulations confirmed the destabilization caused by the mutation S256D (with some long-range effects on stability) and its reduced affinity for Mg-ADP due to the strong destabilization of its binding site (particularly in the apo-state). Our research provides evidence suggesting that modifications in protein stability could potentially enhance the translocation of hPGK1 to the nucleus in cancer. While the structural and energetic basis of its mitochondrial import remain unknown.
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Affiliation(s)
| | | | - Dmitry S Loginov
- Institute of Microbiology - BioCeV, Academy of Sciences of the Czech Republic, Vestec, Czech Republic
| | - Pavla Vankova
- Institute of Biotechnology - BioCeV, Academy of Sciences of the Czech Republic, Vestec, Czech Republic
| | - Petr Man
- Institute of Microbiology - BioCeV, Academy of Sciences of the Czech Republic, Vestec, Czech Republic
| | - Angel L Pey
- Departamento de Química Física, Unidad de Excelencia en Química Aplicada a Biomedicina y Medioambiente e Instituto de Biotecnología, Universidad de Granada, Spain
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4
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Skowicki M, Tarvirdipour S, Kraus M, Schoenenberger CA, Palivan CG. Nanoassemblies designed for efficient nuclear targeting. Adv Drug Deliv Rev 2024; 211:115354. [PMID: 38857762 DOI: 10.1016/j.addr.2024.115354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/23/2024] [Accepted: 06/04/2024] [Indexed: 06/12/2024]
Abstract
One of the key aspects of coping efficiently with complex pathological conditions is delivering the desired therapeutic compounds with precision in both space and time. Therefore, the focus on nuclear-targeted delivery systems has emerged as a promising strategy with high potential, particularly in gene therapy and cancer treatment. Here, we explore the design of supramolecular nanoassemblies as vehicles to deliver specific compounds to the nucleus, with the special focus on polymer and peptide-based carriers that expose nuclear localization signals. Such nanoassemblies aim at maximizing the concentration of genetic and therapeutic agents within the nucleus, thereby optimizing treatment outcomes while minimizing off-target effects. A complex scenario of conditions, including cellular uptake, endosomal escape, and nuclear translocation, requires fine tuning of the nanocarriers' properties. First, we introduce the principles of nuclear import and the role of nuclear pore complexes that reveal strategies for targeting nanosystems to the nucleus. Then, we provide an overview of cargoes that rely on nuclear localization for optimal activity as their integrity and accumulation are crucial parameters to consider when designing a suitable delivery system. Considering that they are in their early stages of research, we present various cargo-loaded peptide- and polymer nanoassemblies that promote nuclear targeting, emphasizing their potential to enhance therapeutic response. Finally, we briefly discuss further advancements for more precise and effective nuclear delivery.
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Affiliation(s)
- Michal Skowicki
- Department of Chemistry, University of Basel, BPR 1096, Mattenstrasse 22, 4058 Basel, Switzerland; NCCR-Molecular Systems Engineering, BPR 1095, Mattenstrasse 24a, 4058 Basel, Switzerland
| | - Shabnam Tarvirdipour
- Department of Chemistry, University of Basel, BPR 1096, Mattenstrasse 22, 4058 Basel, Switzerland
| | - Manuel Kraus
- Department of Chemistry, University of Basel, BPR 1096, Mattenstrasse 22, 4058 Basel, Switzerland
| | - Cora-Ann Schoenenberger
- Department of Chemistry, University of Basel, BPR 1096, Mattenstrasse 22, 4058 Basel, Switzerland; NCCR-Molecular Systems Engineering, BPR 1095, Mattenstrasse 24a, 4058 Basel, Switzerland.
| | - Cornelia G Palivan
- Department of Chemistry, University of Basel, BPR 1096, Mattenstrasse 22, 4058 Basel, Switzerland; NCCR-Molecular Systems Engineering, BPR 1095, Mattenstrasse 24a, 4058 Basel, Switzerland.
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5
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Ferrai C, Schulte C. Mechanotransduction in stem cells. Eur J Cell Biol 2024; 103:151417. [PMID: 38729084 DOI: 10.1016/j.ejcb.2024.151417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 04/28/2024] [Accepted: 04/29/2024] [Indexed: 05/12/2024] Open
Abstract
Nowadays, it is an established concept that the capability to reach a specialised cell identity via differentiation, as in the case of multi- and pluripotent stem cells, is not only determined by biochemical factors, but that also physical aspects of the microenvironment play a key role; interpreted by the cell through a force-based signalling pathway called mechanotransduction. However, the intricate ties between the elements involved in mechanotransduction, such as the extracellular matrix, the glycocalyx, the cell membrane, Integrin adhesion complexes, Cadherin-mediated cell/cell adhesion, the cytoskeleton, and the nucleus, are still far from being understood in detail. Here we report what is currently known about these elements in general and their specific interplay in the context of multi- and pluripotent stem cells. We furthermore merge this overview to a more comprehensive picture, that aims to cover the whole mechanotransductive pathway from the cell/microenvironment interface to the regulation of the chromatin structure in the nucleus. Ultimately, with this review we outline the current picture of the interplay between mechanotransductive cues and epigenetic regulation and how these processes might contribute to stem cell dynamics and fate.
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Affiliation(s)
- Carmelo Ferrai
- Institute of Pathology, University Medical Centre Göttingen, Germany.
| | - Carsten Schulte
- Department of Biomedical and Clinical Sciences and Department of Physics "Aldo Pontremoli", University of Milan, Italy.
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6
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Keuper K, Bartek J, Maya-Mendoza A. The nexus of nuclear envelope dynamics, circular economy and cancer cell pathophysiology. Eur J Cell Biol 2024; 103:151394. [PMID: 38340500 DOI: 10.1016/j.ejcb.2024.151394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 02/01/2024] [Accepted: 02/02/2024] [Indexed: 02/12/2024] Open
Abstract
The nuclear envelope (NE) is a critical component in maintaining the function and structure of the eukaryotic nucleus. The NE and lamina are disassembled during each cell cycle to enable an open mitosis. Nuclear architecture construction and deconstruction is a prime example of a circular economy, as it fulfills a highly efficient recycling program bound to continuous assessment of the quality and functionality of the building blocks. Alterations in the nuclear dynamics and lamina structure have emerged as important contributors to both oncogenic transformation and cancer progression. However, the knowledge of the NE breakdown and reassembly is still limited to a fraction of participating proteins and complexes. As cancer cells contain highly diverse nuclei in terms of DNA content, but also in terms of nuclear number, size, and shape, it is of great interest to understand the intricate relationship between these nuclear features in cancer cell pathophysiology. In this review, we provide insights into how those NE dynamics are regulated, and how lamina destabilization processes may alter the NE circular economy. Moreover, we expand the knowledge of the lamina-associated domain region by using strategic algorithms, including Artificial Intelligence, to infer protein associations, assess their function and location, and predict cancer-type specificity with implications for the future of cancer diagnosis, prognosis and treatment. Using this approach we identified NUP98 and MECP2 as potential proteins that exhibit upregulation in Acute Myeloid Leukemia (LAML) patients with implications for early diagnosis.
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Affiliation(s)
- Kristina Keuper
- DNA Replication and Cancer Group, Danish Cancer Institute, Copenhagen, Denmark; Genome Integrity Group, Danish Cancer Institute, Copenhagen, Denmark
| | - Jiri Bartek
- Genome Integrity Group, Danish Cancer Institute, Copenhagen, Denmark; Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SciLifeLab, Stockholm, Sweden
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7
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Panagaki F, Tapia-Rojo R, Zhu T, Milmoe N, Paracuellos P, Board S, Mora M, Walker J, Rostkova E, Stannard A, Infante E, Garcia-Manyes S. Structural anisotropy results in mechano-directional transport of proteins across nuclear pores. NATURE PHYSICS 2024; 20:1180-1193. [PMID: 39036650 PMCID: PMC11254768 DOI: 10.1038/s41567-024-02438-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 02/08/2024] [Indexed: 07/23/2024]
Abstract
The nuclear pore complex regulates nucleocytoplasmic transport by means of a tightly synchronized suite of biochemical reactions. The physicochemical properties of the translocating cargos are emerging as master regulators of their shuttling dynamics. As well as being affected by molecular weight and surface-exposed amino acids, the kinetics of the nuclear translocation of protein cargos also depend on their nanomechanical properties, yet the mechanisms underpinning the mechanoselectivity of the nuclear pore complex are unclear. Here we show that proteins with locally soft regions in the vicinity of the nuclear-localization sequence exhibit higher nuclear-import rates, and that such mechanoselectivity is specifically impaired upon knocking down nucleoporin 153, a key protein in the nuclear pore complex. This allows us to design a short, easy-to-express and chemically inert unstructured peptide tag that accelerates the nuclear-import rate of stiff protein cargos. We also show that U2OS osteosarcoma cells expressing the peptide-tagged myocardin-related transcription factor import this mechanosensitive protein to the nucleus at higher rates and display faster motility. Locally unstructured regions lower the free-energy barrier of protein translocation and might offer a control mechanism for nuclear mechanotransduction.
