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Mistry AC, Chowdhury D, Chakraborty S, Haldar S. Elucidating the novel mechanisms of molecular chaperones by single-molecule technologies. Trends Biochem Sci 2024; 49:38-51. [PMID: 37980187 DOI: 10.1016/j.tibs.2023.10.009] [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: 05/23/2023] [Revised: 10/26/2023] [Accepted: 10/27/2023] [Indexed: 11/20/2023]
Abstract
Molecular chaperones play central roles in sustaining protein homeostasis and preventing protein aggregation. Most studies of these systems have been performed in bulk, providing averaged measurements, though recent single-molecule approaches have provided an in-depth understanding of the molecular mechanisms of their activities and structural rearrangements during substrate recognition. Chaperone activities have been observed to be substrate specific, with some associated with ATP-dependent structural dynamics and others via interactions with co-chaperones. This Review aims to describe the novel mechanisms of molecular chaperones as revealed by single-molecule approaches, and to provide insights into their functioning and its implications for protein homeostasis and human diseases.
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Affiliation(s)
- Ayush Chandrakant Mistry
- Department of Biology, Trivedi School of Biosciences, Ashoka University, Sonepat, Haryana 131029, India
| | - Debojyoti Chowdhury
- Department of Chemical and Biological Sciences, S.N. Bose National Center for Basic Sciences, Kolkata, West Bengal 700106, India
| | - Soham Chakraborty
- Department of Biology, Trivedi School of Biosciences, Ashoka University, Sonepat, Haryana 131029, India
| | - Shubhasis Haldar
- Department of Biology, Trivedi School of Biosciences, Ashoka University, Sonepat, Haryana 131029, India; Department of Chemical and Biological Sciences, S.N. Bose National Center for Basic Sciences, Kolkata, West Bengal 700106, India; Department of Chemistry, Ashoka University, Sonepat, Haryana 131029, India.
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2
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Cheikh MI, Tchoufag J, Osterfield M, Dean K, Bhaduri S, Zhang C, Mandadapu KK, Doubrovinski K. A comprehensive model of Drosophila epithelium reveals the role of embryo geometry and cell topology in mechanical responses. eLife 2023; 12:e85569. [PMID: 37782009 PMCID: PMC10584372 DOI: 10.7554/elife.85569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 09/29/2023] [Indexed: 10/03/2023] Open
Abstract
In order to understand morphogenesis, it is necessary to know the material properties or forces shaping the living tissue. In spite of this need, very few in vivo measurements are currently available. Here, using the early Drosophila embryo as a model, we describe a novel cantilever-based technique which allows for the simultaneous quantification of applied force and tissue displacement in a living embryo. By analyzing data from a series of experiments in which embryonic epithelium is subjected to developmentally relevant perturbations, we conclude that the response to applied force is adiabatic and is dominated by elastic forces and geometric constraints, or system size effects. Crucially, computational modeling of the experimental data indicated that the apical surface of the epithelium must be softer than the basal surface, a result which we confirmed experimentally. Further, we used the combination of experimental data and comprehensive computational model to estimate the elastic modulus of the apical surface and set a lower bound on the elastic modulus of the basal surface. More generally, our investigations revealed important general features that we believe should be more widely addressed when quantitatively modeling tissue mechanics in any system. Specifically, different compartments of the same cell can have very different mechanical properties; when they do, they can contribute differently to different mechanical stimuli and cannot be merely averaged together. Additionally, tissue geometry can play a substantial role in mechanical response, and cannot be neglected.
