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Filippidi E, Dhiman AK, Li B, Athanasiou T, Vlassopoulos D, Fytas G. Multiscale Elasticity of Epoxy Networks by Rheology and Brillouin Light Spectroscopy. J Phys Chem B 2024; 128:12628-12637. [PMID: 39630480 DOI: 10.1021/acs.jpcb.4c06492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2024]
Abstract
The response of soft materials to an imposed oscillatory stress is typically frequency dependent, with the most utilized frequency range falling in the range of 10-2-102 rad/s. In contrast to most conventional contact techniques for measuring material elasticity, like tensile or shear rheology and atomic force microscopy, or invasive techniques using probes, such as microrheology, Brillouin light spectroscopy (BLS) offers an optical, noncontact, label-free, submicron resolution and three-dimensional (3D) mapping approach to access the mechanical moduli at GHz frequencies. Currently, the correlation between the experimental viscoelastic (at lower frequencies) and elastic (at higher frequencies) moduli has fundamental and practical relevance, but remains unclear. We utilize a series of solvent-free epoxy polymer networks with variable cross-link density as models to compare the storage modulus, G', (in the MPa range) obtained from shear rheology and the longitudinal modulus, M', (in the GPa range) extracted from BLS. Our results show that G' exhibits a much stronger increase with increasing cross-link density than M' (by a factor of about 3.5). This finding is discussed in the context of the phantom network model for G' and Wood's inverse rule of mixtures for M'. The epoxy polymer network displays an unexpectedly fast hypersonic dispersion compared to its uncross-linked precursor. These results testify the importance of obtaining reliable information about the elasticity of networks and will hopefully trigger further investigations in the direction of bridging the elasticity of soft materials at different scales.
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Affiliation(s)
- Emmanouela Filippidi
- Department of Materials Science and Engineering, University of Crete, Heraklion 70013, Greece
- Institute of Electronic Structure and Laser, FORTH, Heraklion 70013, Greece
| | - Anuj K Dhiman
- Faculty of Physics, Adam Mickiewicz University, Uniwersytetu Poznanskiego 2, Poznan 61614, Poland
| | - Benke Li
- Institute of Electronic Structure and Laser, FORTH, Heraklion 70013, Greece
| | | | - Dimitris Vlassopoulos
- Department of Materials Science and Engineering, University of Crete, Heraklion 70013, Greece
- Institute of Electronic Structure and Laser, FORTH, Heraklion 70013, Greece
| | - George Fytas
- Institute of Electronic Structure and Laser, FORTH, Heraklion 70013, Greece
- Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz 55128, Germany
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2
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Shin DS, Son MJ, Bae M, Kim H. Local Stiffness Measurement of Hepatic Steatosis Model Liver Organoid by Fluorescence Imaging-Assisted Probe Indentation. ACS Biomater Sci Eng 2024; 10:7386-7393. [PMID: 39562163 DOI: 10.1021/acsbiomaterials.4c01242] [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] [Indexed: 11/21/2024]
Abstract
Mechanical stiffness of liver organoid is a key indicator for the progress of hepatic steatosis. Probe indentation is a noninvasive methodology to measure Young's modulus (YM); however, the inhomogeneous nature of the liver organoid induces measurement uncertainty requiring a large number of indentations covering a wide scanning area. Here, we demonstrate that lipid-stained fluorescence imaging-assisted probe indentation significantly reduces the number of measurements by specifying the highly lipid-induced area. Lipid-stained hepatic steatosis model liver organoid shows broad fluorescence distributions that are spatially correlated with a decreased YM on a lipid-filled region with bright fluorescence compared with that measured on a blank region with dark fluorescence. The organoid viability remained robust even after exposure to an ambient condition up to 6 h, showing that probe indentations can be noninvasive methods for liver organoid stiffness measurements.
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Affiliation(s)
- Dae-Seop Shin
- Drug Discovery Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Republic of Korea
| | - Myung Jin Son
- Stem Cell Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Department of Functional Genomics, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Myungae Bae
- Drug Discovery Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Republic of Korea
| | - Hyunwoo Kim
- Drug Discovery Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Republic of Korea
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3
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Fan X, Donose B, Jones MWM, Howard D, Torniainen J, Bertling K, Guo X, Kewish CM, Lee KM, Sun AR, Rakic A, Crawford R, Afara IO, Prasadam I. A novel tape-free sample preparation method for human osteochondral cryosections for high throughput hyperspectral imaging. Histochem Cell Biol 2024; 163:16. [PMID: 39621099 DOI: 10.1007/s00418-024-02338-1] [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] [Accepted: 09/27/2024] [Indexed: 12/16/2024]
Abstract
Understanding the osteochondral junction, where non-mineralised cartilage and mineralised bone converge, is crucial for joint health. Current sample preparation techniques are insufficient for detailed spatial hyperspectral imaging analysis. Using the enhanced Kawamoto method, we used the super cryo embedding medium's temperature-dependent properties to transfer high-quality tissue samples onto slides for spatial imaging analysis. We transferred osteochondral samples using a tape-free system and successfully tested them in hematoxylin and eosin (HE), Safranin-O, nanomechanical assessments and nano-Fourier transform infrared (FTIR) mapping. This protocol elucidates the structural and elemental gradients, mechanical characteristics and distinctive biochemical layering, making it a useful tool for analysing biochemical properties' co-distribution in healthy and diseased situations.
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Affiliation(s)
- Xiwei Fan
- Department of Orthopaedic Surgery, The Second Xiangya Hospital of Central South University, Changsha, China
- School of Mechanical, Medical & Process Engineering, Queensland University of Technology, 60 Musk Ave/Cnr. Blamey St, Kelvin Grove, Brisbane, QLD, 4059, Australia
- Centre for Biomedical Technologies, Queensland University of Technology, 60 Musk Ave/Cnr. Blamey St, Kelvin Grove, Brisbane, QLD, 4059, Australia
| | - Bogdan Donose
- School of Electrical Engineering and Computer Science, Faculty of Engineering, Architecture and Information Technology, University of Queensland, Brisbane, Australia
| | - Michael W M Jones
- Central Analytical Research Facility, Queensland University of Technology, Brisbane, Australia
- School of Chemistry and Physics, Queensland University of Technology, Brisbane, Australia
| | - Daryl Howard
- Australian Nuclear Science and Technology Organisation, Australian Synchrotron, Melbourne, Australia
| | - Jari Torniainen
- School of Electrical Engineering and Computer Science, Faculty of Engineering, Architecture and Information Technology, University of Queensland, Brisbane, Australia
| | - Karl Bertling
- School of Electrical Engineering and Computer Science, Faculty of Engineering, Architecture and Information Technology, University of Queensland, Brisbane, Australia
| | - Xiao Guo
- School of Electrical Engineering and Computer Science, Faculty of Engineering, Architecture and Information Technology, University of Queensland, Brisbane, Australia
| | - Cameron M Kewish
- Australian Nuclear Science and Technology Organisation, Australian Synchrotron, Melbourne, Australia
- Department of Chemistry and Physics, La Trobe University, Bundoora, Australia
| | - Kah Meng Lee
- Central Analytical Research Facility, Queensland University of Technology, Brisbane, Australia
| | - Antonia Rujia Sun
- School of Mechanical, Medical & Process Engineering, Queensland University of Technology, 60 Musk Ave/Cnr. Blamey St, Kelvin Grove, Brisbane, QLD, 4059, Australia
- Centre for Biomedical Technologies, Queensland University of Technology, 60 Musk Ave/Cnr. Blamey St, Kelvin Grove, Brisbane, QLD, 4059, Australia
| | - Aleksandar Rakic
- School of Electrical Engineering and Computer Science, Faculty of Engineering, Architecture and Information Technology, University of Queensland, Brisbane, Australia
| | - Ross Crawford
- School of Mechanical, Medical & Process Engineering, Queensland University of Technology, 60 Musk Ave/Cnr. Blamey St, Kelvin Grove, Brisbane, QLD, 4059, Australia
- The Prince Charles Hospital, Brisbane, Australia
| | - Isaac O Afara
- School of Electrical Engineering and Computer Science, Faculty of Engineering, Architecture and Information Technology, University of Queensland, Brisbane, Australia.
