1
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Lesniewska N, Duval JFL, Caillet C, Razafitianamaharavo A, Pinheiro JP, Bihannic I, Gley R, Le Cordier H, Vyas V, Pagnout C, Sohm B, Beaussart A. Physicochemical surface properties of Chlorella vulgaris: a multiscale assessment, from electrokinetic and proton uptake descriptors to intermolecular adhesion forces. NANOSCALE 2024; 16:5149-5163. [PMID: 38265106 DOI: 10.1039/d3nr04740g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
Given the growing scientific and industrial interests in green microalgae, a comprehensive understanding of the forces controlling the colloidal stability of these bioparticles and their interactions with surrounding aqueous microenvironment is required. Accordingly, we addressed here the electrostatic and hydrophobic surface properties of Chlorella vulgaris from the population down to the individual cell levels. We first investigated the organisation of the electrical double layer at microalgae surfaces on the basis of electrophoresis measurements. Interpretation of the results beyond zeta-potential framework underlined the need to account for both the hydrodynamic softness of the algae cells and the heterogeneity of their interface formed with the outer electrolyte solution. We further explored the nature of the structural charge carriers at microalgae interfaces through potentiometric proton titrations. Extraction of the electrostatic descriptors of interest from such data was obscured by cell physiology processes and dependence thereof on prevailing measurement conditions, which includes light, temperature and medium salinity. As an alternative, cell electrostatics was successfully evaluated at the cellular level upon mapping the molecular interactions at stake between (positively and negatively) charged atomic force microscopy tips and algal surface via chemical force microscopy. A thorough comparison between charge-dependent tip-to-algae surface adhesion and hydrophobicity level of microalgae surface evidenced that the contribution of electrostatics to the overall interaction pattern is largest, and that the electrostatic/hydrophobic balance can be largely modulated by pH. Overall, the combination of multiscale physicochemical approaches allowed a drawing of some of the key biosurface properties that govern microalgae cell-cell and cell-surface interactions.
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Affiliation(s)
| | | | - Céline Caillet
- Université de Lorraine, CNRS, LIEC, F-54000 Nancy, France.
| | | | | | | | - Renaud Gley
- Université de Lorraine, CNRS, LIEC, F-54000 Nancy, France.
| | | | - Varun Vyas
- Université de Lorraine, CNRS, LIEC, F-54000 Nancy, France.
| | | | - Bénédicte Sohm
- Université de Lorraine, CNRS, LIEC, F-57000, Metz, France
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2
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Liu B, Li X, Zhang JP, Li X, Yuan Y, Hou GH, Zhang HJ, Zhang H, Li Y, Mezzenga R. Protein Nanotubes as Advanced Material Platforms and Delivery Systems. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2307627. [PMID: 37921269 DOI: 10.1002/adma.202307627] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 10/22/2023] [Indexed: 11/04/2023]
Abstract
Protein nanotubes (PNTs) as state-of-the-art nanocarriers are promising for various potential applications both in the food and pharmaceutical industries. Derived from edible starting sources like α-lactalbumin, lysozyme, and ovalbumin, PNTs bear properties of biocompatibility and biodegradability. Their large specific surface area and hydrophobic core facilitate chemical modification and loading of bioactive substances, respectively. Moreover, their enhanced permeability and penetration ability across biological barriers such as intestinal mucus, extracellular matrix, and thrombus clot, make it promising platforms for health-related applications. Most importantly, their simple preparation processes enable large-scale production, supporting applications in the biomedical and nanotechnological fields. Understanding the self-assembly principles is crucial for controlling their morphology, size, and shape, and thus provides the ground to a multitude of applications. Here, the current state-of-the-art of PNTs including their building materials, physicochemical properties, and self-assembly mechanisms are comprehensively reviewed. The advantages and limitations, as well as challenges and prospects for their successful applications in biomaterial and pharmaceutical sectors are then discussed and highlighted. Potential cytotoxicity of PNTs and the need of regulations as critical factors for enabling in vivo applications are also highlighted. In the end, a brief summary and future prospects for PNTs as advanced platforms and delivery systems are included.