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Affiliation(s)
- Mohamad Ibrahim Cheikh
- Department of Biophysics, University of Texas Southwestern Medical CenterDallasUnited States
| | - Joel Tchoufag
- Department of Chemical and Biomolecular Engineering, University of California, BerkeleyBerkeleyUnited States
- Chemical Sciences Division, Lawrence Berkeley National LaboratoryBerkeleyUnited States
| | - Miriam Osterfield
- Department of Biophysics, University of Texas Southwestern Medical CenterDallasUnited States
| | - Kevin Dean
- Department of Bioinformatics, University of Texas Southwestern Medical CenterDallasUnited States
| | - Swayamdipta Bhaduri
- Department of Biophysics, University of Texas Southwestern Medical CenterDallasUnited States
| | - Chuzhong Zhang
- Department of Material Science and Engineering, University of Texas at ArlingtonArlingtonUnited States
| | - Kranthi Kiran Mandadapu
- Department of Chemical and Biomolecular Engineering, University of California, BerkeleyBerkeleyUnited States
- Chemical Sciences Division, Lawrence Berkeley National LaboratoryBerkeleyUnited States
| | - Konstantin Doubrovinski
- Department of Biophysics, University of Texas Southwestern Medical CenterDallasUnited States
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Scott S, Weiss M, Selhuber-Unkel C, Barooji YF, Sabri A, Erler JT, Metzler R, Oddershede LB. Extracting, quantifying, and comparing dynamical and biomechanical properties of living matter through single particle tracking. Phys Chem Chem Phys 2023; 25:1513-1537. [PMID: 36546878 DOI: 10.1039/d2cp01384c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A panoply of new tools for tracking single particles and molecules has led to an explosion of experimental data, leading to novel insights into physical properties of living matter governing cellular development and function, health and disease. In this Perspective, we present tools to investigate the dynamics and mechanics of living systems from the molecular to cellular scale via single-particle techniques. In particular, we focus on methods to measure, interpret, and analyse complex data sets that are associated with forces, materials properties, transport, and emergent organisation phenomena within biological and soft-matter systems. Current approaches, challenges, and existing solutions in the associated fields are outlined in order to support the growing community of researchers at the interface of physics and the life sciences. Each section focuses not only on the general physical principles and the potential for understanding living matter, but also on details of practical data extraction and analysis, discussing limitations, interpretation, and comparison across different experimental realisations and theoretical frameworks. Particularly relevant results are introduced as examples. While this Perspective describes living matter from a physical perspective, highlighting experimental and theoretical physics techniques relevant for such systems, it is also meant to serve as a solid starting point for researchers in the life sciences interested in the implementation of biophysical methods.
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Affiliation(s)
- Shane Scott
- Institute of Physiology, Kiel University, Hermann-Rodewald-Straße 5, 24118 Kiel, Germany
| | - Matthias Weiss
- Experimental Physics I, University of Bayreuth, Universitätsstr. 30, D-95447 Bayreuth, Germany
| | - Christine Selhuber-Unkel
- Institute for Molecular Systems Engineering, Heidelberg University, D-69120 Heidelberg, Germany.,Max Planck School Matter to Life, Jahnstraße 29, D-69120 Heidelberg, Germany
| | - Younes F Barooji
- Niels Bohr Institute, Blegdamsvej 17, DK-2100 Copenhagen, Denmark.
| | - Adal Sabri
- Experimental Physics I, University of Bayreuth, Universitätsstr. 30, D-95447 Bayreuth, Germany
| | - Janine T Erler
- BRIC, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark.
| | - Ralf Metzler
- Institute of Physics and Astronomy, University of Potsdam, Karl-Liebknecht Str. 24/25, D-14476 Potsdam, Germany.,Asia Pacific Center for Theoretical Physics, Pohang 37673, Republic of Korea
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Wang H, Zhou F, Guo Y, Ju LA. Micropipette-based biomechanical nanotools on living cells. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2022; 51:119-133. [PMID: 35171346 PMCID: PMC8964576 DOI: 10.1007/s00249-021-01587-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 08/30/2021] [Accepted: 12/13/2021] [Indexed: 12/14/2022]
Abstract
Mechanobiology is an emerging field at the interface of biology and mechanics, investigating the roles of mechanical forces within biomolecules, organelles, cells, and tissues. As a highlight, the recent advances of micropipette-based aspiration assays and dynamic force spectroscopies such as biomembrane force probe (BFP) provide unprecedented mechanobiological insights with excellent live-cell compatibility. In their classic applications, these assays measure force-dependent ligand-receptor-binding kinetics, protein conformational changes, and cellular mechanical properties such as cortical tension and stiffness. In recent years, when combined with advanced microscopies in high spatial and temporal resolutions, these biomechanical nanotools enable characterization of receptor-mediated cell mechanosensing and subsequent organelle behaviors at single-cellular and molecular level. In this review, we summarize the latest developments of these assays for live-cell mechanobiology studies. We also provide perspectives on their future upgrades with multimodal integration and high-throughput capability.
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Affiliation(s)
- Haoqing Wang
- School of Biomedical Engineering, Faculty of Engineering, The University of Sydney, Darlington, NSW, Australia.,Charles Perkins Centre, The University of Sydney, Camperdown, NSW, Australia.,Heart Research Institute, Newtown, NSW, Australia
| | - Fang Zhou
- School of Biomedical Engineering, Faculty of Engineering, The University of Sydney, Darlington, NSW, Australia
| | - Yuze Guo
- School of Biomedical Engineering, Faculty of Engineering, The University of Sydney, Darlington, NSW, Australia
| | - Lining Arnold Ju
- School of Biomedical Engineering, Faculty of Engineering, The University of Sydney, Darlington, NSW, Australia. .,Charles Perkins Centre, The University of Sydney, Camperdown, NSW, Australia. .,Heart Research Institute, Newtown, NSW, Australia.