- Department of Technical Physics, University of Eastern Finland, Kuopio, Finland.
| | - Indira Prasadam
- School of Mechanical, Medical & Process Engineering, Queensland University of Technology, 60 Musk Ave/Cnr. Blamey St, Kelvin Grove, Brisbane, QLD, 4059, Australia.
- Centre for Biomedical Technologies, Queensland University of Technology, 60 Musk Ave/Cnr. Blamey St, Kelvin Grove, Brisbane, QLD, 4059, Australia.
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4
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O’Dowling AT, Rodriguez BJ, Gallagher TK, Thorpe SD. Machine learning and artificial intelligence: Enabling the clinical translation of atomic force microscopy-based biomarkers for cancer diagnosis. Comput Struct Biotechnol J 2024; 24:661-671. [PMID: 39525667 PMCID: PMC11543504 DOI: 10.1016/j.csbj.2024.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Revised: 10/02/2024] [Accepted: 10/02/2024] [Indexed: 11/16/2024] Open
Abstract
The influence of biomechanics on cell function has become increasingly defined over recent years. Biomechanical changes are known to affect oncogenesis; however, these effects are not yet fully understood. Atomic force microscopy (AFM) is the gold standard method for measuring tissue mechanics on the micro- or nano-scale. Due to its complexity, however, AFM has yet to become integrated in routine clinical diagnosis. Artificial intelligence (AI) and machine learning (ML) have the potential to make AFM more accessible, principally through automation of analysis. In this review, AFM and its use for the assessment of cell and tissue mechanics in cancer is described. Research relating to the application of artificial intelligence and machine learning in the analysis of AFM topography and force spectroscopy of cancer tissue and cells are reviewed. The application of machine learning and artificial intelligence to AFM has the potential to enable the widespread use of nanoscale morphologic and biomechanical features as diagnostic and prognostic biomarkers in cancer treatment.
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Affiliation(s)
- Aidan T. O’Dowling
- UCD School of Medicine, University College Dublin, Dublin, Ireland
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
- Department of Hepatobiliary and Transplant Surgery, St Vincent’s University Hospital, Dublin, Ireland
| | - Brian J. Rodriguez
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
- UCD School of Physics, University College Dublin, Dublin, Ireland
| | - Tom K. Gallagher
- UCD School of Medicine, University College Dublin, Dublin, Ireland
- Department of Hepatobiliary and Transplant Surgery, St Vincent’s University Hospital, Dublin, Ireland
| | - Stephen D. Thorpe
- UCD School of Medicine, University College Dublin, Dublin, Ireland
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
- Trinity Centre for Bioengineering, Trinity College Dublin, Dublin, Ireland
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5
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Li M. Atomic force microscopy as a nanomechanical tool for cancer liquid biopsy. Biochem Biophys Res Commun 2024; 734:150637. [PMID: 39226737 DOI: 10.1016/j.bbrc.2024.150637] [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: 07/25/2024] [Revised: 08/24/2024] [Accepted: 08/30/2024] [Indexed: 09/05/2024]
Abstract
Liquid biopsies have been receiving tremendous attention for their potential to reshape cancer management. Though current studies of cancer liquid biopsy primarily focus on applying biochemical assays to characterize the genetic/molecular profiles of circulating tumor cells (CTCs) and their secondary products shed from tumor sites in bodily fluids, delineating the nanomechanical properties of tumor-associated materials in liquid biopsy specimens yields complementary insights into the biology of tumor dissemination and evolution. Particularly, atomic force microscopy (AFM) has become a standard and versatile toolbox for characterizing the mechanical properties of living biological systems at the micro/nanoscale, and AFM has been increasingly utilized to probe the nanomechanical properties of various tumor-derived analytes in liquid biopsies, including CTCs, tumor-associated cells, circulating tumor DNA (ctDNA) molecules, and extracellular vesicles (EVs), offering additional possibilities for understanding cancer pathogenesis from the perspective of mechanobiology. Herein, the applications of AFM in cancer liquid biopsy are summarized, and the challenges and future directions of AFM as a nanomechanical analysis tool in cancer liquid biopsy towards clinical utility are discussed and envisioned.
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Affiliation(s)
- Mi Li
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang, 110016, China.
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Dos Santos Natividade R, Dumitru AC, Nicoli A, Strebl M, Sutherland DM, Welsh OL, Ghulam M, Stehle T, Dermody TS, Di Pizio A, Koehler M, Alsteens D. Viral capsid structural assembly governs the reovirus binding interface to NgR1. NANOSCALE HORIZONS 2024; 9:1925-1937. [PMID: 39347978 PMCID: PMC11441417 DOI: 10.1039/d4nh00315b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Accepted: 09/13/2024] [Indexed: 10/01/2024]
Abstract
Understanding the mechanisms underlying viral entry is crucial for controlling viral diseases. In this study, we investigated the interactions between reovirus and Nogo-receptor 1 (NgR1), a key mediator of reovirus entry into the host central nervous system. NgR1 exhibits a unique bivalent interaction with the reovirus capsid, specifically binding at the interface between adjacent heterohexamers arranged in a precise structural pattern on the curved virus surface. Using single-molecule techniques, we explored for the first time how the capsid molecular architecture and receptor polymorphism influence virus binding. We compared the binding affinities of human and mouse NgR1 to reovirus μ1/σ3 proteins in their isolated form, self-assembled in 2D capsid patches, and within the native 3D viral topology. Our results underscore the essential role of the concave side of NgR1 and emphasize that the spatial organization and curvature of the virus are critical determinants of the stability of the reovirus-NgR1 complex. This study highlights the importance of characterizing interactions in physiologically relevant spatial configurations, providing precise insights into virus-host interactions and opening new avenues for therapeutic interventions against viral infections.
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Affiliation(s)
- Rita Dos Santos Natividade
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium.
| | - Andra C Dumitru
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium.
| | - Alessandro Nicoli
- Leibniz Institute for Food Systems Biology, Technical University of Munich, Freising, Germany.
- Chemoinformatics and Protein Modelling, Department of Molecular Life Sciences, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Michael Strebl
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Danica M Sutherland
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Institute of Infection, Inflammation, and Immunity, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Olivia L Welsh
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Institute of Infection, Inflammation, and Immunity, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Mustafa Ghulam
- Leibniz Institute for Food Systems Biology, Technical University of Munich, Freising, Germany.
| | - Thilo Stehle
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Terence S Dermody
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Institute of Infection, Inflammation, and Immunity, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Antonella Di Pizio
- Leibniz Institute for Food Systems Biology, Technical University of Munich, Freising, Germany.
- Chemoinformatics and Protein Modelling, Department of Molecular Life Sciences, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Melanie Koehler
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium.
- Leibniz Institute for Food Systems Biology, Technical University of Munich, Freising, Germany.
| | - David Alsteens
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium.