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Affiliation(s)
- Bin Liu
- Key Laboratory of Precision Nutrition and Food Quality, Research Center of Food Colloids and Delivery of Functionality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China
- Department of Nutrition and Health, China Agricultural University, Beijing, 100091, P. R. China
| | - Xing Li
- Key Laboratory of Precision Nutrition and Food Quality, Research Center of Food Colloids and Delivery of Functionality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China
| | - Ji Peng Zhang
- Key Laboratory of Precision Nutrition and Food Quality, Research Center of Food Colloids and Delivery of Functionality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China
| | - Xin Li
- Key Laboratory of Precision Nutrition and Food Quality, Research Center of Food Colloids and Delivery of Functionality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China
| | - Yu Yuan
- Key Laboratory of Precision Nutrition and Food Quality, Research Center of Food Colloids and Delivery of Functionality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China
| | - Guo Hua Hou
- Key Laboratory of Precision Nutrition and Food Quality, Research Center of Food Colloids and Delivery of Functionality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China
| | - Hui Juan Zhang
- Key Laboratory of Precision Nutrition and Food Quality, Research Center of Food Colloids and Delivery of Functionality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China
| | - Hui Zhang
- Key Laboratory of Precision Nutrition and Food Quality, Research Center of Food Colloids and Delivery of Functionality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China
| | - Yuan Li
- Key Laboratory of Precision Nutrition and Food Quality, Research Center of Food Colloids and Delivery of Functionality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China
| | - Raffaele Mezzenga
- Department of Health Sciences and Technology, ETH Zurich, Zürich, 8092, Switzerland
- Department of Materials, ETH Zurich, Zürich, 8092, Switzerland
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3
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Moretti M, Limongi T, Testi C, Milanetti E, De Angelis MT, Parrotta EI, Scalise S, Santamaria G, Allione M, Lopatin S, Torre B, Zhang P, Marini M, Perozziello G, Candeloro P, Pirri CF, Ruocco G, Cuda G, Di Fabrizio E. Direct Visualization and Identification of Membrane Voltage-Gated Sodium Channels from Human iPSC-Derived Neurons by Multiple Imaging and Light Enhanced Spectroscopy. SMALL METHODS 2022; 6:e2200402. [PMID: 35595684 DOI: 10.1002/smtd.202200402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/22/2022] [Indexed: 06/15/2023]
Abstract
In this study, transmission electron microscopy atomic force microscopy, and surface enhanced Raman spectroscopy are combined through a direct imaging approach, to gather structural and chemical information of complex molecular systems such as ion channels in their original plasma membrane. Customized microfabricated sample holder allows to characterize Nav channels embedded in the original plasma membrane extracted from neuronal cells that are derived from healthy human induced pluripotent stem cells. The identification of the channels is accomplished by using two different approaches, one of them widely used in cryo-EM (the particle analysis method) and the other based on a novel Zernike Polynomial expansion of the images bitmap. This approach allows to carry out a whole series of investigations, one complementary to the other, on the same sample, preserving its state as close as possible to the original membrane configuration.
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Affiliation(s)
- Manola Moretti
- King Abdullah University of Science and Technology, SMILEs lab, PSE Division, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Tania Limongi
- Dipartimento di Scienza Applicata e Tecnologia, Politecnico di Torino, Corso Duca Degli Abruzzi 24, 10129, Torino, Italy
| | - Claudia Testi
- Center for Life Nanoscience, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161, Rome, Italy
| | - Edoardo Milanetti
- Center for Life Nanoscience, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161, Rome, Italy
- Department of Physics, Sapienza University, Piazzale Aldo Moro 5, Rome, 00185, Italy
| | - Maria Teresa De Angelis
- Laboratory of Stem Cell Biology, Department of Experimental and Clinical Medicine, University Magna Graecia, Campus S. Venuta, Viale Europa, Catanzaro, 88100, Italy
| | - Elvira I Parrotta
- Laboratory of Stem Cell Biology, Department of Experimental and Clinical Medicine, University Magna Graecia, Campus S. Venuta, Viale Europa, Catanzaro, 88100, Italy
| | - Stefania Scalise
- Laboratory of Stem Cell Biology, Department of Experimental and Clinical Medicine, University Magna Graecia, Campus S. Venuta, Viale Europa, Catanzaro, 88100, Italy
| | - Gianluca Santamaria
- Laboratory of Stem Cell Biology, Department of Experimental and Clinical Medicine, University Magna Graecia, Campus S. Venuta, Viale Europa, Catanzaro, 88100, Italy
| | - Marco Allione
- King Abdullah University of Science and Technology, SMILEs lab, PSE Division, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Sergei Lopatin
- King Abdullah University of Science and Technology, Imaging and Characterization Core lab, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Bruno Torre