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Affiliation(s)
- Fani Panagaki
- Single Molecule Mechanobiology Laboratory, The Francis Crick Institute, London, UK
- Department of Physics, Randall Centre for Cell and Molecular Biophysics, Centre for the Physical Science of Life and London Centre for Nanotechnology, King’s College London, London, UK
| | - Rafael Tapia-Rojo
- Single Molecule Mechanobiology Laboratory, The Francis Crick Institute, London, UK
- Department of Physics, Randall Centre for Cell and Molecular Biophysics, Centre for the Physical Science of Life and London Centre for Nanotechnology, King’s College London, London, UK
| | - Tong Zhu
- Single Molecule Mechanobiology Laboratory, The Francis Crick Institute, London, UK
- Department of Physics, Randall Centre for Cell and Molecular Biophysics, Centre for the Physical Science of Life and London Centre for Nanotechnology, King’s College London, London, UK
| | - Natalie Milmoe
- Single Molecule Mechanobiology Laboratory, The Francis Crick Institute, London, UK
- Department of Physics, Randall Centre for Cell and Molecular Biophysics, Centre for the Physical Science of Life and London Centre for Nanotechnology, King’s College London, London, UK
| | - Patricia Paracuellos
- Single Molecule Mechanobiology Laboratory, The Francis Crick Institute, London, UK
- Department of Physics, Randall Centre for Cell and Molecular Biophysics, Centre for the Physical Science of Life and London Centre for Nanotechnology, King’s College London, London, UK
| | - Stephanie Board
- Single Molecule Mechanobiology Laboratory, The Francis Crick Institute, London, UK
- Department of Physics, Randall Centre for Cell and Molecular Biophysics, Centre for the Physical Science of Life and London Centre for Nanotechnology, King’s College London, London, UK
| | - Marc Mora
- Single Molecule Mechanobiology Laboratory, The Francis Crick Institute, London, UK
- Department of Physics, Randall Centre for Cell and Molecular Biophysics, Centre for the Physical Science of Life and London Centre for Nanotechnology, King’s College London, London, UK
| | - Jane Walker
- Single Molecule Mechanobiology Laboratory, The Francis Crick Institute, London, UK
- Department of Physics, Randall Centre for Cell and Molecular Biophysics, Centre for the Physical Science of Life and London Centre for Nanotechnology, King’s College London, London, UK
| | - Elena Rostkova
- Department of Physics, Randall Centre for Cell and Molecular Biophysics, Centre for the Physical Science of Life and London Centre for Nanotechnology, King’s College London, London, UK
| | - Andrew Stannard
- Department of Physics, Randall Centre for Cell and Molecular Biophysics, Centre for the Physical Science of Life and London Centre for Nanotechnology, King’s College London, London, UK
| | - Elvira Infante
- Single Molecule Mechanobiology Laboratory, The Francis Crick Institute, London, UK
- Department of Physics, Randall Centre for Cell and Molecular Biophysics, Centre for the Physical Science of Life and London Centre for Nanotechnology, King’s College London, London, UK
| | - Sergi Garcia-Manyes
- Single Molecule Mechanobiology Laboratory, The Francis Crick Institute, London, UK
- Department of Physics, Randall Centre for Cell and Molecular Biophysics, Centre for the Physical Science of Life and London Centre for Nanotechnology, King’s College London, London, UK
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8
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Mistriotis P, Wisniewski EO, Si BR, Kalab P, Konstantopoulos K. Coordinated in confined migration: crosstalk between the nucleus and ion channel-mediated mechanosensation. Trends Cell Biol 2024:S0962-8924(24)00001-1. [PMID: 38290913 PMCID: PMC11284253 DOI: 10.1016/j.tcb.2024.01.001] [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: 09/03/2023] [Revised: 12/22/2023] [Accepted: 01/05/2024] [Indexed: 02/01/2024]
Abstract
Cell surface and intracellular mechanosensors enable cells to perceive different geometric, topographical, and physical cues. Mechanosensitive ion channels (MICs) localized at the cell surface and on the nuclear envelope (NE) are among the first to sense and transduce these signals. Beyond compartmentalizing the genome of the cell and its transcription, the nucleus also serves as a mechanical gauge of different physical and topographical features of the tissue microenvironment. In this review, we delve into the intricate mechanisms by which the nucleus and different ion channels regulate cell migration in confinement. We review evidence suggesting an interplay between macromolecular nuclear-cytoplasmic transport (NCT) and ionic transport across the cell membrane during confined migration. We also discuss the roles of the nucleus and ion channel-mediated mechanosensation, whether acting independently or in tandem, in orchestrating migratory mechanoresponses. Understanding nuclear and ion channel sensing, and their crosstalk, is critical to advancing our knowledge of cell migration in health and disease.
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Affiliation(s)
| | - Emily O Wisniewski
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, MD 21218, USA; Johns Hopkins Institute for NanoBioTechnology, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Bishwa R Si
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, MD 21218, USA; Johns Hopkins Institute for NanoBioTechnology, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Petr Kalab
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, MD 21218, USA.
| | - Konstantinos Konstantopoulos
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, MD 21218, USA; Johns Hopkins Institute for NanoBioTechnology, The Johns Hopkins University, Baltimore, MD 21218, USA; Department of Biomedical Engineering, The Johns Hopkins University, Baltimore, MD 21218, USA; Department of Oncology, The Johns Hopkins University, Baltimore, MD 21205, USA.
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9
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Mora M, Tapia-Rojo R, Garcia-Manyes S. Unfolding and Refolding Proteins Using Single-Molecule AFM. Methods Mol Biol 2024; 2694:339-354. [PMID: 37824012 DOI: 10.1007/978-1-0716-3377-9_16] [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: 10/13/2023]
Abstract
Single-molecule atomic force microscopy (AFM) allows capturing the conformational dynamics of an individual molecule under force. In this chapter, we describe a protocol for conducting a protein nanomechanical experiment using AFM, covering both the force-extension and force-clamp modes. Combined, these experiments provide an integrated vista of the molecular mechanisms-and their associated kinetics-underpinning the mechanical unfolding and refolding of individual proteins when exposed to mechanical load.
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Affiliation(s)
- Marc Mora
- Department of Physics, Randall Centre for Cell and Molecular Biophysics and London Centre for Nanotechnology, King's College London, London, UK
| | - Rafael Tapia-Rojo
- Department of Physics, Randall Centre for Cell and Molecular Biophysics and London Centre for Nanotechnology, King's College London, London, UK
| | - Sergi Garcia-Manyes
- Department of Physics, Randall Centre for Cell and Molecular Biophysics and London Centre for Nanotechnology, King's College London, London, UK.