- WELBIO department, WEL Research Institute, 1300 Wavre, Belgium
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7
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Huang S, Su G, Yang L, Yue L, Chen L, Huang J, Yang F. Single-Molecule-Level Quantification Based on Atomic Force Microscopy Data Reveals the Interaction between Melittin and Lipopolysaccharide in Gram-Negative Bacteria. Int J Mol Sci 2024; 25:10508. [PMID: 39408837 PMCID: PMC11477153 DOI: 10.3390/ijms251910508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2024] [Revised: 09/26/2024] [Accepted: 09/27/2024] [Indexed: 10/20/2024] Open
Abstract
The interaction forces and mechanical properties of the interaction between melittin (Mel) and lipopolysaccharide (LPS) are considered to be crucial driving forces for Mel when killing Gram-negative bacteria (GNB). However, how their interaction forces perform at the single-molecule level and the dissociation kinetic characteristics of the Mel/LPS complex remain poorly understood. In this study, the single-molecule-level interaction forces between Mel and LPSs from E. coli K-12, O55:B5, O111:B4, and O128:B12 were explored using atomic force microscopy (AFM)-based single-molecule force spectroscopy (SMFS). AFM-based dynamic force spectroscopy (DFS) and an advanced analytical model were employed to investigate the kinetic characteristics of the Mel/LPS complex dissociation. The results indicated that Mel could interact with both rough (R)-form LPS (E. coli K-12) and smooth (S)-form LPSs (E. coli O55:B5, O111:B4, and O128:B12). The S-form LPS showed a more robust interaction with Mel than the R-form LPS, and a slight difference existed in the interaction forces between Mel and the diverse S-form LPS. Mel interactions with the S-form LPSs showed greater specific and non-specific interaction forces than the R-form LPS (p < 0.05), as determined by AFM-based SMFS. However, there was no significant difference in the specific and non-specific interaction forces among the three samples of S-form LPSs (p > 0.05), indicating that the variability in the O-antigen did not affect the interaction between Mel and LPSs. The DFS result showed that the Mel/S-form LPS complexes had a lower dissociation rate constant, a shorter energy barrier width, a longer bond lifetime, and a higher energy barrier height, demonstrating that Mel interacted with S-form LPS to form more stable complexes. This research enhances the existing knowledge of the interaction micromechanics and kinetic characteristics of Mel and LPS at the single-molecule level. Our research may help with the design and evaluation of new anti-GNB drugs.
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Affiliation(s)
- Sheng Huang
- Animal Nutrition Institute, Chongqing Academy of Animal Science, Chongqing 402460, China; (S.H.); (G.S.); (L.C.)
- Institute of Nutrition and Feed, National Center of Technology Innovation for Pigs, Chongqing 402460, China; (L.Y.); (L.Y.)
| | - Guoqi Su
- Animal Nutrition Institute, Chongqing Academy of Animal Science, Chongqing 402460, China; (S.H.); (G.S.); (L.C.)
- Institute of Nutrition and Feed, National Center of Technology Innovation for Pigs, Chongqing 402460, China; (L.Y.); (L.Y.)
| | - Li Yang
- Institute of Nutrition and Feed, National Center of Technology Innovation for Pigs, Chongqing 402460, China; (L.Y.); (L.Y.)
| | - Liangguang Yue
- Institute of Nutrition and Feed, National Center of Technology Innovation for Pigs, Chongqing 402460, China; (L.Y.); (L.Y.)
| | - Li Chen
- Animal Nutrition Institute, Chongqing Academy of Animal Science, Chongqing 402460, China; (S.H.); (G.S.); (L.C.)
- Institute of Nutrition and Feed, National Center of Technology Innovation for Pigs, Chongqing 402460, China; (L.Y.); (L.Y.)
| | - Jinxiu Huang
- Animal Nutrition Institute, Chongqing Academy of Animal Science, Chongqing 402460, China; (S.H.); (G.S.); (L.C.)
- Institute of Nutrition and Feed, National Center of Technology Innovation for Pigs, Chongqing 402460, China; (L.Y.); (L.Y.)
| | - Feiyun Yang
- Animal Nutrition Institute, Chongqing Academy of Animal Science, Chongqing 402460, China; (S.H.); (G.S.); (L.C.)
- Institute of Nutrition and Feed, National Center of Technology Innovation for Pigs, Chongqing 402460, China; (L.Y.); (L.Y.)
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8
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Yang X, Li M. Label-free and rapid mechanics of single cells under high-density co-culture conditions by deep learning image recognition-assisted atomic force microscopy. Acta Biochim Biophys Sin (Shanghai) 2024. [PMID: 39295485 DOI: 10.3724/abbs.2024158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/21/2024] Open
Affiliation(s)
- Xuliang Yang
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang 110016, China
- School of Artificial Intelligence, Shenyang University of Technology, Shenyang 110870, China
| | - Mi Li
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang 110016, China
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9
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Edgecomb J, Nguyen DT, Tan S, Murugesan V, Johnson GE, Prabhakaran V. Electrochemical Imaging of Precisely-Defined Redox and Reactive Interfaces. Angew Chem Int Ed Engl 2024; 63:e202405846. [PMID: 38871656 DOI: 10.1002/anie.202405846] [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: 03/26/2024] [Revised: 06/13/2024] [Accepted: 06/13/2024] [Indexed: 06/15/2024]
Abstract
Understanding the diverse electrochemical reactions occurring at electrode-electrolyte interfaces (EEIs) is a critical challenge to developing more efficient energy conversion and storage technologies. Establishing a predictive molecular-level understanding of solid electrolyte interphases (SEIs) is challenging due to the presence of multiple intertwined chemical and electrochemical processes occurring at battery electrodes. Similarly, chemical conversions in reactive electrochemical systems are often influenced by the heterogeneous distribution of active sites, surface defects, and catalyst particle sizes. In this mini review, we highlight an emerging field of interfacial science that isolates the impact of specific chemical species by preparing precisely-defined EEIs and visualizing the reactivity of their individual components using single-entity characterization techniques. We highlight the broad applicability and versatility of these methods, along with current state-of-the-art instrumentation and future opportunities for these approaches to address key scientific challenges related to batteries, chemical separations, and fuel cells. We establish that controlled preparation of well-defined electrodes combined with single entity characterization will be crucial to filling key knowledge gaps and advancing the theories used to describe and predict chemical and physical processes occurring at EEIs and accelerating new materials discovery for energy applications.
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Affiliation(s)
- Joseph Edgecomb
- Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | | | - Shuai Tan
- Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | | | - Grant E Johnson
- Pacific Northwest National Laboratory, Richland, WA 99352, USA
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Kogut-Günthel MM, Zara Z, Nicoli A, Steuer A, Lopez-Balastegui M, Selent J, Karanth S, Koehler M, Ciancetta A, Abiko LA, Hagn F, Di Pizio A. The path to the G protein-coupled receptor structural landscape: Major milestones and future directions. Br J Pharmacol 2024. [PMID: 39209310 DOI: 10.1111/bph.17314] [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: 12/20/2023] [Revised: 06/14/2024] [Accepted: 06/28/2024] [Indexed: 09/04/2024] Open
Abstract
G protein-coupled receptors (GPCRs) play a crucial role in cell function by transducing signals from the extracellular environment to the inside of the cell. They mediate the effects of various stimuli, including hormones, neurotransmitters, ions, photons, food tastants and odorants, and are renowned drug targets. Advancements in structural biology techniques, including X-ray crystallography and cryo-electron microscopy (cryo-EM), have driven the elucidation of an increasing number of GPCR structures. These structures reveal novel features that shed light on receptor activation, dimerization and oligomerization, dichotomy between orthosteric and allosteric modulation, and the intricate interactions underlying signal transduction, providing insights into diverse ligand-binding modes and signalling pathways. However, a substantial portion of the GPCR repertoire and their activation states remain structurally unexplored. Future efforts should prioritize capturing the full structural diversity of GPCRs across multiple dimensions. To do so, the integration of structural biology with biophysical and computational techniques will be essential. We describe in this review the progress of nuclear magnetic resonance (NMR) to examine GPCR plasticity and conformational dynamics, of atomic force microscopy (AFM) to explore the spatial-temporal dynamics and kinetic aspects of GPCRs, and the recent breakthroughs in artificial intelligence for protein structure prediction to characterize the structures of the entire GPCRome. In summary, the journey through GPCR structural biology provided in this review illustrates how far we have come in decoding these essential proteins architecture and function. Looking ahead, integrating cutting-edge biophysics and computational tools offers a path to navigating the GPCR structural landscape, ultimately advancing GPCR-based applications.