- King Abdullah University of Science and Technology, SMILEs lab, PSE Division, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Peng Zhang
- King Abdullah University of Science and Technology, SMILEs lab, PSE Division, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Monica Marini
- Dipartimento di Scienza Applicata e Tecnologia, Politecnico di Torino, Corso Duca Degli Abruzzi 24, 10129, Torino, Italy
| | - Gerardo Perozziello
- BionNEM lab and Nanotechnology Research Center, Department of Experimental and Clinical Medicine, University Magna Graecia, Campus S. Venuta, Viale Europa, Catanzaro, 88100, Italy
| | - Patrizio Candeloro
- BionNEM lab and Nanotechnology Research Center, Department of Experimental and Clinical Medicine, University Magna Graecia, Campus S. Venuta, Viale Europa, Catanzaro, 88100, Italy
| | - Candido Fabrizio Pirri
- Dipartimento di Scienza Applicata e Tecnologia, Politecnico di Torino, Corso Duca Degli Abruzzi 24, 10129, Torino, Italy
| | - Giancarlo Ruocco
- Department of Physics, Sapienza University, Piazzale Aldo Moro 5, Rome, 00185, Italy
| | - Giovanni Cuda
- Laboratory of Stem Cell Biology, Department of Experimental and Clinical Medicine, University Magna Graecia, Campus S. Venuta, Viale Europa, Catanzaro, 88100, Italy
| | - Enzo Di Fabrizio
- Dipartimento di Scienza Applicata e Tecnologia, Politecnico di Torino, Corso Duca Degli Abruzzi 24, 10129, Torino, Italy
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4
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Laskowski PR, Pluhackova K, Haase M, Lang BM, Nagler G, Kuhn A, Müller DJ. Monitoring the binding and insertion of a single transmembrane protein by an insertase. Nat Commun 2021; 12:7082. [PMID: 34873152 PMCID: PMC8648943 DOI: 10.1038/s41467-021-27315-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 11/11/2021] [Indexed: 11/27/2022] Open
Abstract
Cells employ highly conserved families of insertases and translocases to insert and fold proteins into membranes. How insertases insert and fold membrane proteins is not fully known. To investigate how the bacterial insertase YidC facilitates this process, we here combine single-molecule force spectroscopy and fluorescence spectroscopy approaches, and molecular dynamics simulations. We observe that within 2 ms, the cytoplasmic α-helical hairpin of YidC binds the polypeptide of the membrane protein Pf3 at high conformational variability and kinetic stability. Within 52 ms, YidC strengthens its binding to the substrate and uses the cytoplasmic α-helical hairpin domain and hydrophilic groove to transfer Pf3 to the membrane-inserted, folded state. In this inserted state, Pf3 exposes low conformational variability such as typical for transmembrane α-helical proteins. The presence of YidC homologues in all domains of life gives our mechanistic insight into insertase-mediated membrane protein binding and insertion general relevance for membrane protein biogenesis.
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Affiliation(s)
- Pawel R. Laskowski
- grid.5801.c0000 0001 2156 2780Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | - Kristyna Pluhackova
- grid.5801.c0000 0001 2156 2780Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | - Maximilian Haase
- grid.9464.f0000 0001 2290 1502Molecular Microbiology, Biology Institute, Universität Hohenheim, 70599 Stuttgart, Germany
| | - Brian M. Lang
- grid.5801.c0000 0001 2156 2780Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | - Gisela Nagler
- grid.9464.f0000 0001 2290 1502Molecular Microbiology, Biology Institute, Universität Hohenheim, 70599 Stuttgart, Germany
| | - Andreas Kuhn
- grid.9464.f0000 0001 2290 1502Molecular Microbiology, Biology Institute, Universität Hohenheim, 70599 Stuttgart, Germany
| | - Daniel J. Müller
- grid.5801.c0000 0001 2156 2780Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
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5
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Li M, Xi N, Liu L. Peak force tapping atomic force microscopy for advancing cell and molecular biology. NANOSCALE 2021; 13:8358-8375. [PMID: 33913463 DOI: 10.1039/d1nr01303c] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The advent of atomic force microscopy (AFM) provides an exciting tool to detect molecular and cellular behaviors under aqueous conditions. AFM is able to not only visualize the surface topography of the specimens, but also can quantify the mechanical properties of the specimens by force spectroscopy assay. Nevertheless, integrating AFM topographic imaging with force spectroscopy assay has long been limited due to the low spatiotemporal resolution. In recent years, the appearance of a new AFM imaging mode called peak force tapping (PFT) has shattered this limit. PFT allows AFM to simultaneously acquire the topography and mechanical properties of biological samples with unprecedented spatiotemporal resolution. The practical applications of PFT in the field of life sciences in the past decade have demonstrated the excellent capabilities of PFT in characterizing the fine structures and mechanics of living biological systems in their native states, offering novel possibilities to reveal the underlying mechanisms guiding physiological/pathological activities. In this paper, the recent progress in cell and molecular biology that has been made with the utilization of PFT is summarized, and future perspectives for further progression and biomedical applications of PFT are provided.