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10
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Kofler M, Kapus A. Nuclear Import and Export of YAP and TAZ. Cancers (Basel) 2023; 15:4956. [PMID: 37894323 PMCID: PMC10605228 DOI: 10.3390/cancers15204956] [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: 09/04/2023] [Revised: 10/05/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
Yes-associated Protein (YAP) and its paralog Transcriptional Coactivator with PDZ-binding Motif (TAZ) are major regulators of gene transcription/expression, primarily controlled by the Hippo pathway and the cytoskeleton. Integrating an array of chemical and mechanical signals, they impact growth, differentiation, and regeneration. Accordingly, they also play key roles in tumorigenesis and metastasis formation. Their activity is primarily regulated by their localization, that is, Hippo pathway- and/or cytoskeleton-controlled cytosolic or nuclear sequestration. While many details of such prevailing retention models have been elucidated, much less is known about their actual nuclear traffic: import and export. Although their size is not far from the cutoff for passive diffusion through the nuclear pore complex (NPC), and they do not contain any classic nuclear localization (NLS) or nuclear export signal (NES), evidence has been accumulating that their shuttling involves mediated and thus regulatable/targetable processes. The aim of this review is to summarize emerging information/concepts about their nucleocytoplasmic shuttling, encompassing the relevant structural requirements (NLS, NES), nuclear transport receptors (NTRs, karyophererins), and NPC components, along with the potential transport mechanisms and their regulation. While dissecting retention vs. transport is often challenging, the emerging picture suggests that YAP/TAZ shuttles across the NPC via multiple, non-exclusive, mediated mechanisms, constituting a novel and intriguing facet of YAP/TAZ biology.
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Affiliation(s)
- Michael Kofler
- Keenan Research Centre for Biomedical Science of the St. Michael’s Hospital, Toronto, ON M5B 1W8, Canada;
| | - András Kapus
- Keenan Research Centre for Biomedical Science of the St. Michael’s Hospital, Toronto, ON M5B 1W8, Canada;
- Department of Surgery, University of Toronto, Toronto, ON M5T 1P5, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON M5B 1T8, Canada
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11
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Beedle AE, Roca-Cusachs P. The reversibility of cellular mechano-activation. Curr Opin Cell Biol 2023; 84:102229. [PMID: 37633090 DOI: 10.1016/j.ceb.2023.102229] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 07/22/2023] [Accepted: 07/31/2023] [Indexed: 08/28/2023]
Abstract
The cellular microenvironment is highly heterogeneous and dynamic. Therefore, cells must be equipped with molecular tools to adapt and respond to constantly fluctuating inputs. One such input is mechanical force, which activates signalling and regulates cell behaviour in the process of mechanotransduction. Whereas the mechanisms activating mechanotransduction are well studied, the reversibility of this process, whereby cells disassemble and reverse force-activated signalling pathways upon cessation of mechanical stimulation is far less understood. In this review we will outline some of the key experimental techniques to investigate the reversibility of mechanical signalling, and key discoveries arising from them.
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Affiliation(s)
- Amy Em Beedle
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain; Department of Physics, King's College London, London WC2R 2LS, UK.
| | - Pere Roca-Cusachs
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain; University of Barcelona, 08028 Barcelona, Spain.
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12
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De Silva S, Fan Z, Kang B, Shanahan CM, Zhang Q. Nesprin-1: novel regulator of striated muscle nuclear positioning and mechanotransduction. Biochem Soc Trans 2023; 51:1331-1345. [PMID: 37171063 PMCID: PMC10317153 DOI: 10.1042/bst20221541] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 04/20/2023] [Accepted: 04/20/2023] [Indexed: 05/13/2023]
Abstract
Nesprins (nuclear envelope spectrin repeat proteins) are multi-isomeric scaffolding proteins. Giant nesprin-1 and -2 localise to the outer nuclear membrane, interact with SUN (Sad1p/UNC-84) domain-containing proteins at the inner nuclear membrane to form the LInker of Nucleoskeleton and Cytoskeleton (LINC) complex, which, in association with lamin A/C and emerin, mechanically couples the nucleus to the cytoskeleton. Despite ubiquitous expression of nesprin giant isoforms, pathogenic mutations in nesprin-1 and -2 are associated with tissue-specific disorders, particularly related to striated muscle such as dilated cardiomyopathy and Emery-Dreifuss muscular dystrophy. Recent evidence suggests this muscle-specificity might be attributable in part, to the small muscle specific isoform, nesprin-1α2, which has a novel role in striated muscle function. Our current understanding of muscle-specific functions of nesprin-1 and its isoforms will be summarised in this review to provide insight into potential pathological mechanisms of nesprin-related muscle disease and may inform potential targets of therapeutic modulation.
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Affiliation(s)
- Shanelle De Silva
- King's College London British Heart Foundation Centre of Research Excellence, School of Cardiovascular and Metabolic Medicine & Sciences, London SE5 9NU, U.K
| | - Zhijuan Fan
- King's College London British Heart Foundation Centre of Research Excellence, School of Cardiovascular and Metabolic Medicine & Sciences, London SE5 9NU, U.K
- Clinical Laboratory, Tianjin Third Central Hospital, Tianjin 300170, China
| | - Baoqiang Kang
- King's College London British Heart Foundation Centre of Research Excellence, School of Cardiovascular and Metabolic Medicine & Sciences, London SE5 9NU, U.K
| | - Catherine M. Shanahan
- King's College London British Heart Foundation Centre of Research Excellence, School of Cardiovascular and Metabolic Medicine & Sciences, London SE5 9NU, U.K
| | - Qiuping Zhang
- King's College London British Heart Foundation Centre of Research Excellence, School of Cardiovascular and Metabolic Medicine & Sciences, London SE5 9NU, U.K
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13
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Beedle AEM, Garcia-Manyes S. The role of single protein elasticity in mechanobiology. NATURE REVIEWS. MATERIALS 2023; 8:10-24. [PMID: 37469679 PMCID: PMC7614781 DOI: 10.1038/s41578-022-00488-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 09/07/2022] [Indexed: 07/21/2023]
Abstract
In addition to biochemical signals and genetic considerations, mechanical forces are rapidly emerging as a master regulator of human physiology. Yet the molecular mechanisms that regulate force-induced functionalities across a wide range of scales, encompassing the cell, tissue or organ levels, are comparatively not so well understood. With the advent, development and refining of single molecule nanomechanical techniques, enabling to exquisitely probe the conformational dynamics of individual proteins under the effect of a calibrated force, we have begun to acquire a comprehensive knowledge on the rich plethora of physicochemical principles that regulate the elasticity of single proteins. Here we review the major advances underpinning our current understanding of how the elasticity of single proteins regulates mechanosensing and mechanotransduction. We discuss the present limitations and future challenges of such a prolific and burgeoning field.
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Affiliation(s)
- Amy EM Beedle
- Department of Physics, Randall Centre for Cell and Molecular Biophysics, Centre for the Physical Science of Life and London Centre for Nanotechnology, King’s College London, Strand, WC2R 2LS London, United Kingdom
- Institute for Bioengineering of Catalonia (IBEC), the Barcelona Institute of Technology (BIST), 08028 Barcelona, Spain
| | - Sergi Garcia-Manyes
- Department of Physics, Randall Centre for Cell and Molecular Biophysics, Centre for the Physical Science of Life and London Centre for Nanotechnology, King’s College London, Strand, WC2R 2LS London, United Kingdom
- Single Molecule Mechanobiology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, London, UK
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14
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Cardiac fibroblasts and mechanosensation in heart development, health and disease. Nat Rev Cardiol 2022; 20:309-324. [PMID: 36376437 DOI: 10.1038/s41569-022-00799-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/04/2022] [Indexed: 11/16/2022]
Abstract
The term 'mechanosensation' describes the capacity of cells to translate mechanical stimuli into the coordinated regulation of intracellular signals, cellular function, gene expression and epigenetic programming. This capacity is related not only to the sensitivity of the cells to tissue motion, but also to the decryption of tissue geometric arrangement and mechanical properties. The cardiac stroma, composed of fibroblasts, has been historically considered a mechanically passive component of the heart. However, the latest research suggests that the mechanical functions of these cells are an active and necessary component of the developmental biology programme of the heart that is involved in myocardial growth and homeostasis, and a crucial determinant of cardiac repair and disease. In this Review, we discuss the general concept of cell mechanosensation and force generation as potent regulators in heart development and pathology, and describe the integration of mechanical and biohumoral pathways predisposing the heart to fibrosis and failure. Next, we address the use of 3D culture systems to integrate tissue mechanics to mimic cardiac remodelling. Finally, we highlight the potential of mechanotherapeutic strategies, including pharmacological treatment and device-mediated left ventricular unloading, to reverse remodelling in the failing heart.