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Affiliation(s)
| | - Zeenat Zara
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
- Faculty of Science, University of South Bohemia in Ceske Budejovice, České Budějovice, Czech Republic
| | - Alessandro Nicoli
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
- Professorship for Chemoinformatics and Protein Modelling, Department of Molecular Life Science, School of Life Science, Technical University of Munich, Freising, Germany
| | - Alexandra Steuer
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
- Professorship for Chemoinformatics and Protein Modelling, Department of Molecular Life Science, School of Life Science, Technical University of Munich, Freising, Germany
| | - Marta Lopez-Balastegui
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute & Pompeu Fabra University, Barcelona, Spain
| | - Jana Selent
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute & Pompeu Fabra University, Barcelona, Spain
| | - Sanjai Karanth
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
| | - Melanie Koehler
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
- TUM Junior Fellow at the Chair of Nutritional Systems Biology, Technical University of Munich, Freising, Germany
| | - Antonella Ciancetta
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Ferrara, Italy
| | - Layara Akemi Abiko
- Focal Area Structural Biology and Biophysics, Biozentrum, University of Basel, Basel, Switzerland
| | - Franz Hagn
- Structural Membrane Biochemistry, Bavarian NMR Center, Dept. Bioscience, School of Natural Sciences, Technical University of Munich, Munich, Germany
- Institute of Structural Biology (STB), Helmholtz Munich, Neuherberg, Germany
| | - Antonella Di Pizio
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
- Professorship for Chemoinformatics and Protein Modelling, Department of Molecular Life Science, School of Life Science, Technical University of Munich, Freising, Germany
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11
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Tatulian SA. Analysis of protein-protein and protein-membrane interactions by isotope-edited infrared spectroscopy. Phys Chem Chem Phys 2024; 26:21930-21953. [PMID: 39108200 DOI: 10.1039/d4cp01136h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
Abstract
The objective of this work is to highlight the power of isotope-edited Fourier transform infrared (FTIR) spectroscopy in resolving important problems encountered in biochemistry, biophysics, and biomedical research, focusing on protein-protein and protein membrane interactions that play key roles in practically all life processes. An overview of the effects of isotope substitutions in (bio)molecules on spectral frequencies and intensities is given. Data are presented demonstrating how isotope-labeled proteins and/or lipids can be used to elucidate enzymatic mechanisms, the mode of membrane binding of peripheral proteins, regulation of membrane protein function, protein aggregation, and local and global structural changes in proteins during functional transitions. The use of polarized attenuated total reflection FTIR spectroscopy to identify the spatial orientation and the secondary structure of a membrane-bound interfacial enzyme and the mode of lipid hydrolysis is described. Methods of production of site-directed, segmental, and domain-specific labeling of proteins by the synthetic, semisynthetic, and recombinant strategies, including advanced protein engineering technologies such as nonsense suppression and frameshift quadruplet codons are overviewed.
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Affiliation(s)
- Suren A Tatulian
- Department of Physics, University of Central Florida, Orlando, FL 32816, USA.
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12
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Sae-Ueng U, Bunsuwansakul C, Showpanish K, Phironrit N, Thadajarassiri J, Nehls C. Nanomechanical resilience and thermal stability of RSJ2 phage. Sci Rep 2024; 14:19389. [PMID: 39169068 PMCID: PMC11339380 DOI: 10.1038/s41598-024-70056-8] [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: 02/23/2024] [Accepted: 08/12/2024] [Indexed: 08/23/2024] Open
Abstract
As the world moves toward a green economy and sustainable agriculture, bacterial viruses or bacteriophages (phages) become attractive biocontrol agents for controlling crop diseases. Effective utilization of phages in farms requires integrated knowledge of crops, pathogens, phages, and surroundings. Phages must encounter environmental fluctuations, including temperature, and must remain infectious for successful bacteria lysis. This work studied a soilborne RSJ2 phage discovered in Thailand, which can eliminate Ralstonia solanacearum, causing bacterial wilt disease in chili. We investigated how phage infectivity and nanomechanics responded to thermal changes. The plaque-based assay showed that the infectivity of the RSJ2 phage was stable within 24-40 °C, an average temperature fluctuation in tropical regions. The structural examination also showed that the phage remained intact. The nanomechanical property of the phage was inspected by the atomic force microscopy-based nanoindentation. The result revealed that the phage stiffness within 24-40 °C was statistically similar (0.05-0.06 N/m). Upon heating at 40 °C for 1, 5, and 10 h and resting at 25 °C, the stiffness of the phage particles increased to 0.09-0.11 N/m (54-83% increase). The stiffness results suggest structural adaptation of the protein subunits as a response to thermal alteration. The study exhibits that the phage structure is highly dynamic and can nanomechanically respond to varying temperatures. The phage stiffness may reveal insight into phage adaptation to environmental factors. Equipped with the knowledge of phage infectivity, structure, and nanomechanics, we can design practical guidelines for effective phage usage in farming and propelling green and safe agriculture.
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Affiliation(s)
- Udom Sae-Ueng
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand.
| | - Chooseel Bunsuwansakul
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Kittiya Showpanish
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Namthip Phironrit
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Jidapa Thadajarassiri
- Department of Mathematics, Faculty of Science, Srinakharinwirot University, Bangkok, 10110, Thailand
| | - Christians Nehls
- Research Center Borstel - Leibniz Lung Center (FZB), Borstel, Germany
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
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13
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Khakimzhan A, Izri Z, Thompson S, Dmytrenko O, Fischer P, Beisel C, Noireaux V. Cell-free expression with a quartz crystal microbalance enables rapid, dynamic, and label-free characterization of membrane-interacting proteins. Commun Biol 2024; 7:1005. [PMID: 39152195 PMCID: PMC11329788 DOI: 10.1038/s42003-024-06690-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 08/06/2024] [Indexed: 08/19/2024] Open
Abstract
Integral and interacting membrane proteins (IIMPs) constitute a vast family of biomolecules that perform essential functions in all forms of life. However, characterizing their interactions with lipid bilayers remains limited due to challenges in purifying and reconstituting IIMPs in vitro or labeling IIMPs without disrupting their function in vivo. Here, we report cell-free transcription-translation in a quartz crystal microbalance with dissipation (TXTL-QCMD) to dynamically characterize interactions between diverse IIMPs and membranes without protein purification or labeling. As part of TXTL-QCMD, IIMPs are synthesized using cell-free transcription-translation (TXTL), and their interactions with supported lipid bilayers are measured using a quartz crystal microbalance with dissipation (QCMD). TXTL-QCMD reconstitutes known IIMP-membrane dependencies, including specific association with prokaryotic or eukaryotic membranes, and the multiple-IIMP dynamical pattern-forming association of the E. coli division-coordinating proteins MinCDE. Applying TXTL-QCMD to the recently discovered Zorya anti-phage system that is unamenable to labeling, we discovered that ZorA and ZorB integrate within the lipids found at the poles of bacteria while ZorE diffuses freely on the non-pole membrane. These efforts establish the potential of TXTL-QCMD to broadly characterize the large diversity of IIMPs.