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Affiliation(s)
- Mi Li
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang 110016, China and Institutes for Robotics and Intelligent Manufacturing, Chinese Academy of Sciences, Shenyang 110169, China and University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Ning Xi
- Department of Industrial and Manufacturing Systems Engineering, The University of Hong Kong, Hong Kong 999077, China
| | - Lianqing Liu
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang 110016, China and Institutes for Robotics and Intelligent Manufacturing, Chinese Academy of Sciences, Shenyang 110169, China and University of Chinese Academy of Sciences, Beijing 100049, China.
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6
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Müller DJ, Dumitru AC, Lo Giudice C, Gaub HE, Hinterdorfer P, Hummer G, De Yoreo JJ, Dufrêne YF, Alsteens D. Atomic Force Microscopy-Based Force Spectroscopy and Multiparametric Imaging of Biomolecular and Cellular Systems. Chem Rev 2020; 121:11701-11725. [PMID: 33166471 DOI: 10.1021/acs.chemrev.0c00617] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
During the last three decades, a series of key technological improvements turned atomic force microscopy (AFM) into a nanoscopic laboratory to directly observe and chemically characterize molecular and cell biological systems under physiological conditions. Here, we review key technological improvements that have established AFM as an analytical tool to observe and quantify native biological systems from the micro- to the nanoscale. Native biological systems include living tissues, cells, and cellular components such as single or complexed proteins, nucleic acids, lipids, or sugars. We showcase the procedures to customize nanoscopic chemical laboratories by functionalizing AFM tips and outline the advantages and limitations in applying different AFM modes to chemically image, sense, and manipulate biosystems at (sub)nanometer spatial and millisecond temporal resolution. We further discuss theoretical approaches to extract the kinetic and thermodynamic parameters of specific biomolecular interactions detected by AFM for single bonds and extend the discussion to multiple bonds. Finally, we highlight the potential of combining AFM with optical microscopy and spectroscopy to address the full complexity of biological systems and to tackle fundamental challenges in life sciences.
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Affiliation(s)
- Daniel J Müller
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, Mattenstrasse 28, 4056 Basel, Switzerland
| | - Andra C Dumitru
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain (UCLouvain), Croix du Sud, 4-5, bte L7.07.07, B-1348 Louvain-la-Neuve, Belgium
| | - Cristina Lo Giudice
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain (UCLouvain), Croix du Sud, 4-5, bte L7.07.07, B-1348 Louvain-la-Neuve, Belgium
| | - Hermann E Gaub
- Applied Physics, Ludwig-Maximilians-Universität Munich, Amalienstrasse 54, 80799 München, Germany
| | - Peter Hinterdorfer
- Institute of Biophysics, Johannes Kepler University of Linz, Gruberstrasse 40, 4020 Linz, Austria
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics and Department of Physics, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - James J De Yoreo
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States.,Department of Materials Science and Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Yves F Dufrêne
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain (UCLouvain), Croix du Sud, 4-5, bte L7.07.07, B-1348 Louvain-la-Neuve, Belgium
| | - David Alsteens
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain (UCLouvain), Croix du Sud, 4-5, bte L7.07.07, B-1348 Louvain-la-Neuve, Belgium
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7
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Stauffer M, Hirschi S, Ucurum Z, Harder D, Schlesinger R, Fotiadis D. Engineering and Production of the Light-Driven Proton Pump Bacteriorhodopsin in 2D Crystals for Basic Research and Applied Technologies. Methods Protoc 2020; 3:mps3030051. [PMID: 32707904 PMCID: PMC7563565 DOI: 10.3390/mps3030051] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 07/18/2020] [Accepted: 07/19/2020] [Indexed: 11/16/2022] Open
Abstract
The light-driven proton pump bacteriorhodopsin (BR) from the extreme halophilic archaeon Halobacterium salinarum is a retinal-binding protein, which forms highly ordered and thermally stable 2D crystals in native membranes (termed purple membranes). BR and purple membranes (PMs) have been and are still being intensively studied by numerous researchers from different scientific disciplines. Furthermore, PMs are being successfully used in new, emerging technologies such as bioelectronics and bionanotechnology. Most published studies used the wild-type form of BR, because of the intrinsic difficulty to produce genetically modified versions in purple membranes homologously. However, modification and engineering is crucial for studies in basic research and, in particular, to tailor BR for specific applications in applied sciences. We present an extensive and detailed protocol ranging from the genetic modification and cultivation of H. salinarum to the isolation, and biochemical, biophysical and functional characterization of BR and purple membranes. Pitfalls and problems of the homologous expression of BR versions in H. salinarum are discussed and possible solutions presented. The protocol is intended to facilitate the access to genetically modified BR versions for researchers of different scientific disciplines, thus increasing the application of this versatile biomaterial.