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15
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Kim JK, Han SB, Park SI, Kim IS, Kim DH. Nuclear transport of STAT6 determines the matrix rigidity dependent M2 activation of macrophages. Biomaterials 2022; 290:121859. [DOI: 10.1016/j.biomaterials.2022.121859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 10/04/2022] [Accepted: 10/09/2022] [Indexed: 11/28/2022]
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16
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Andreu I, Granero-Moya I, Chahare NR, Clein K, Molina-Jordán M, Beedle AEM, Elosegui-Artola A, Abenza JF, Rossetti L, Trepat X, Raveh B, Roca-Cusachs P. Mechanical force application to the nucleus regulates nucleocytoplasmic transport. Nat Cell Biol 2022; 24:896-905. [PMID: 35681009 PMCID: PMC7614780 DOI: 10.1038/s41556-022-00927-7] [Citation(s) in RCA: 59] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 04/26/2022] [Indexed: 12/30/2022]
Abstract
Mechanical force controls fundamental cellular processes in health and disease, and increasing evidence shows that the nucleus both experiences and senses applied forces. Such forces can lead to the nuclear translocation of proteins, but whether force controls nucleocytoplasmic transport, and how, remains unknown. Here we show that nuclear forces differentially control passive and facilitated nucleocytoplasmic transport, setting the rules for the mechanosensitivity of shuttling proteins. We demonstrate that nuclear force increases permeability across nuclear pore complexes, with a dependence on molecular weight that is stronger for passive than for facilitated diffusion. Owing to this differential effect, force leads to the translocation of cargoes into or out of the nucleus within a given range of molecular weight and affinity for nuclear transport receptors. Further, we show that the mechanosensitivity of several transcriptional regulators can be both explained by this mechanism and engineered exogenously by introducing appropriate nuclear localization signals. Our work unveils a mechanism of mechanically induced signalling, probably operating in parallel with others, with potential applicability across signalling pathways.
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Affiliation(s)
- Ion Andreu
- Institute for Bioengineering of Catalonia (IBEC), the Barcelona Institute of Technology (BIST), Barcelona, Spain.
- Universidad de Navarra, TECNUN Escuela de Ingeniería, Donostia-San Sebastián, Spain.
| | - Ignasi Granero-Moya
- Institute for Bioengineering of Catalonia (IBEC), the Barcelona Institute of Technology (BIST), Barcelona, Spain
- Universitat de Barcelona, Barcelona, Spain
| | - Nimesh R Chahare
- Institute for Bioengineering of Catalonia (IBEC), the Barcelona Institute of Technology (BIST), Barcelona, Spain
| | - Kessem Clein
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Marc Molina-Jordán
- Institute for Bioengineering of Catalonia (IBEC), the Barcelona Institute of Technology (BIST), Barcelona, Spain
- Universitat de Barcelona, Barcelona, Spain
| | - Amy E M Beedle
- Institute for Bioengineering of Catalonia (IBEC), the Barcelona Institute of Technology (BIST), Barcelona, Spain
- Department of Physics, King's College London, London, UK
| | - Alberto Elosegui-Artola
- Institute for Bioengineering of Catalonia (IBEC), the Barcelona Institute of Technology (BIST), Barcelona, Spain
- Department of Physics, King's College London, London, UK
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
- Cell and Tissue Mechanobiology Laboratory, The Francis Crick Institute, London, UK
| | - Juan F Abenza
- Institute for Bioengineering of Catalonia (IBEC), the Barcelona Institute of Technology (BIST), Barcelona, Spain
| | - Leone Rossetti
- Institute for Bioengineering of Catalonia (IBEC), the Barcelona Institute of Technology (BIST), Barcelona, Spain
| | - Xavier Trepat
- Institute for Bioengineering of Catalonia (IBEC), the Barcelona Institute of Technology (BIST), Barcelona, Spain
- Universitat de Barcelona, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Barcelona, Spain
| | - Barak Raveh
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Pere Roca-Cusachs
- Institute for Bioengineering of Catalonia (IBEC), the Barcelona Institute of Technology (BIST), Barcelona, Spain.
- Universitat de Barcelona, Barcelona, Spain.
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17
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Andreu I, Granero-Moya I, Garcia-Manyes S, Roca-Cusachs P. Understanding the role of mechanics in nucleocytoplasmic transport. APL Bioeng 2022; 6:020901. [PMID: 35783457 PMCID: PMC9246425 DOI: 10.1063/5.0076034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 02/03/2022] [Indexed: 01/26/2023] Open
Abstract
Cell nuclei are submitted to mechanical forces, which in turn affect nuclear and cell functions. Recent evidence shows that a crucial mechanically regulated nuclear function is nucleocytoplasmic transport, mediated by nuclear pore complexes (NPCs). Mechanical regulation occurs at two levels: first, by force application to the nucleus, which increases NPC permeability likely through NPC stretch. Second, by the mechanical properties of the transported proteins themselves, as mechanically labile proteins translocate through NPCs faster than mechanically stiff ones. In this perspective, we discuss this evidence and the associated mechanisms by which mechanics can regulate the nucleo-cytoplasmic partitioning of proteins. Finally, we analyze how mechanical regulation of nucleocytoplasmic transport can provide a systematic approach to the study of mechanobiology and open new avenues both in fundamental and applied research.
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Affiliation(s)
- Ion Andreu
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Technology (BIST), 08028 Barcelona, Spain
| | | | - Sergi Garcia-Manyes
- Department of Physics, Randall Centre for Cell and Molecular Biophysics, King's College London, WC2R 2LS London, United Kingdom; Single Molecule Mechanobiology Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom
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18
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Rico-Pasto M, Zaltron A, Davis SJ, Frutos S, Ritort F. Molten globule-like transition state of protein barnase measured with calorimetric force spectroscopy. Proc Natl Acad Sci U S A 2022; 119:e2112382119. [PMID: 35271392 PMCID: PMC8931224 DOI: 10.1073/pnas.2112382119] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 01/31/2022] [Indexed: 01/11/2023] Open
Abstract
SignificanceUnderstanding the molecular forces driving the unfolded polypeptide chain to self-assemble into a functional native structure remains an open question. However, identifying the states visited during protein folding (e.g., the transition state between the unfolded and native states) is tricky due to their transient nature. Here, we introduce calorimetric force spectroscopy in a temperature jump optical trap to determine the enthalpy, entropy, and heat capacity of the transition state of protein barnase. We find that the transition state has the properties of a dry molten globule, that is, high free energy and low configurational entropy, being structurally similar to the native state. This experimental single-molecule study characterizes the thermodynamic properties of the transition state in funneled energy landscapes.
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Affiliation(s)
- Marc Rico-Pasto
- Small Biosystems Lab, Condensed Matter Physics Department, University of Barcelona, 08028 Barcelona, Spain
| | - Annamaria Zaltron
- Physics and Astronomy Department, University of Padova, 35131 Padova, Italy
| | - Sebastian J. Davis
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, Ecole Polytechnique Federale de Lausanne, 1015 Lausanne, Switzerland
| | | | - Felix Ritort
- Small Biosystems Lab, Condensed Matter Physics Department, University of Barcelona, 08028 Barcelona, Spain
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19
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Matsuda A, Mofrad MRK. On the nuclear pore complex and its emerging role in cellular mechanotransduction. APL Bioeng 2022; 6:011504. [PMID: 35308827 PMCID: PMC8916845 DOI: 10.1063/5.0080480] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 02/21/2022] [Indexed: 12/13/2022] Open
Abstract
The nuclear pore complex (NPC) is a large protein assembly that perforates the nuclear envelope and provides a sole gateway for traffic between the cytoplasm and the nucleus. The NPC controls the nucleocytoplasmic transport by selectively allowing cargoes such as proteins and mRNA to pass through its central channel, thereby playing a vital role in protecting the nuclear component and regulating gene expression and protein synthesis. The selective transport through the NPC originates from its exquisite molecular structure featuring a large scaffold and the intrinsically disordered central channel domain, but the exact mechanism underlying the selective transport remains elusive and is the subject of various, often conflicting, hypotheses. Moreover, recent studies have suggested a new role for the NPC as a mechanosensor, where the NPC changes its channel diameter depending on the nuclear envelope tension, altering the molecular transportability through this nanopore. In this mini-review, we summarize the current understandings of the selective nature of the NPC and discuss its emerging role in cellular mechanotransduction.