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Affiliation(s)
- Aset Khakimzhan
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Ziane Izri
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Seth Thompson
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Oleg Dmytrenko
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Centre for Infection Research (HZI), 97080, Würzburg, Germany
| | - Patrick Fischer
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Centre for Infection Research (HZI), 97080, Würzburg, Germany
| | - Chase Beisel
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Centre for Infection Research (HZI), 97080, Würzburg, Germany
- Medical Faculty, University of Würzburg, 97080, Würzburg, Germany
| | - Vincent Noireaux
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, 55455, USA.
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14
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Eliahoo P, Setayesh H, Hoffman T, Wu Y, Li S, Treweek JB. Viscoelasticity in 3D Cell Culture and Regenerative Medicine: Measurement Techniques and Biological Relevance. ACS MATERIALS AU 2024; 4:354-384. [PMID: 39006396 PMCID: PMC11240420 DOI: 10.1021/acsmaterialsau.3c00038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 10/08/2023] [Accepted: 10/10/2023] [Indexed: 07/16/2024]
Abstract
The field of mechanobiology is gaining prominence due to recent findings that show cells sense and respond to the mechanical properties of their environment through a process called mechanotransduction. The mechanical properties of cells, cell organelles, and the extracellular matrix are understood to be viscoelastic. Various technologies have been researched and developed for measuring the viscoelasticity of biological materials, which may provide insight into both the cellular mechanisms and the biological functions of mechanotransduction. Here, we explain the concept of viscoelasticity and introduce the major techniques that have been used to measure the viscoelasticity of various soft materials in different length- and timescale frames. The topology of the material undergoing testing, the geometry of the probe, the magnitude of the exerted stress, and the resulting deformation should be carefully considered to choose a proper technique for each application. Lastly, we discuss several applications of viscoelasticity in 3D cell culture and tissue models for regenerative medicine, including organoids, organ-on-a-chip systems, engineered tissue constructs, and tunable viscoelastic hydrogels for 3D bioprinting and cell-based therapies.
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Affiliation(s)
- Payam Eliahoo
- Department of Biomedical Engineering, University of Southern California, Los Angeles, California 90089 United States
| | - Hesam Setayesh
- Department of Biomedical Engineering, University of Southern California, Los Angeles, California 90089 United States
| | - Tyler Hoffman
- Department of Bioengineering, University of California Los Angeles, Los Angeles, California 90095 United States
| | - Yifan Wu
- Department of Bioengineering, University of California Los Angeles, Los Angeles, California 90095 United States
| | - Song Li
- Department of Bioengineering, University of California Los Angeles, Los Angeles, California 90095 United States
| | - Jennifer B Treweek
- Department of Biomedical Engineering, University of Southern California, Los Angeles, California 90089 United States
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15
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Karanth S, Benthin J, Wiesenfarth M, Somoza V, Koehler M. Nanodisc Technology: Direction toward Physicochemical Characterization of Chemosensory Membrane Proteins in Food Flavor Research. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:14521-14529. [PMID: 38906535 PMCID: PMC11228972 DOI: 10.1021/acs.jafc.4c01827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 05/31/2024] [Accepted: 06/11/2024] [Indexed: 06/23/2024]
Abstract
Chemosensory membrane proteins such as G-protein-coupled receptors (GPCRs) drive flavor perception of food formulations. To achieve this, a detailed understanding of the structure and function of these membrane proteins is needed, which is often limited by the extraction and purification methods involved. The proposed nanodisc methodology helps overcome some of these existing challenges such as protein stability and solubilization along with their reconstitution from a native cell-membrane environment. Being well-established in structural biology procedures, nanodiscs offer this elegant solution by using, e.g., a membrane scaffold protein (MSP) or styrene-maleic acid (SMA) polymer, which interacts directly with the cell membrane during protein reconstitution. Such derived proteins retain their biophysical properties without compromising the membrane architecture. Here, we seek to show that these lipidic systems can be explored for insights with a focus on chemosensory membrane protein morphology and structure, conformational dynamics of protein-ligand interactions, and binding kinetics to answer pending questions in flavor research. Additionally, the compatibility of nanodiscs across varied (labeled or label-free) techniques offers significant leverage, which has been highlighted here.
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Affiliation(s)
- Sanjai Karanth
- Leibniz
Institute for Food Systems Biology at the Technical University of
Munich, Lise-Meitner-Strasse 34, 85354 Freising, Germany
| | - Julia Benthin
- Leibniz
Institute for Food Systems Biology at the Technical University of
Munich, Lise-Meitner-Strasse 34, 85354 Freising, Germany
- TUM
Graduate School, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Alte Akademie 8, 85354 Freising, Germany
| | - Marina Wiesenfarth
- Leibniz
Institute for Food Systems Biology at the Technical University of
Munich, Lise-Meitner-Strasse 34, 85354 Freising, Germany
- TUM
Graduate School, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Alte Akademie 8, 85354 Freising, Germany
| | - Veronika Somoza
- Leibniz
Institute for Food Systems Biology at the Technical University of
Munich, Lise-Meitner-Strasse 34, 85354 Freising, Germany
- Chair
of Nutritional Systems Biology, Technical
University of Munich, 85354 Freising, Germany
- Department
of Physiological Chemistry, Faculty of Chemistry, University of Vienna, Vienna 1090, Austria
| | - Melanie Koehler
- Leibniz
Institute for Food Systems Biology at the Technical University of
Munich, Lise-Meitner-Strasse 34, 85354 Freising, Germany
- TUM
Junior Fellow at the Chair of Nutritional Systems Biology, Technical University of Munich, 85354 Freising, Germany
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16
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Mensah GAK, Schaefer KG, Roberts AG, King GM, Bartlett MG. Probing the Mechanisms Underlying the Transport of the Vinca Alkaloids by P-glycoprotein. J Pharm Sci 2024; 113:1960-1974. [PMID: 38527618 DOI: 10.1016/j.xphs.2024.03.014] [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: 10/26/2023] [Revised: 03/18/2024] [Accepted: 03/18/2024] [Indexed: 03/27/2024]
Abstract
The efficacy of many cancer drugs is hindered by P-glycoprotein (Pgp), a cellular pump that removes drugs from cells. To improve chemotherapy, drugs capable of evading Pgp must be developed. Despite similarities in structure, vinca alkaloids (VAs) show disparate Pgp-mediated efflux ratios. ATPase activity and binding affinity studies show at least two binding sites for the VAs: high- and low-affinity sites that stimulate and inhibit the ATPase activity rate, respectively. The affinity for ATP from the ATPase kinetics curve for vinblastine (VBL) at the high-affinity site was 2- and 9-fold higher than vinorelbine (VRL) and vincristine (VCR), respectively. Conversely, VBL had the highest Km (ATP) for the low-affinity site. The dissociation constants (KDs) determined by protein fluorescence quenching were in the order VBL < VRL< VCR. The order of the KDs was reversed at higher substrate concentrations. Acrylamide quenching of protein fluorescence indicate that the VAs, either at 10 µM or 150 µM, predominantly maintain Pgp in an open-outward conformation. When 3.2 mM AMPPNP was present, 10 µM of either VBL, VRL, or VCR cause Pgp to shift to an open-outward conformation, while 150 µM of the VAs shifted the conformation of Pgp to an intermediate orientation, between opened inward and open-outward. However, the conformational shift induced by saturating AMPPNP and VCR condition was less than either VBL or VRL in the presence of AMPPNP. At 150 µM, atomic force microscopy (AFM) revealed that the VAs shift Pgp population to a predominantly open-inward conformation. Additionally, STDD NMR studies revealed comparable groups in VBL, VRL, and VCR are in contact with the protein during binding. Our results, when coupled with VAs-microtubule structure-activity relationship studies, could lay the foundation for developing next-generation VAs that are effective as anti-tumor agents. A model that illustrates the intricate process of Pgp-mediated transport of the VAs is presented.