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Affiliation(s)
- Mirko Stauffer
- Institute of Biochemistry and Molecular Medicine, and Swiss National Centre of Competence in Research (NCCR) TransCure, University of Bern, 3012 Bern, Switzerland; (M.S.); (S.H.); (Z.U.); (D.H.)
| | - Stephan Hirschi
- Institute of Biochemistry and Molecular Medicine, and Swiss National Centre of Competence in Research (NCCR) TransCure, University of Bern, 3012 Bern, Switzerland; (M.S.); (S.H.); (Z.U.); (D.H.)
| | - Zöhre Ucurum
- Institute of Biochemistry and Molecular Medicine, and Swiss National Centre of Competence in Research (NCCR) TransCure, University of Bern, 3012 Bern, Switzerland; (M.S.); (S.H.); (Z.U.); (D.H.)
| | - Daniel Harder
- Institute of Biochemistry and Molecular Medicine, and Swiss National Centre of Competence in Research (NCCR) TransCure, University of Bern, 3012 Bern, Switzerland; (M.S.); (S.H.); (Z.U.); (D.H.)
| | - Ramona Schlesinger
- Department of Physics, Genetic Biophysics, Freie Universität Berlin, 14195 Berlin, Germany
- Correspondence: (R.S.); (D.F.)
| | - Dimitrios Fotiadis
- Institute of Biochemistry and Molecular Medicine, and Swiss National Centre of Competence in Research (NCCR) TransCure, University of Bern, 3012 Bern, Switzerland; (M.S.); (S.H.); (Z.U.); (D.H.)
- Correspondence: (R.S.); (D.F.)
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8
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Desbiolles BXE, Hannebelle MTM, de Coulon E, Bertsch A, Rohr S, Fantner GE, Renaud P. Volcano-Shaped Scanning Probe Microscopy Probe for Combined Force-Electrogram Recordings from Excitable Cells. NANO LETTERS 2020; 20:4520-4529. [PMID: 32426984 PMCID: PMC7291358 DOI: 10.1021/acs.nanolett.0c01319] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 05/19/2020] [Indexed: 05/30/2023]
Abstract
Atomic force microscopy based approaches have led to remarkable advances in the field of mechanobiology. However, linking the mechanical cues to biological responses requires complementary techniques capable of recording these physiological characteristics. In this study, we present an instrument for combined optical, force, and electrical measurements based on a novel type of scanning probe microscopy cantilever composed of a protruding volcano-shaped nanopatterned microelectrode (nanovolcano probe) at the tip of a suspended microcantilever. This probe enables simultaneous force and electrical recordings from single cells. Successful impedance measurements on mechanically stimulated neonatal rat cardiomyocytes in situ were achieved using these nanovolcano probes. Furthermore, proof of concept experiments demonstrated that extracellular field potentials (electrogram) together with contraction displacement curves could simultaneously be recorded. These features render the nanovolcano probe especially suited for mechanobiological studies aiming at linking mechanical stimuli to electrophysiological responses of single cells.