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Affiliation(s)
- Atsushi Matsuda
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California Berkeley, Berkeley, California 94720, USA
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20
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Nie J, Deng Y, Tian F, Shi S, Zheng P. Detection of weak non-covalent cation-π interactions in NGAL by single-molecule force spectroscopy. NANO RESEARCH 2022; 15:4251-4257. [PMID: 35574260 PMCID: PMC9077643 DOI: 10.1007/s12274-021-4065-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 11/23/2021] [Accepted: 12/09/2021] [Indexed: 05/14/2023]
Abstract
Cation-π interaction is an electrostatic interaction between a cation and an electron-rich arene. It plays an essential role in many biological systems as a vital driving force for protein folding, stability, and receptor-ligand interaction/recognition. To date, the discovery of most cation-π interactions in proteins relies on the statistical analyses of available three-dimensional (3D) protein structures and corresponding computational calculations. However, their experimental verification and quantification remain sparse at the molecular level, mainly due to the limited methods to dynamically measure such a weak non-covalent interaction in proteins. Here, we use atomic force microscopy-based single-molecule force spectroscopy (AFM-SMFS) to measure the stability of protein neutrophil gelatinase-associated lipocalin (also known as NGAL, siderocalin, lipocalin 2) that can bind iron through the cation-π interactions between its three cationic residues and the iron-binding tri-catechols. Based on a site-specific cysteine engineering and anchoring method, we first characterized the stability and unfolding pathways of apo-NGAL. Then, the same NGAL but bound with the iron-catechol complexes through the cation-π interactions as a holo-form was characterized. AFM measurements demonstrated stronger stabilities and kinetics of the holo-NGAL from two pulling sites, F122 and F133. Here, NGAL is stretched from the designed cysteine close to the cationic residues for a maximum unfolding effect. Thus, our work demonstrates high-precision detection of the weak cation-π interaction in NGAL. Electronic Supplementary Material Supplementary material (additional SDS-PAGE, UV-vis, protein sequences, and more experimental methods) is available in the online version of this article at 10.1007/s12274-021-4065-9.
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Affiliation(s)
- Jingyuan Nie
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Road, Nanjing, 210023 China
| | - Yibing Deng
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Road, Nanjing, 210023 China
| | - Fang Tian
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Road, Nanjing, 210023 China
| | - Shengchao Shi
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Road, Nanjing, 210023 China
| | - Peng Zheng
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Road, Nanjing, 210023 China
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21
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Abstract
Cells generate and sense mechanical forces that trigger biochemical signals to elicit cellular responses that control cell fate changes. Mechanical forces also physically distort neighboring cells and the surrounding connective tissue, which propagate mechanochemical signals over long distances to guide tissue patterning, organogenesis, and adult tissue homeostasis. As the largest and stiffest organelle, the nucleus is particularly sensitive to mechanical force and deformation. Nuclear responses to mechanical force include adaptations in chromatin architecture and transcriptional activity that trigger changes in cell state. These force-driven changes also influence the mechanical properties of chromatin and nuclei themselves to prevent aberrant alterations in nuclear shape and help maintain genome integrity. This review will discuss principles of nuclear mechanotransduction and chromatin mechanics and their role in DNA damage and cell fate regulation.
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Affiliation(s)
- Yekaterina A Miroshnikova
- Helsinki Institute of Life Science, Biomedicum Helsinki, University of Helsinki, Helsinki 00014, Finland
- Wihuri Research Institute, Biomedicum Helsinki, University of Helsinki, Helsinki 00290, Finland
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki 00014, Finland
- Max Planck Institute for Biology of Ageing, Cologne 50931, Germany
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Sara A Wickström
- Helsinki Institute of Life Science, Biomedicum Helsinki, University of Helsinki, Helsinki 00014, Finland
- Wihuri Research Institute, Biomedicum Helsinki, University of Helsinki, Helsinki 00290, Finland
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki 00014, Finland
- Max Planck Institute for Biology of Ageing, Cologne 50931, Germany
- Cluster of Excellence Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne 50931, Germany
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22
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Petrosyan R, Narayan A, Woodside MT. Single-Molecule Force Spectroscopy of Protein Folding. J Mol Biol 2021; 433:167207. [PMID: 34418422 DOI: 10.1016/j.jmb.2021.167207] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/11/2021] [Accepted: 08/11/2021] [Indexed: 10/20/2022]
Abstract
The use of force probes to induce unfolding and refolding of single molecules through the application of mechanical tension, known as single-molecule force spectroscopy (SMFS), has proven to be a powerful tool for studying the dynamics of protein folding. Here we provide an overview of what has been learned about protein folding using SMFS, from small, single-domain proteins to large, multi-domain proteins. We highlight the ability of SMFS to measure the energy landscapes underlying folding, to map complex pathways for native and non-native folding, to probe the mechanisms of chaperones that assist with native folding, to elucidate the effects of the ribosome on co-translational folding, and to monitor the folding of membrane proteins.
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Affiliation(s)
- Rafayel Petrosyan
- Department of Physics, University of Alberta, Edmonton, AB T6G 2E1, Canada
| | - Abhishek Narayan
- Department of Physics, University of Alberta, Edmonton, AB T6G 2E1, Canada
| | - Michael T Woodside
- Department of Physics, University of Alberta, Edmonton, AB T6G 2E1, Canada
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23
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Alegre-Cebollada J. Protein nanomechanics in biological context. Biophys Rev 2021; 13:435-454. [PMID: 34466164 PMCID: PMC8355295 DOI: 10.1007/s12551-021-00822-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 07/05/2021] [Indexed: 12/20/2022] Open
Abstract
How proteins respond to pulling forces, or protein nanomechanics, is a key contributor to the form and function of biological systems. Indeed, the conventional view that proteins are able to diffuse in solution does not apply to the many polypeptides that are anchored to rigid supramolecular structures. These tethered proteins typically have important mechanical roles that enable cells to generate, sense, and transduce mechanical forces. To fully comprehend the interplay between mechanical forces and biology, we must understand how protein nanomechanics emerge in living matter. This endeavor is definitely challenging and only recently has it started to appear tractable. Here, I introduce the main in vitro single-molecule biophysics methods that have been instrumental to investigate protein nanomechanics over the last 2 decades. Then, I present the contemporary view on how mechanical force shapes the free energy of tethered proteins, as well as the effect of biological factors such as post-translational modifications and mutations. To illustrate the contribution of protein nanomechanics to biological function, I review current knowledge on the mechanobiology of selected muscle and cell adhesion proteins including titin, talin, and bacterial pilins. Finally, I discuss emerging methods to modulate protein nanomechanics in living matter, for instance by inducing specific mechanical loss-of-function (mLOF). By interrogating biological systems in a causative manner, these new tools can contribute to further place protein nanomechanics in a biological context.
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24
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Novev JK, Heltberg ML, Jensen MH, Doostmohammadi A. Spatiotemporal model of cellular mechanotransduction via Rho and YAP. Integr Biol (Camb) 2021; 13:197-209. [PMID: 34278428 DOI: 10.1093/intbio/zyab012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 04/29/2021] [Accepted: 06/15/2021] [Indexed: 01/20/2023]
Abstract
How cells sense and respond to mechanical stimuli remains an open question. Recent advances have identified the translocation of Yes-associated protein (YAP) between nucleus and cytoplasm as a central mechanism for sensing mechanical forces and regulating mechanotransduction. We formulate a spatiotemporal model of the mechanotransduction signalling pathway that includes coupling of YAP with the cell force-generation machinery through the Rho family of GTPases. Considering the active and inactive forms of a single Rho protein (GTP/GDP-bound) and of YAP (non-phosphorylated/phosphorylated), we study the cross-talk between cell polarization due to active Rho and YAP activation through its nuclear localization. For fixed mechanical stimuli, our model predicts stationary nuclear-to-cytoplasmic YAP ratios consistent with experimental data at varying adhesive cell area. We further predict damped and even sustained oscillations in the YAP nuclear-to-cytoplasmic ratio by accounting for recently reported positive and negative YAP-Rho feedback. Extending the framework to time-varying mechanical stimuli that simulate cyclic stretching and compression, we show that the YAP nuclear-to-cytoplasmic ratio's time dependence follows that of the cyclic mechanical stimulus. The model presents one of the first frameworks for understanding spatiotemporal YAP mechanotransduction, providing several predictions of possible YAP localization dynamics, and suggesting new directions for experimental and theoretical studies.