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Affiliation(s)
- Gershon A K Mensah
- Department of Pharmaceutical and Biomedical Science, University of Georgia, Athens, GA 30602, USA
| | - Katherine G Schaefer
- Department of Physics and Astronomy, University of Missouri, Columbia, MO 65211, USA
| | - Arthur G Roberts
- Department of Pharmaceutical and Biomedical Science, University of Georgia, Athens, GA 30602, USA.
| | - Gavin M King
- Department of Physics and Astronomy, University of Missouri, Columbia, MO 65211, USA; Joint with Biochemistry, University of Missouri, Columbia, MO 65211, USA.
| | - Michael G Bartlett
- Department of Pharmaceutical and Biomedical Science, University of Georgia, Athens, GA 30602, USA.
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17
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Lira RB, Dillingh LS, Schuringa JJ, Yahioglu G, Suhling K, Roos WH. Fluorescence lifetime imaging microscopy of flexible and rigid dyes probes the biophysical properties of synthetic and biological membranes. Biophys J 2024; 123:1592-1609. [PMID: 38702882 PMCID: PMC11214022 DOI: 10.1016/j.bpj.2024.04.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 03/22/2024] [Accepted: 04/30/2024] [Indexed: 05/06/2024] Open
Abstract
Sensing of the biophysical properties of membranes using molecular reporters has recently regained widespread attention. This was elicited by the development of new probes of exquisite optical properties and increased performance, combined with developments in fluorescence detection. Here, we report on fluorescence lifetime imaging of various rigid and flexible fluorescent dyes to probe the biophysical properties of synthetic and biological membranes at steady state as well as upon the action of external membrane-modifying agents. We tested the solvatochromic dyes Nile red and 1,2-dimyristoyl-sn-glycero-3-phosphoethanolamine-N-(7-nitro-2-1,3-benzoxadiazol-4-yl) (ammonium salt) (NBD), the viscosity sensor Bodipy C12, the flipper dye FliptR, as well as the dyes 3,3'-dioctadecyloxacarbocyanine perchlorate (DiO), Bodipy C16, lissamine-rhodamine, and Atto647, which are dyes with no previous reported environmental sensitivity. The performance of the fluorescent probes, many of which are commercially available, was benchmarked with well-known environmental reporters, with Nile red and Bodipy C12 being specific reporters of medium hydration and viscosity, respectively. We show that some widely used ordinary dyes with no previous report of sensing capabilities can exhibit competing performance compared to highly sensitive commercially available or custom-based solvatochromic dyes, molecular rotors, or flipper in a wide range of biophysics experiments. Compared to other methods, fluorescence lifetime imaging is a minimally invasive and nondestructive method with optical resolution. It enables biophysical mapping at steady state or assessment of the changes induced by membrane-active molecules at subcellular level in both synthetic and biological membranes when intensity measurements fail to do so. The results have important consequences for the specific choice of the sensor and take into consideration factors such as probe sensitivity, response to environmental changes, ease and speed of data analysis, and the probe's intracellular distribution, as well as potential side effects induced by labeling and imaging.
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Affiliation(s)
- Rafael B Lira
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, the Netherlands.
| | - Laura S Dillingh
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, the Netherlands; Department of Hematology, Universitair Medisch Centrum Groningen & Rijksuniversiteit Groningen, Groningen, the Netherlands
| | - Jan-Jacob Schuringa
- Department of Hematology, Universitair Medisch Centrum Groningen & Rijksuniversiteit Groningen, Groningen, the Netherlands
| | | | - Klaus Suhling
- Department of Physics, King's College London, Strand, London, UK.
| | - Wouter H Roos
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, the Netherlands
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18
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Zhai Y, Li S, Wang H, Shan Y. Revealing the dynamic mechanism of cell-penetrating peptides across cell membranes at the single-molecule level. J Mater Chem B 2024; 12:5589-5593. [PMID: 38741568 DOI: 10.1039/d4tb00522h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Cell-penetrating peptides (CPPs) have gained prominence in cellular drug delivery due to their extremely low toxicity and rapid cell internalization properties. Understanding the effect of CPPs' physicochemical properties on trans-membrane behavior will provide a better screening scheme for designing effective CPP-conjugated nano-drugs. Herein, the efficiency of the CPPs interacting with the cell membrane and the subsequent trans-membrane is revealed at the single-molecule level using single-molecule force spectroscopy (SMFS) and force tracing technique based on atomic force spectroscopy (AFM). The dynamic force spectroscopy (DFS) analysis indicates that cationic TAT48-60 and amphipathic MAP are more effective during the interaction with cell membrane due to the strong electrostatic interaction between CPPs and cell membrane. However, for the subsequent trans-membrane process, the hydrophobicity of Pep-7 plays a key role, showing a higher trans-membrane speed at the single-molecule level. Meanwhile, Pep-7 shows lower trans-membrane speed and probability on normal cells (Vero), which makes it more suitable as a peptide-based nano-drug to treat tumors avoiding harming normal cells. The dynamic parameters obtained in this study offer guidance for screening and modifying effective CPPs, targeting specific cell lines or tissues during the nano-drug design.
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Affiliation(s)
- Yuhang Zhai
- School of Chemistry and Life Science, Advanced Institute of Materials Science, Changchun University of Technology, Changchun 130012, China.
| | - Siying Li
- School of Chemistry and Life Science, Advanced Institute of Materials Science, Changchun University of Technology, Changchun 130012, China.
| | - Hui Wang
- School of Chemistry and Life Science, Advanced Institute of Materials Science, Changchun University of Technology, Changchun 130012, China.
| | - Yuping Shan
- School of Chemistry and Life Science, Advanced Institute of Materials Science, Changchun University of Technology, Changchun 130012, China.
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19
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Li XH, Duan JL, Ma JY, Liu XY, Sun XD, Wang Y, Tan MM, Yuan XZ. Probing the Surface Layer Modulation on Archaeal Mechanics and Adhesion at the Single-Cell Level. Anal Chem 2024; 96:8981-8989. [PMID: 38758609 DOI: 10.1021/acs.analchem.4c00038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2024]
Abstract
Addressing the challenge of understanding how cellular interfaces dictate the mechanical resilience and adhesion of archaeal cells, this study demonstrates the role of the surface layer (S-layer) in methanogenic archaea. Using a combination of atomic force microscopy and single-cell force spectroscopy, we quantified the impact of S-layer disruption on cell morphology, mechanical properties, and adhesion capabilities. We demonstrate that the S-layer is crucial for maintaining cell morphology, where its removal induces significant cellular enlargement and deformation. Mechanical stability of the cell surface is substantially compromised upon S-layer disruption, as evidenced by decreased Young's modulus values. Adhesion experiments revealed that the S-layer primarily facilitates hydrophobic interactions, which are significantly reduced after its removal, affecting both cell-cell and cell-bubble interactions. Our findings illuminate the S-layer's fundamental role in methanogen architecture and provide a chemical understanding of archaeal cell surfaces, with implications for enhancing methane production in biotechnological applications.