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Affiliation(s)
- B. X. E. Desbiolles
- Laboratory
of Microsystems LMIS4, Ecole Polytechnique
Fédérale de Lausanne, Lausanne 1015, Switzerland
| | - M. T. M Hannebelle
- Laboratory
of Bio- and Nano- Instrumentation, Ecole
Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
| | - E. de Coulon
- Laboratory
of Cellular Optics II, Department of Physiology, University of Bern, Bern 3012, Switzerland
| | - A. Bertsch
- Laboratory
of Microsystems LMIS4, Ecole Polytechnique
Fédérale de Lausanne, Lausanne 1015, Switzerland
| | - S. Rohr
- Laboratory
of Cellular Optics II, Department of Physiology, University of Bern, Bern 3012, Switzerland
| | - G. E. Fantner
- Laboratory
of Bio- and Nano- Instrumentation, Ecole
Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
| | - P. Renaud
- Laboratory
of Microsystems LMIS4, Ecole Polytechnique
Fédérale de Lausanne, Lausanne 1015, Switzerland
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9
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Abstract
Microbial adhesion and biofilm formation are usually studied using molecular and cellular biology assays, optical and electron microscopy, or laminar flow chamber experiments. Today, atomic force microscopy (AFM) represents a valuable addition to these approaches, enabling the measurement of forces involved in microbial adhesion at the single-molecule level. In this minireview, we discuss recent discoveries made applying state-of-the-art AFM techniques to microbial specimens in order to understand the strength and dynamics of adhesive interactions. These studies shed new light on the molecular mechanisms of adhesion and demonstrate an intimate relationship between force and function in microbial adhesins.
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10
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Synchronous, Crosstalk-free Correlative AFM and Confocal Microscopies/Spectroscopies. Sci Rep 2020; 10:7098. [PMID: 32341407 PMCID: PMC7184616 DOI: 10.1038/s41598-020-62529-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 03/14/2020] [Indexed: 11/08/2022] Open
Abstract
Microscopies have become pillars of our characterization tools to observe biological systems and assemblies. Correlative and synchronous use of different microscopies relies on the fundamental assumption of non-interference during images acquisitions. In this work, by exploring the correlative use of Atomic Force Microscopy and confocal-Fluorescence-Lifetime Imaging Microscopy (AFM-FLIM), we quantify cross-talk effects occurring during synchronous acquisition. We characterize and minimize optomechanical forces on different AFM cantilevers interfering with normal AFM operation as well as spurious luminescence from the tip and cantilever affecting time-resolved fluorescence detection. By defining non-interfering experimental imaging parameters, we show accurate real-time acquisition and two-dimensional mapping of interaction force, fluorescence lifetime and intensity characterizing morphology (AFM) and local viscosity (FLIM) of gel and fluid phases separation of supported lipid model membranes. Finally, as proof of principle by means of synchronous force and fluorescence spectroscopies, we precisely tune the lifetime of a fluorescent nanodiamond positioned on the AFM tip by controlling its distance from a metallic surface. This opens up a novel pathway of quench sensing to image soft biological samples such as membranes since it does not require tip-sample mechanical contact in contrast with conventional AFM in liquid.
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11
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Nirmalraj PN, List J, Battacharya S, Howe G, Xu L, Thompson D, Mayer M. Complete aggregation pathway of amyloid β (1-40) and (1-42) resolved on an atomically clean interface. SCIENCE ADVANCES 2020; 6:eaaz6014. [PMID: 32285004 PMCID: PMC7141833 DOI: 10.1126/sciadv.aaz6014] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 01/14/2020] [Indexed: 05/22/2023]
Abstract
To visualize amyloid β (Aβ) aggregates requires an uncontaminated and artifact-free interface. This paper demonstrates the interface between graphene and pure water (verified to be atomically clean using tunneling microscopy) as an ideal platform for resolving size, shape, and morphology (measured by atomic force microscopy) of Aβ-40 and Aβ-42 peptide assemblies from 0.5 to 150 hours at a 5-hour time interval with single-particle resolution. After confirming faster aggregation of Aβ-42 in comparison to Aβ-40, a stable set of oligomers with a diameter distribution of ~7 to 9 nm was prevalently observed uniquely for Aβ-42 even after fibril appearance. The interaction energies between a distinct class of amyloid aggregates (dodecamers) and graphene was then quantified using molecular dynamics simulations. Last, differences in Aβ-40 and Aβ-42 networks were resolved, wherein only Aβ-42 fibrils were aligned through lateral interactions over micrometer-scale lengths, a property that could be exploited in the design of biofunctional materials.