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Affiliation(s)
- Javor K Novev
- Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100 Copenhagen Ø, Denmark
| | - Mathias L Heltberg
- Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100 Copenhagen Ø, Denmark.,Laboratoire de Physique, Ecole Normale Superieure, Rue Lhomond 15, Paris 07505, France
| | - Mogens H Jensen
- Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100 Copenhagen Ø, Denmark
| | - Amin Doostmohammadi
- Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100 Copenhagen Ø, Denmark
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25
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Ross JA, Stroud MJ. THE NUCLEUS: Mechanosensing in cardiac disease. Int J Biochem Cell Biol 2021; 137:106035. [PMID: 34242685 DOI: 10.1016/j.biocel.2021.106035] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 06/28/2021] [Accepted: 06/30/2021] [Indexed: 11/17/2022]
Abstract
The nucleus provides a physical and selective chemical boundary to segregate the genome from the cytoplasm. The contents of the nucleus are surrounded by the nuclear envelope, which acts as a hub of mechanosensation, transducing forces from the external cytoskeleton to the nucleus, thus impacting on nuclear morphology, genome organisation, gene transcription and signalling pathways. Muscle tissues such as the heart are unique in that they actively generate large contractile forces, resulting in a distinctive mechanical environment which impacts nuclear properties, function and mechanosensing. In light of this, mutations that affect the function of the nuclear envelope (collectively known as nuclear envelopathies and laminopathies) disproportionately result in striated muscle diseases, which include dilated and arrhythmogenic cardiomyopathies. Here we review the nucleus and its role in mechanotransduction, as well as associated defects that lead to cardiac dysfunction.
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Affiliation(s)
- Jacob A Ross
- British Heart Foundation Centre of Excellence, School of Cardiovascular Medicine and Sciences, King's College London, London, UK
| | - Matthew J Stroud
- British Heart Foundation Centre of Excellence, School of Cardiovascular Medicine and Sciences, King's College London, London, UK.
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26
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Li Y, Tang W, Guo M. The Cell as Matter: Connecting Molecular Biology to Cellular Functions. MATTER 2021; 4:1863-1891. [PMID: 35495565 PMCID: PMC9053450 DOI: 10.1016/j.matt.2021.03.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Viewing cell as matter to understand the intracellular biomolecular processes and multicellular tissue behavior represents an emerging research area at the interface of physics and biology. Cellular material displays various physical and mechanical properties, which can strongly affect both intracellular and multicellular biological events. This review provides a summary of how cells, as matter, connect molecular biology to cellular and multicellular scale functions. As an impact in molecular biology, we review recent progresses in utilizing cellular material properties to direct cell fate decisions in the communities of immune cells, neurons, stem cells, and cancer cells. Finally, we provide an outlook on how to integrate cellular material properties in developing biophysical methods for engineered living systems, regenerative medicine, and disease treatments.
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Affiliation(s)
- Yiwei Li
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Wenhui Tang
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ming Guo
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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27
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Stannard A, Mora M, Beedle AE, Castro-López M, Board S, Garcia-Manyes S. Molecular Fluctuations as a Ruler of Force-Induced Protein Conformations. NANO LETTERS 2021; 21:2953-2961. [PMID: 33765390 PMCID: PMC7610714 DOI: 10.1021/acs.nanolett.1c00051] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Molecular fluctuations directly reflect the underlying energy landscape. Variance analysis examines protein dynamics in several biochemistry-driven approaches, yet measurement of probe-independent fluctuations in proteins exposed to mechanical forces remains only accessible through steered molecular dynamics simulations. Using single molecule magnetic tweezers, here we conduct variance analysis to show that individual unfolding and refolding transitions occurring in dynamic equilibrium in a single protein under force are hallmarked by a change in the protein's end-to-end fluctuations, revealing a change in protein stiffness. By unfolding and refolding three structurally distinct proteins under a wide range of constant forces, we demonstrate that the associated change in protein compliance to reach force-induced thermodynamically stable states scales with the protein's contour length increment, in agreement with the sequence-independent freely jointed chain model of polymer physics. Our findings will help elucidate the conformational dynamics of proteins exposed to mechanical force at high resolution which are of central importance in mechanosensing and mechanotransduction.
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Affiliation(s)
- Andrew Stannard
- Department of Physics, Randall Centre for Cell and Molecular Biophysics and London Centre for Nanotechnology, King’s College London, Strand, WC2R 2LS London, United Kingdom
| | - Marc Mora
- Department of Physics, Randall Centre for Cell and Molecular Biophysics and London Centre for Nanotechnology, King’s College London, Strand, WC2R 2LS London, United Kingdom
| | - Amy E.M. Beedle
- Department of Physics, Randall Centre for Cell and Molecular Biophysics and London Centre for Nanotechnology, King’s College London, Strand, WC2R 2LS London, United Kingdom
| | - Marta Castro-López
- Department of Physics, Randall Centre for Cell and Molecular Biophysics and London Centre for Nanotechnology, King’s College London, Strand, WC2R 2LS London, United Kingdom
| | - Stephanie Board
- Department of Physics, Randall Centre for Cell and Molecular Biophysics and London Centre for Nanotechnology, King’s College London, Strand, WC2R 2LS London, United Kingdom
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, London, UK
| | - Sergi Garcia-Manyes
- Department of Physics, Randall Centre for Cell and Molecular Biophysics and London Centre for Nanotechnology, King’s College London, Strand, WC2R 2LS London, United Kingdom
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, London, UK
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28
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Wang Y, Yang Y, Wang X, Yoshitomi T, Kawazoe N, Yang Y, Chen G. Micropattern-controlled chirality of focal adhesions regulates the cytoskeletal arrangement and gene transfection of mesenchymal stem cells. Biomaterials 2021; 271:120751. [PMID: 33740614 DOI: 10.1016/j.biomaterials.2021.120751] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 02/26/2021] [Accepted: 03/02/2021] [Indexed: 02/07/2023]
Abstract
Cell chirality has been demonstrated to be important for controlling cell functions. However, it is not clear how the chirality of the extracellular microenvironment regulates cell adhesion and cytoskeletal structures and therefore affects gene transfection. In this study, the chirality of focal adhesions and the cytoskeleton of single human mesenchymal stem cells (hMSCs) was controlled by specially designed micropatterns, and its influence on gene transfection was investigated. Micropatterns with different cell adhesion areas and swirling stripe lines were prepared by micropatterning fibronectin on polystyrene surfaces. The chiral micropatterns induced the formation of chiral focal adhesions and chiral cytoskeletal structures. Gene transfection efficiency was enhanced with increasing adhesion area, while hMSCs on left-handed and right-handed swirling micropatterns showed the same level of gene transfection. When the swirling angle was changed from 0°, 30°, and 60° to 90°, the gene transfection efficiency at a swirling angle of 60° was the lowest. The influence of cell chirality on gene transfection was strongly associated with cellular uptake capacity, DNA synthesis and cytoskeletal mechanics. The results demonstrated that cytoskeletal swirling had a significant influence on gene transfection.
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Affiliation(s)
- Yongtao Wang
- Research Center for Functional Materials, National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki, 305-0044, Japan; Department of Materials Science and Engineering, Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Yingjun Yang
- Research Center for Functional Materials, National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki, 305-0044, Japan; Department of Materials Science and Engineering, Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Xinlong Wang
- Research Center for Functional Materials, National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki, 305-0044, Japan; Department of Materials Science and Engineering, Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Toru Yoshitomi
- Research Center for Functional Materials, National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki, 305-0044, Japan
| | - Naoki Kawazoe
- Research Center for Functional Materials, National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki, 305-0044, Japan
| | - Yingnan Yang
- Graduate School of Life and Environmental Science, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan
| | - Guoping Chen
- Research Center for Functional Materials, National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki, 305-0044, Japan; Department of Materials Science and Engineering, Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan.