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Affiliation(s)
- Xiao-Hua Li
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong 266237, P. R. China
| | - Jian-Lu Duan
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong 266237, P. R. China
| | - Jing-Ya Ma
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong 266237, P. R. China
| | - Xiao-Yu Liu
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong 266237, P. R. China
| | - Xiao-Dong Sun
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong 266237, P. R. China
| | - Yue Wang
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong 266237, P. R. China
| | - Miao-Miao Tan
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong 266237, P. R. China
| | - Xian-Zheng Yuan
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong 266237, P. R. China
- Sino-French Research Institute for Ecology and Environment (ISFREE), Shandong University, Qingdao, Shandong 266237, P. R. China
- Weihai Research Institute of Industrial Technology, Shandong University, Weihai, Shandong 264209, P. R. China
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20
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Dzyhovskyi V, Romani A, Pula W, Bondi A, Ferrara F, Melloni E, Gonelli A, Pozza E, Voltan R, Sguizzato M, Secchiero P, Esposito E. Characterization Methods for Nanoparticle-Skin Interactions: An Overview. Life (Basel) 2024; 14:599. [PMID: 38792620 PMCID: PMC11122446 DOI: 10.3390/life14050599] [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: 03/29/2024] [Revised: 05/02/2024] [Accepted: 05/04/2024] [Indexed: 05/26/2024] Open
Abstract
Research progresses have led to the development of different kinds of nanoplatforms to deliver drugs through different biological membranes. Particularly, nanocarriers represent a precious means to treat skin pathologies, due to their capability to solubilize lipophilic and hydrophilic drugs, to control their release, and to promote their permeation through the stratum corneum barrier. A crucial point in the development of nano-delivery systems relies on their characterization, as well as in the assessment of their interaction with tissues, in order to predict their fate under in vivo administration. The size of nanoparticles, their shape, and the type of matrix can influence their biodistribution inside the skin strata and their cellular uptake. In this respect, an overview of some characterization methods employed to investigate nanoparticles intended for topical administration is presented here, namely dynamic light scattering, zeta potential, scanning and transmission electron microscopy, X-ray diffraction, atomic force microscopy, Fourier transform infrared and Raman spectroscopy. In addition, the main fluorescence methods employed to detect the in vitro nanoparticles interaction with skin cell lines, such as fluorescence-activated cell sorting or confocal imaging, are described, considering different examples of applications. Finally, recent studies on the techniques employed to determine the nanoparticle presence in the skin by ex vivo and in vivo models are reported.
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Affiliation(s)
- Valentyn Dzyhovskyi
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy; (V.D.); (A.R.); (E.M.); (E.P.)
| | - Arianna Romani
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy; (V.D.); (A.R.); (E.M.); (E.P.)
- Laboratorio per le Tecnologie delle Terapie Avanzate (LTTA) Centre, University of Ferrara, 44121 Ferrara, Italy;
| | - Walter Pula
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, 44121 Ferrara, Italy; (W.P.); (A.B.); (F.F.); (M.S.)
| | - Agnese Bondi
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, 44121 Ferrara, Italy; (W.P.); (A.B.); (F.F.); (M.S.)
| | - Francesca Ferrara
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, 44121 Ferrara, Italy; (W.P.); (A.B.); (F.F.); (M.S.)
| | - Elisabetta Melloni
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy; (V.D.); (A.R.); (E.M.); (E.P.)
- Laboratorio per le Tecnologie delle Terapie Avanzate (LTTA) Centre, University of Ferrara, 44121 Ferrara, Italy;
| | - Arianna Gonelli
- Department of Environmental and Prevention Sciences, University of Ferrara, 44121 Ferrara, Italy;
| | - Elena Pozza
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy; (V.D.); (A.R.); (E.M.); (E.P.)
| | - Rebecca Voltan
- Laboratorio per le Tecnologie delle Terapie Avanzate (LTTA) Centre, University of Ferrara, 44121 Ferrara, Italy;
- Department of Environmental and Prevention Sciences, University of Ferrara, 44121 Ferrara, Italy;
| | - Maddalena Sguizzato
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, 44121 Ferrara, Italy; (W.P.); (A.B.); (F.F.); (M.S.)
| | - Paola Secchiero
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy; (V.D.); (A.R.); (E.M.); (E.P.)
- Laboratorio per le Tecnologie delle Terapie Avanzate (LTTA) Centre, University of Ferrara, 44121 Ferrara, Italy;
| | - Elisabetta Esposito
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, 44121 Ferrara, Italy; (W.P.); (A.B.); (F.F.); (M.S.)
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21
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Li M. Harnessing atomic force microscopy-based single-cell analysis to advance physical oncology. Microsc Res Tech 2024; 87:631-659. [PMID: 38053519 DOI: 10.1002/jemt.24467] [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: 08/22/2023] [Revised: 11/21/2023] [Accepted: 11/23/2023] [Indexed: 12/07/2023]
Abstract
Single-cell analysis is an emerging and promising frontier in the field of life sciences, which is expected to facilitate the exploration of fundamental laws of physiological and pathological processes. Single-cell analysis allows experimental access to cell-to-cell heterogeneity to reveal the distinctive behaviors of individual cells, offering novel opportunities to dissect the complexity of severe human diseases such as cancers. Among the single-cell analysis tools, atomic force microscopy (AFM) is a powerful and versatile one which is able to nondestructively image the fine topographies and quantitatively measure multiple mechanical properties of single living cancer cells in their native states under aqueous conditions with unprecedented spatiotemporal resolution. Over the past few decades, AFM has been widely utilized to detect the structural and mechanical behaviors of individual cancer cells during the process of tumor formation, invasion, and metastasis, yielding numerous unique insights into tumor pathogenesis from the biomechanical perspective and contributing much to the field of cancer mechanobiology. Here, the achievements of AFM-based analysis of single cancer cells to advance physical oncology are comprehensively summarized, and challenges and future perspectives are also discussed. RESEARCH HIGHLIGHTS: Achievements of AFM in characterizing the structural and mechanical behaviors of single cancer cells are summarized, and future directions are discussed. AFM is not only capable of visualizing cellular fine structures, but can also measure multiple cellular mechanical properties as well as cell-generated mechanical forces. There is still plenty of room for harnessing AFM-based single-cell analysis to advance physical oncology.