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Selvaggi L, Ackermann M, Pasakarnis L, Brunner D, Aegerter CM. Force measurements of Myosin II waves at the yolk surface during Drosophila dorsal closure. Biophys J 2022; 121:410-420. [PMID: 34971619 PMCID: PMC8822616 DOI: 10.1016/j.bpj.2021.12.038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 11/19/2021] [Accepted: 12/23/2021] [Indexed: 02/03/2023] Open
Abstract
The mechanical properties and the forces involved during tissue morphogenesis have been the focus of much research in the last years. Absolute values of forces during tissue closure events have not yet been measured. This is also true for a common force-producing mechanism involving Myosin II waves that results in pulsed cell surface contractions. Our patented magnetic tweezer, CAARMA, integrated into a spinning disk confocal microscope, provides a powerful explorative tool for quantitatively measuring forces during tissue morphogenesis. Here, we used this tool to quantify the in vivo force production of Myosin II waves that we observed at the dorsal surface of the yolk cell in stage 13 Drosophila melanogaster embryos. In addition to providing for the first time to our knowledge quantitative values on an active Myosin-driven force, we elucidated the dynamics of the Myosin II waves by measuring their periodicity in both absence and presence of external perturbations, and we characterized the mechanical properties of the dorsal yolk cell surface.
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Affiliation(s)
- Lara Selvaggi
- Physik-Institut, Universität Zürich, Zürich, Switzerland,Department of Molecular Life Science, Universität Zürich, Zürich, Switzerland
| | | | - Laurynas Pasakarnis
- Department of Molecular Life Science, Universität Zürich, Zürich, Switzerland
| | - Damian Brunner
- Department of Molecular Life Science, Universität Zürich, Zürich, Switzerland
| | - Christof M. Aegerter
- Physik-Institut, Universität Zürich, Zürich, Switzerland,Department of Molecular Life Science, Universität Zürich, Zürich, Switzerland,Corresponding author
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Banerjee S, Chakraborty S, Sreepada A, Banerji D, Goyal S, Khurana Y, Haldar S. Cutting-Edge Single-Molecule Technologies Unveil New Mechanics in Cellular Biochemistry. Annu Rev Biophys 2021; 50:419-445. [PMID: 33646813 DOI: 10.1146/annurev-biophys-090420-083836] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Single-molecule technologies have expanded our ability to detect biological events individually, in contrast to ensemble biophysical technologies, where the result provides averaged information. Recent developments in atomic force microscopy have not only enabled us to distinguish the heterogeneous phenomena of individual molecules, but also allowed us to view up to the resolution of a single covalent bond. Similarly, optical tweezers, due to their versatility and precision, have emerged as a potent technique to dissect a diverse range of complex biological processes, from the nanomechanics of ClpXP protease-dependent degradation to force-dependent processivity of motor proteins. Despite the advantages of optical tweezers, the time scales used in this technology were inconsistent with physiological scenarios, which led to the development of magnetic tweezers, where proteins are covalently linked with the glass surface, which in turn increases the observation window of a single biomolecule from minutes to weeks. Unlike optical tweezers, magnetic tweezers use magnetic fields to impose torque, which makes them convenient for studying DNA topology and topoisomerase functioning. Using modified magnetic tweezers, researchers were able to discover the mechanical role of chaperones, which support their substrate proteinsby pulling them during translocation and assist their native folding as a mechanical foldase. In this article, we provide a focused review of many of these new roles of single-molecule technologies, ranging from single bond breaking to complex chaperone machinery, along with the potential to design mechanomedicine, which would be a breakthrough in pharmacological interventions against many diseases.