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Affiliation(s)
- Peter Niraj Nirmalraj
- Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, CH-1700 Fribourg, Switzerland
- Transport at Nanoscale Interfaces Laboratory, Swiss Federal Laboratories for Materials Science and Technology, Dübendorf CH-8600, Switzerland
- Corresponding author.
| | - Jonathan List
- Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, CH-1700 Fribourg, Switzerland
| | - Shayon Battacharya
- Department of Physics, Bernal Institute, University of Limerick, Limerick V94T9PX, Ireland
| | - Geoffrey Howe
- Department of Physics, Bernal Institute, University of Limerick, Limerick V94T9PX, Ireland
| | - Liang Xu
- Department of Physics, Bernal Institute, University of Limerick, Limerick V94T9PX, Ireland
| | - Damien Thompson
- Department of Physics, Bernal Institute, University of Limerick, Limerick V94T9PX, Ireland
| | - Michael Mayer
- Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, CH-1700 Fribourg, Switzerland
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12
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Visser MJ, Pretorius E. Atomic Force Microscopy: The Characterisation of Amyloid Protein Structure in Pathology. Curr Top Med Chem 2020; 19:2958-2973. [DOI: 10.2174/1568026619666191121143240] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 09/24/2019] [Accepted: 09/27/2019] [Indexed: 12/28/2022]
Abstract
:
Proteins are versatile macromolecules that perform a variety of functions and participate in
virtually all cellular processes. The functionality of a protein greatly depends on its structure and alterations
may result in the development of diseases. Most well-known of these are protein misfolding disorders,
which include Alzheimer’s and Parkinson’s diseases as well as type 2 diabetes mellitus, where
soluble proteins transition into insoluble amyloid fibrils. Atomic Force Microscopy (AFM) is capable of
providing a topographical map of the protein and/or its aggregates, as well as probing the nanomechanical
properties of a sample. Moreover, AFM requires relatively simple sample preparation, which presents
the possibility of combining this technique with other research modalities, such as confocal laser
scanning microscopy, Raman spectroscopy and stimulated emission depletion microscopy. In this review,
the basic principles of AFM are discussed, followed by a brief overview of how it has been applied
in biological research. Finally, we focus specifically on its use as a characterisation method to
study protein structure at the nanoscale in pathophysiological conditions, considering both molecules
implicated in disease pathogenesis and the plasma protein fibrinogen. In conclusion, AFM is a userfriendly
tool that supplies multi-parametric data, rendering it a most valuable technique.
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Affiliation(s)
- Maria J.E. Visser
- Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Stellenbosch, Private Bag X1 Matieland, 7602, South Africa
| | - Etheresia Pretorius
- Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Stellenbosch, Private Bag X1 Matieland, 7602, South Africa
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13
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Li M, Xi N, Wang Y, Liu L. Atomic Force Microscopy as a Powerful Multifunctional Tool for Probing the Behaviors of Single Proteins. IEEE Trans Nanobioscience 2020; 19:78-99. [DOI: 10.1109/tnb.2019.2954099] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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14
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Mulvihill E, Pfreundschuh M, Thoma J, Ritzmann N, Müller DJ. High-Resolution Imaging of Maltoporin LamB while Quantifying the Free-Energy Landscape and Asymmetry of Sugar Binding. NANO LETTERS 2019; 19:6442-6453. [PMID: 31385710 DOI: 10.1021/acs.nanolett.9b02674] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Maltoporins are a family of membrane proteins that facilitate the diffusion of hydrophilic molecules and maltosaccharides across the outer membrane of Gram-negative bacteria. Two contradicting models propose the sugar binding, uptake, and transport by maltoporins to be either symmetric or asymmetric. Here, we address this contradiction and introduce force-distance-based atomic force microscopy to image single maltoporin LamB trimers in the membrane at sub-nanometer resolution and simultaneously quantify the binding of different malto-oligosaccharides. We assay subtle differences of the binding free-energy landscape of maltotriose, maltotetraose, and maltopentaose, which quantifies how binding strength and affinity increase with the malto-oligosaccharide chain length. The ligand-binding parameters change considerably by mutating the extracellular loop 3, which folds into and constricts the transmembrane pore of LamB. By recording LamB topographs and structurally mapping binding events at sub-nanometer resolution, we observe LamB to preferentially bind maltodextrin from the periplasmic side, which shows sugar binding and uptake to be asymmetric. The study introduces atomic force microscopy as an analytical nanoscopic tool that can differentiate among the factors modulating and models describing the binding and uptake of substrates by membrane proteins.