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29
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Vilhena JG, Ortega M, Uhlig MR, Garcia R, Pérez R. Practical Guide to Single-Protein AFM Nanomechanical Spectroscopy Mapping: Insights and Pitfalls As Unraveled by All-Atom MD Simulations on Immunoglobulin G. ACS Sens 2021; 6:553-564. [PMID: 33503368 DOI: 10.1021/acssensors.0c02241] [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: 12/31/2022]
Abstract
Atomic force microscopy is an invaluable characterization tool in almost every biophysics laboratory. However, obtaining atomic/sub-nanometer resolution on single proteins has thus far remained elusive-a feat long achieved on hard substrates. In this regard, nanomechanical spectroscopy mapping may provide a viable approach to overcome this limitation. By complementing topography with mechanical properties measured locally, one may thus enhance spatial resolution at the single-protein level. In this work, we perform all-atom molecular dynamics simulations of the indentation process on a single immunoglobulin G (IgG) adsorbed on a graphene slab. Our simulations reveal three different stages as a function of strain: a noncontact regime-where the mechanical response is linked to the presence of the water environment- followed by an elastic response and a final plastic deformation regime. In the noncontact regime, we are able to identify hydrophobic/hydrophilic patches over the protein. This regime provides the most local mechanical information that allows one to discern different regions with similar height/topography and leads to the best spatial resolution. In the elastic regime, we conclude that the Young modulus is a well-defined property only within mechanically decoupled domains. This is caused by the fact that the elastic deformation is associated with a global reorganization of the domain. Differences in the mechanical response are large enough to clearly resolve domains within a single protein, such as the three subunits forming the IgG. Two events, unfolding or protein slipping, are observed in the plastic regime. Our simulations allow us to characterize these two processes and to provide a strategy to identify them in the force curves. Finally, we elaborate on possible challenges that could hamper the interpretation of such experiments/simulations and how to overcome them. All in all, our simulations provide a detailed picture of nanomechanical spectroscopy mapping on single proteins, showing its potential and the challenges that need to be overcome to unlock its full potential.
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Affiliation(s)
- J. G. Vilhena
- Department of Physics, University of Basel, Klingelbergstrasse 82, 4056 Basel, Switzerland
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
| | - Maria Ortega
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
| | - Manuel R. Uhlig
- Materials Science Factory, Instituto de Ciencia de Materiales de Madrid (ICMM), CSIC, 28049 Madrid, Spain
| | - Ricardo Garcia
- Materials Science Factory, Instituto de Ciencia de Materiales de Madrid (ICMM), CSIC, 28049 Madrid, Spain
| | - Rubén Pérez
- Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
- Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, E-28049 Madrid, Spain
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30
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Paci G, Caria J, Lemke EA. Cargo transport through the nuclear pore complex at a glance. J Cell Sci 2021; 134:237315. [PMID: 33495357 DOI: 10.1242/jcs.247874] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Bidirectional transport of macromolecules across the nuclear envelope is a hallmark of eukaryotic cells, in which the genetic material is compartmentalized inside the nucleus. The nuclear pore complex (NPC) is the major gateway to the nucleus and it regulates nucleocytoplasmic transport, which is key to processes including transcriptional regulation and cell cycle control. Accordingly, components of the nuclear transport machinery are often found to be dysregulated or hijacked in diseases. In this Cell Science at a Glance article and accompanying poster, we provide an overview of our current understanding of cargo transport through the NPC, from the basic transport signals and machinery to more emerging aspects, all from a 'cargo perspective'. Among these, we discuss the transport of large cargoes (>15 nm), as well as the roles of different cargo properties to nuclear transport, from size and number of bound nuclear transport receptors (NTRs), to surface and mechanical properties.
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Affiliation(s)
- Giulia Paci
- Biocentre, Johannes Gutenberg-University Mainz, Hans-Dieter-Hüsch-Weg 15, 555128 Mainz, Germany.,Institute of Molecular Biology, Ackermannweg 4, 55128 Mainz, Germany.,European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Joana Caria
- Biocentre, Johannes Gutenberg-University Mainz, Hans-Dieter-Hüsch-Weg 15, 555128 Mainz, Germany.,Institute of Molecular Biology, Ackermannweg 4, 55128 Mainz, Germany.,European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Edward A Lemke
- Biocentre, Johannes Gutenberg-University Mainz, Hans-Dieter-Hüsch-Weg 15, 555128 Mainz, Germany .,Institute of Molecular Biology, Ackermannweg 4, 55128 Mainz, Germany.,European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
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31
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Yang B, Liu H, Liu Z, Doenen R, Nash MA. Influence of Fluorination on Single-Molecule Unfolding and Rupture Pathways of a Mechanostable Protein Adhesion Complex. NANO LETTERS 2020; 20:8940-8950. [PMID: 33191756 PMCID: PMC7729889 DOI: 10.1021/acs.nanolett.0c04178] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/08/2020] [Indexed: 05/25/2023]
Abstract
We investigated the influence of fluorination on unfolding and unbinding reaction pathways of a mechanostable protein complex comprising the tandem dyad XModule-Dockerin bound to Cohesin. Using single-molecule atomic force spectroscopy, we mapped the energy landscapes governing the unfolding and unbinding reactions. We then used sense codon suppression to substitute trifluoroleucine in place of canonical leucine globally in XMod-Doc. Although TFL substitution thermally destabilized XMod-Doc, it had little effect on XMod-Doc:Coh binding affinity at equilibrium. When we mechanically dissociated global TFL-substituted XMod-Doc from Coh, we observed the emergence of a new unbinding pathway with a lower energy barrier. Counterintuitively, when fluorination was restricted to Doc, we observed mechano-stabilization of the non-fluorinated neighboring XMod domain. This suggests that intramolecular deformation is modulated by fluorination and highlights the differences between equilibrium thermostability and non-equilibrium mechanostability. Future work is poised to investigate fluorination as a means to modulate mechanical properties of synthetic proteins and hydrogels.
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Affiliation(s)
- Byeongseon Yang
- Department
of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
| | - Haipei Liu
- Department
of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
| | - Zhaowei Liu
- Department
of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
| | - Regina Doenen
- Department
of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
| | - Michael A. Nash
- Department
of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
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32
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Sonar P, Bellucci L, Mossa A, Heidarsson PO, Kragelund BB, Cecconi C. Effects of Ligand Binding on the Energy Landscape of Acyl-CoA-Binding Protein. Biophys J 2020; 119:1821-1832. [PMID: 33080224 PMCID: PMC7677128 DOI: 10.1016/j.bpj.2020.09.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 08/14/2020] [Accepted: 09/08/2020] [Indexed: 12/19/2022] Open
Abstract
Binding of ligands is often crucial for function yet the effects of ligand binding on the mechanical stability and energy landscape of proteins are incompletely understood. Here, we use a combination of single-molecule optical tweezers and MD simulations to investigate the effect of ligand binding on the energy landscape of acyl-coenzyme A (CoA)-binding protein (ACBP). ACBP is a topologically simple and highly conserved four-α-helix bundle protein that acts as an intracellular transporter and buffer for fatty-acyl-CoA and is active in membrane assembly. We have previously described the behavior of ACBP under tension, revealing a highly extended transition state (TS) located almost halfway between the unfolded and native states. Here, we performed force-ramp and force-jump experiments, in combination with advanced statistical analysis, to show that octanoyl-CoA binding increases the activation free energy for the unfolding reaction of ACBP without affecting the position of the transition state along the reaction coordinate. It follows that ligand binding enhances the mechanical resistance and thermodynamic stability of the protein, without changing its mechanical compliance. Steered molecular dynamics simulations allowed us to rationalize the results in terms of key interactions that octanoyl-CoA establishes with the four α-helices of ACBP and showed that the unfolding pathway is marginally affected by the ligand. The results show that ligand-induced mechanical stabilization effects can be complex and may prove useful for the rational design of stabilizing ligands.
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Affiliation(s)
- Punam Sonar
- Physik-Department E22, Technische Universität München, Garching Germany
| | - Luca Bellucci
- NEST, Istituto Nanoscienze-CNR and Scuola Normale Superiore, Piazza San Silvestro 12, Pisa, Italy
| | - Alessandro Mossa
- INFN Firenze, Sesto Fiorentino, Italy; Istituto Statale di Istruzione Superiore "Leonardo da Vinci", Firenze, Italy.
| | - Pétur O Heidarsson
- Department of Biochemistry, Science Institute, University of Iceland, Reykjavík, Iceland.