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Affiliation(s)
- Souradeep Banerjee
- Department of Biological Sciences, Ashoka University, Sonipat, Haryana 131029, India;
| | - Soham Chakraborty
- Department of Biological Sciences, Ashoka University, Sonipat, Haryana 131029, India;
| | - Abhijit Sreepada
- Department of Biological Sciences, Ashoka University, Sonipat, Haryana 131029, India;
| | - Devshuvam Banerji
- Department of Biological Sciences, Ashoka University, Sonipat, Haryana 131029, India;
| | - Shashwat Goyal
- Department of Biological Sciences, Ashoka University, Sonipat, Haryana 131029, India;
| | - Yajushi Khurana
- Department of Biological Sciences, Ashoka University, Sonipat, Haryana 131029, India;
| | - Shubhasis Haldar
- Department of Biological Sciences, Ashoka University, Sonipat, Haryana 131029, India;
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Aermes C, Hayn A, Fischer T, Mierke CT. Environmentally controlled magnetic nano-tweezer for living cells and extracellular matrices. Sci Rep 2020; 10:13453. [PMID: 32778758 PMCID: PMC7417586 DOI: 10.1038/s41598-020-70428-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Accepted: 07/16/2020] [Indexed: 01/08/2023] Open
Abstract
The magnetic tweezer technique has become a versatile tool for unfolding or folding of individual molecules, mainly DNA. In addition to single molecule analysis, the magnetic tweezer can be used to analyze the mechanical properties of cells and extracellular matrices. We have established a magnetic tweezer that is capable of measuring the linear and non-linear viscoelastic behavior of a wide range of soft matter in precisely controlled environmental conditions, such as temperature, CO2 and humidity. The magnetic tweezer presented in this study is suitable to detect specific differences in the mechanical properties of different cell lines, such as human breast cancer cells and mouse embryonic fibroblasts, as well as collagen matrices of distinct concentrations in the presence and absence of fibronectin crosslinks. The precise calibration and control mechanism employed in the presented magnetic tweezer setup provides the ability to apply physiological force up to 5 nN on 4.5 µm superparamagnetic beads coated with fibronectin and coupled to the cells or collagen matrices. These measurements reveal specific local linear and non-linear viscoelastic behavior of the investigated samples. The viscoelastic response of cells and collagen matrices to the force application is best described by a weak power law behavior. Our results demonstrate that the stress stiffening response and the fluidization of cells is cell type specific and varies largely between differently invasive and aggressive cancer cells. Finally, we showed that the viscoelastic behavior of collagen matrices with and without fibronectin crosslinks measured by the magnetic tweezer can be related to the microstructure of these matrices.
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Affiliation(s)
- Christian Aermes
- Faculty of Physics and Earth Science, Peter Debye Institute of Soft Matter Physics, Biological Physics Division, University of Leipzig, Linnéstr. 5, 04103, Leipzig, Germany
| | - Alexander Hayn
- Faculty of Physics and Earth Science, Peter Debye Institute of Soft Matter Physics, Biological Physics Division, University of Leipzig, Linnéstr. 5, 04103, Leipzig, Germany
| | - Tony Fischer
- Faculty of Physics and Earth Science, Peter Debye Institute of Soft Matter Physics, Biological Physics Division, University of Leipzig, Linnéstr. 5, 04103, Leipzig, Germany
| | - Claudia Tanja Mierke
- Faculty of Physics and Earth Science, Peter Debye Institute of Soft Matter Physics, Biological Physics Division, University of Leipzig, Linnéstr. 5, 04103, Leipzig, Germany.
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Atzeni F, Lanfranconi F, Aegerter CM. Disentangling geometrical, viscoelastic and hyperelastic effects in force-displacement relationships of folded biological tissues. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2019; 42:47. [PMID: 31011840 DOI: 10.1140/epje/i2019-11807-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 03/07/2019] [Indexed: 06/09/2023]
Abstract
Drosophila wing discs show a remarkable variability when subject to mechanical perturbation. We developed a stretching bench that allows accurate measurements of instantaneous and time-dependent material behaviour of the disc as a whole, while determining the exact three-dimensional structure of the disc during stretching. Our experiments reveal force relaxation dynamics on timescales that are significant for development, along with a surprisingly nonlinear force-displacement relationship. Concurrently our imaging indicates that the disc is a highly heterogeneous tissue with a complex geometry. Using image-based 3D finite element modelling we are able to identify the contributions of size, shape and materials parameters to the measured force-displacement relations. In particular, we find that simulating the stretching of a disc with stiffness patterns in the extra-cellular matrix (ECM) recapitulates the experimentally found stretched geometries. In our simulations, linear hyperelasticity explains the measured nonlinearity to a surprising extent. To fully match the experimental force-displacement curves, we use an exponentially elastic material, which, when coupled to material relaxation also explains time-dependent experiments. Our simulations predict that as the disc develops, two counteracting effects, namely the discs foldedness and the hardening of the ECM lead to force-relative displacement curves that are nearly conserved during development.
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Affiliation(s)
- Francesco Atzeni
- Physics Institute, University of Zurich, Zurich, Switzerland
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- Life Science Zurich Graduate School, ETH Zurich and University of Zurich, Zurich, Switzerland
| | | | - Christof M Aegerter
- Physics Institute, University of Zurich, Zurich, Switzerland.
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.
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