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Affiliation(s)
- Estefania Mulvihill
- Department of Biosystems Science and Engineering , Eidgenössische Technische Hochschule (ETH) Zurich , Mattenstrasse 26 , 4058 Basel , Switzerland
| | - Moritz Pfreundschuh
- Department of Biosystems Science and Engineering , Eidgenössische Technische Hochschule (ETH) Zurich , Mattenstrasse 26 , 4058 Basel , Switzerland
| | - Johannes Thoma
- Department of Biosystems Science and Engineering , Eidgenössische Technische Hochschule (ETH) Zurich , Mattenstrasse 26 , 4058 Basel , Switzerland
| | - Noah Ritzmann
- Department of Biosystems Science and Engineering , Eidgenössische Technische Hochschule (ETH) Zurich , Mattenstrasse 26 , 4058 Basel , Switzerland
| | - Daniel J Müller
- Department of Biosystems Science and Engineering , Eidgenössische Technische Hochschule (ETH) Zurich , Mattenstrasse 26 , 4058 Basel , Switzerland
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15
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Lo Giudice C, Dumitru AC, Alsteens D. Probing ligand-receptor bonds in physiologically relevant conditions using AFM. Anal Bioanal Chem 2019; 411:6549-6559. [PMID: 31410537 DOI: 10.1007/s00216-019-02077-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 07/30/2019] [Accepted: 08/07/2019] [Indexed: 12/16/2022]
Abstract
Cell surface receptors, often called transmembrane receptors, are key cellular components as they control and mediate cell communication and signalling, converting extracellular signals into intracellular signals. Elucidating the molecular details of ligand binding (cytokine, growth factors, hormones, pathogens,...) to cell surface receptors and how this binding triggers conformational changes that initiate intracellular signalling is needed to improve our understanding of cellular processes and for rational drug design. Unfortunately, the molecular complexity and high hydrophobicity of membrane proteins significantly hamper their structural and functional characterization in conditions mimicking their native environment. With its piconewton force sensitivity and (sub)nanometer spatial resolution, together with the capability of operating in liquid environment and at physiological temperature, atomic force microscopy (AFM) has proven to be one of the most powerful tools to image and quantify receptor-ligand bonds in situ under physiologically relevant conditions. In this article, a brief overview of the rapid evolution of AFM towards quantitative biological mapping will be given, followed by selected examples highlighting the main advances that AFM-based ligand-receptor studies have brought to the fields of cell biology, immunology, microbiology, and virology, along with future prospects and challenges. Graphical abstract.
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Affiliation(s)
- Cristina Lo Giudice
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Croix du sud 4-5, 1348, Louvain-la-Neuve, Belgium
| | - Andra C Dumitru
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Croix du sud 4-5, 1348, Louvain-la-Neuve, Belgium
| | - David Alsteens
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Croix du sud 4-5, 1348, Louvain-la-Neuve, Belgium.
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16
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Hirschi S, Fischer N, Kalbermatter D, Laskowski PR, Ucurum Z, Müller DJ, Fotiadis D. Design and assembly of a chemically switchable and fluorescently traceable light-driven proton pump system for bionanotechnological applications. Sci Rep 2019; 9:1046. [PMID: 30705382 PMCID: PMC6355921 DOI: 10.1038/s41598-018-37260-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 11/29/2018] [Indexed: 02/07/2023] Open
Abstract
Energy-supplying modules are essential building blocks for the assembly of functional multicomponent nanoreactors in synthetic biology. Proteorhodopsin, a light-driven proton pump, is an ideal candidate to provide the required energy in form of an electrochemical proton gradient. Here we present an advanced proteoliposome system equipped with a chemically on-off switchable proteorhodopsin variant. The proton pump was engineered to optimize the specificity and efficiency of chemical deactivation and reactivation. To optically track and characterize the proteoliposome system using fluorescence microscopy and nanoparticle tracking analysis, fluorescenlty labelled lipids were implemented. Fluorescence is a highly valuable feature that enables detection and tracking of nanoreactors in complex media. Cryo-transmission electron microscopy, and correlative atomic force and confocal microscopy revealed that our procedure yields polylamellar proteoliposomes, which exhibit enhanced mechanical stability. The combination of these features makes the presented energizing system a promising foundation for the engineering of complex nanoreactors.
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Affiliation(s)
- S Hirschi
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
| | - N Fischer
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
| | - D Kalbermatter
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
| | - P R Laskowski
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Z Ucurum
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
| | - D J Müller
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - D Fotiadis
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland.
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QIN GG, LI WH, XU JC, KOU XL, ZHAO R, LUO F, FANG XH. Development of Integrated Atomic Force Microscopy and Fluorescence Microscopy for Single-Molecule Analysis in Living Cells. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2017. [DOI: 10.1016/s1872-2040(17)61056-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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