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen N, Denmark.
| | - Ciro Cecconi
- Department of Physics, Informatics and Mathematics, University of Modena and Reggio Emilia, Modena, Italy; Center S3, CNR Institute Nanoscience, Modena, Italy.
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33
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Sharma S, Subramani S, Popa I. Does protein unfolding play a functional role in vivo? FEBS J 2020; 288:1742-1758. [PMID: 32761965 DOI: 10.1111/febs.15508] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/09/2020] [Accepted: 08/03/2020] [Indexed: 12/21/2022]
Abstract
Unfolding and refolding of multidomain proteins under force have yet to be recognized as a major mechanism of function for proteins in vivo. In this review, we discuss the inherent properties of multidomain proteins under a force vector from a structural and functional perspective. We then characterize three main systems where multidomain proteins could play major roles through mechanical unfolding: muscular contraction, cellular mechanotransduction, and bacterial adhesion. We analyze how key multidomain proteins for each system can produce a gain-of-function from the perspective of a fine-tuned quantized response, a molecular battery, delivery of mechanical work through refolding, elasticity tuning, protection and exposure of cryptic sites, and binding-induced mechanical changes. Understanding how mechanical unfolding and refolding affect function will have important implications in designing mechano-active drugs against conditions such as muscular dystrophy, cancer, or novel antibiotics.
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Affiliation(s)
- Sabita Sharma
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Smrithika Subramani
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Ionel Popa
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
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34
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Paci G, Zheng T, Caria J, Zilman A, Lemke EA. Molecular determinants of large cargo transport into the nucleus. eLife 2020; 9:e55963. [PMID: 32692309 PMCID: PMC7375812 DOI: 10.7554/elife.55963] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 06/18/2020] [Indexed: 01/03/2023] Open
Abstract
Nucleocytoplasmic transport is tightly regulated by the nuclear pore complex (NPC). Among the thousands of molecules that cross the NPC, even very large (>15 nm) cargoes such as pathogens, mRNAs and pre-ribosomes can pass the NPC intact. For these cargoes, there is little quantitative understanding of the requirements for their nuclear import, especially the role of multivalent binding to transport receptors via nuclear localisation sequences (NLSs) and the effect of size on import efficiency. Here, we assayed nuclear import kinetics of 30 large cargo models based on four capsid-like particles in the size range of 17-36 nm, with tuneable numbers of up to 240 NLSs. We show that the requirements for nuclear transport can be recapitulated by a simple two-parameter biophysical model that correlates the import flux with the energetics of large cargo transport through the NPC. Together, our results reveal key molecular determinants of large cargo import in cells.
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Affiliation(s)
- Giulia Paci
- Biocentre, Johannes Gutenberg-University MainzMainzGermany
- Institute of Molecular BiologyMainzGermany
- European Molecular Biology LaboratoryHeidelbergGermany
| | - Tiantian Zheng
- Department of Physics, University of TorontoTorontoCanada
| | - Joana Caria
- Biocentre, Johannes Gutenberg-University MainzMainzGermany
- Institute of Molecular BiologyMainzGermany
- European Molecular Biology LaboratoryHeidelbergGermany
| | - Anton Zilman
- Department of Physics, University of TorontoTorontoCanada
- Institute for Biomaterials and Biomedical Engineering (IBBME), University of TorontoTorontoCanada
| | - Edward A Lemke
- Biocentre, Johannes Gutenberg-University MainzMainzGermany
- Institute of Molecular BiologyMainzGermany
- European Molecular Biology LaboratoryHeidelbergGermany
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35
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Nuclear mechanotransduction in stem cells. Curr Opin Cell Biol 2020; 64:97-104. [DOI: 10.1016/j.ceb.2020.05.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 04/20/2020] [Accepted: 05/05/2020] [Indexed: 12/17/2022]
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36
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Deng Y, Shi S, Zheng B, Wu T, Zheng P. Enzymatic Construction of Protein Polymer/Polyprotein Using OaAEP1 and TEV Protease. Bio Protoc 2020; 10:e3596. [PMID: 33659562 PMCID: PMC7842765 DOI: 10.21769/bioprotoc.3596] [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: 09/23/2019] [Revised: 02/24/2020] [Accepted: 02/26/2020] [Indexed: 04/01/2024] Open
Abstract
The development of chemical and biological coupling technologies in recent years has made possible of protein polymers engineering. We have developed an enzymatic method for building polyproteins using a protein ligase OaAEP1 (asparagine endopeptidase 1) and protease TEV (tobacco etching virus). Using a mobile TEV protease site compatible with the OaAEP1 ligation, we achieved a stepwise polymerization of the protein on the surface. The produced polyprotein can be verified by protein unfolding scenario using atomic force microscopy-based single-molecule force spectroscopy (AFM-SMFS). Thus, this study provides an alternative method for polyprotein engineering and immobilization.
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Affiliation(s)
- Yibing Deng
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 21002, China
| | - Shengchao Shi
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 21002, China
| | - Bin Zheng
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 21002, China
| | - Tao Wu
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 21002, China
| | - Peng Zheng
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 21002, China
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37
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Mora M, Stannard A, Garcia-Manyes S. The nanomechanics of individual proteins. Chem Soc Rev 2020; 49:6816-6832. [DOI: 10.1039/d0cs00426j] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
This tutorial review provides an overview of the single protein force spectroscopy field, including the main techniques and the basic tools for analysing the data obtained from the single molecule experiments.
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Affiliation(s)
- Marc Mora
- Department of Physics and Randall Centre for Cell and Molecular Biophysics
- King's College London
- London
- UK
- The Francis Crick Institute
| | - Andrew Stannard
- Department of Physics and Randall Centre for Cell and Molecular Biophysics
- King's College London
- London
- UK
- The Francis Crick Institute
| | - Sergi Garcia-Manyes
- Department of Physics and Randall Centre for Cell and Molecular Biophysics
- King's College London
- London
- UK
- The Francis Crick Institute
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38
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Li Y, Cao Y. The molecular mechanisms underlying mussel adhesion. NANOSCALE ADVANCES 2019; 1:4246-4257. [PMID: 36134404 PMCID: PMC9418609 DOI: 10.1039/c9na00582j] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Accepted: 10/09/2019] [Indexed: 06/12/2023]
Abstract
Marine mussels are able to firmly affix on various wet surfaces by the overproduction of special mussel foot proteins (mfps). Abundant fundamental studies have been conducted to understand the molecular basis of mussel adhesion, where the catecholic amino acid, l-3,4-dihydroxyphenylalanine (DOPA) has been found to play the major role. These studies continue to inspire the engineering of novel adhesives and coatings with improved underwater performances. Despite the fact that the recent advances of adhesives and coatings inspired by mussel adhesive proteins have been intensively reviewed in literature, the fundamental biochemical and biophysical studies on the origin of the strong and versatile wet adhesion have not been fully covered. In this review, we show how the force measurements at the molecular level by surface force apparatus (SFA) and single molecule atomic force microscopy (AFM) can be used to reveal the direct link between DOPA and the wet adhesion strength of mussel proteins. We highlight a few important technical details that are critical to the successful experimental design. We also summarize many new insights going beyond DOPA adhesion, such as the surface environment and protein sequence dependent synergistic and cooperative binding. We also provide a perspective on a few uncharted but outstanding questions for future studies. A comprehensive understanding on mussel adhesion will be beneficial to the design of novel synthetic wet adhesives for various biomedical applications.
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Affiliation(s)
- Yiran Li
- Shenzhen Research Institute of Nanjing University Shenzhen 518057 China
- Department of Physics, Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Soli State Microstructure, Nanjing University Nanjing 210093 China
| | - Yi Cao
- Shenzhen Research Institute of Nanjing University Shenzhen 518057 China
- Department of Physics, Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Soli State Microstructure, Nanjing University Nanjing 210093 China
- Chemistry and Biomedicine Innovation Center, Nanjing University Nanjing 210093 China
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