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Affiliation(s)
- Mi Li
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang, China
- Institutes for Robotics and Intelligent Manufacturing, Chinese Academy of Sciences, Shenyang, China
- University of Chinese Academy of Sciences, Beijing, China
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22
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Wang B, Dong J, Yang F, Ju T, Wang J, Qu K, Wang Y, Tian Y, Wang Z. Determining the degree of chromosomal instability in breast cancer cells by atomic force microscopy. Analyst 2024; 149:1988-1997. [PMID: 38420857 DOI: 10.1039/d3an01815f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Chromosomal instability (CIN) is a source of genetic variation and is highly linked to the malignance of cancer. Determining the degree of CIN is necessary for understanding the role that it plays in tumor development. There is currently a lack of research on high-resolution characterization of CIN and the relationship between CIN and cell mechanics. Here, a method to determine CIN of breast cancer cells by high resolution imaging with atomic force microscopy (AFM) is explored. The numerical and structural changes of chromosomes in human breast cells (MCF-10A), moderately malignant breast cells (MCF-7) and highly malignant breast cells (MDA-MB-231) were observed and analyzed by AFM. Meanwhile, the nuclei, cytoskeleton and cell mechanics of the three kinds of cells were also investigated. The results showed the differences in CIN between the benign and cancer cells. Also, the degree of structural CIN increased with enhanced malignancy of cancer cells. This was also demonstrated by calculating the probability of micronucleus formation in these three kinds of cells. Meanwhile, we found that the area of the nucleus was related to the number of chromosomes in the nucleus. In addition, reduced or even aggregated actin fibers led to decreased elasticities in MCF-7 and MDA-MB-231 cells. It was found that the rearrangement of actin fibers would affect the nucleus, and then lead to wrong mitosis and CIN. Using AFM to detect chromosomal changes in cells with different malignancy degrees provides a new detection method for the study of cell carcinogenesis with a perspective for targeted therapy of cancer.
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Affiliation(s)
- Bowei Wang
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, China.
- Centre for Opto/Bio-Nano Measurement and Manufacturing, Zhongshan Institute of Changchun University of Science and Technology, Zhongshan 528437, China
| | - Jianjun Dong
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, China.
- Centre for Opto/Bio-Nano Measurement and Manufacturing, Zhongshan Institute of Changchun University of Science and Technology, Zhongshan 528437, China
| | - Fan Yang
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, China.
- Centre for Opto/Bio-Nano Measurement and Manufacturing, Zhongshan Institute of Changchun University of Science and Technology, Zhongshan 528437, China
| | - Tuoyu Ju
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, China.
- Centre for Opto/Bio-Nano Measurement and Manufacturing, Zhongshan Institute of Changchun University of Science and Technology, Zhongshan 528437, China
| | - Junxi Wang
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, China.
- Centre for Opto/Bio-Nano Measurement and Manufacturing, Zhongshan Institute of Changchun University of Science and Technology, Zhongshan 528437, China
| | - Kaige Qu
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, China.
- Centre for Opto/Bio-Nano Measurement and Manufacturing, Zhongshan Institute of Changchun University of Science and Technology, Zhongshan 528437, China
| | - Ying Wang
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, China.
- Centre for Opto/Bio-Nano Measurement and Manufacturing, Zhongshan Institute of Changchun University of Science and Technology, Zhongshan 528437, China
| | - Yanling Tian
- School of Engineering, University of Warwick, Coventry CV4 7AL, UK
| | - Zuobin Wang
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun 130022, China.
- Centre for Opto/Bio-Nano Measurement and Manufacturing, Zhongshan Institute of Changchun University of Science and Technology, Zhongshan 528437, China
- JR3CN & IRAC, University of Bedfordshire, Luton LU1 3JU, UK
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23
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Wu Z, Bayón JL, Kouznetsova TB, Ouchi T, Barkovich KJ, Hsu SK, Craig SL, Steinmetz NF. Virus-like Particles Armored by an Endoskeleton. NANO LETTERS 2024; 24:2989-2997. [PMID: 38294951 DOI: 10.1021/acs.nanolett.3c03806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2024]
Abstract
Many virus-like particles (VLPs) have good chemical, thermal, and mechanical stabilities compared to those of other biologics. However, their stability needs to be improved for the commercialization and use in translation of VLP-based materials. We developed an endoskeleton-armored strategy for enhancing VLP stability. Specifically, the VLPs of physalis mottle virus (PhMV) and Qβ were used to demonstrate this concept. We built an internal polymer "backbone" using a maleimide-PEG15-maleimide cross-linker to covalently interlink viral coat proteins inside the capsid cavity, while the native VLPs are held together by only noncovalent bonding between subunits. Endoskeleton-armored VLPs exhibited significantly improved thermal stability (95 °C for 15 min), increased resistance to denaturants (i.e., surfactants, pHs, chemical denaturants, and organic solvents), and enhanced mechanical performance. Single-molecule force spectroscopy demonstrated a 6-fold increase in rupture distance and a 1.9-fold increase in rupture force of endoskeleton-armored PhMV. Overall, this endoskeleton-armored strategy provides more opportunities for the development and applications of materials.
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Affiliation(s)
- Zhuohong Wu
- Department of NanoEngineering, University of California, San Diego, La Jolla, California 92093, United States
- Center for Nano-ImmunoEngineering, University of California, San Diego, La Jolla, California 92093, United States
- Moores Cancer Center, University of California, San Diego, La Jolla, California 92093, United States
- Shu and K. C. Chien and Peter Farrell Collaboratory, University of California, San Diego, La Jolla, California 92093, United States
| | - Jorge L Bayón
- Department of NanoEngineering, University of California, San Diego, La Jolla, California 92093, United States
- Center for Nano-ImmunoEngineering, University of California, San Diego, La Jolla, California 92093, United States
- Moores Cancer Center, University of California, San Diego, La Jolla, California 92093, United States
- Shu and K. C. Chien and Peter Farrell Collaboratory, University of California, San Diego, La Jolla, California 92093, United States
| | - Tatiana B Kouznetsova
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Tetsu Ouchi
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Krister J Barkovich
- Center for Nano-ImmunoEngineering, University of California, San Diego, La Jolla, California 92093, United States
- Moores Cancer Center, University of California, San Diego, La Jolla, California 92093, United States
- Shu and K. C. Chien and Peter Farrell Collaboratory, University of California, San Diego, La Jolla, California 92093, United States
- Department of Radiology, University of California, San Diego, La Jolla, California 92093, United States
| | - Sean K Hsu
- Center for Nano-ImmunoEngineering, University of California, San Diego, La Jolla, California 92093, United States
- Moores Cancer Center, University of California, San Diego, La Jolla, California 92093, United States
- Shu and K. C. Chien and Peter Farrell Collaboratory, University of California, San Diego, La Jolla, California 92093, United States
- Department of Molecular Biology, University of California, San Diego, La Jolla, California 92093, United States
| | - Stephen L Craig
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Nicole F Steinmetz
- Department of NanoEngineering, University of California, San Diego, La Jolla, California 92093, United States
- Center for Nano-ImmunoEngineering, University of California, San Diego, La Jolla, California 92093, United States
- Moores Cancer Center, University of California, San Diego, La Jolla, California 92093, United States
- Shu and K. C. Chien and Peter Farrell Collaboratory, University of California, San Diego, La Jolla, California 92093, United States
- Department of Radiology, University of California, San Diego, La Jolla, California 92093, United States
- Department of Molecular Biology, University of California, San Diego, La Jolla, California 92093, United States
- Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, United States
- Institute for Materials Discovery and Design, University of California, San Diego, La Jolla, California 92093, United States
- Center for Engineering in Cancer, Institute for Engineering in Medicine, University of California, San Diego, La Jolla, California 92093, United States
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24
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Yang S, Wang M, Tian D, Zhang X, Cui K, Lü S, Wang HH, Long M, Nie Z. DNA-functionalized artificial mechanoreceptor for de novo force-responsive signaling. Nat Chem Biol 2024:10.1038/s41589-024-01572-x. [PMID: 38448735 DOI: 10.1038/s41589-024-01572-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 02/07/2024] [Indexed: 03/08/2024]
Abstract
Synthetic signaling receptors enable programmable cellular responses coupling with customized inputs. However, engineering a designer force-sensing receptor to rewire mechanotransduction remains largely unexplored. Herein, we introduce nongenetically engineered artificial mechanoreceptors (AMRs) capable of reprogramming non-mechanoresponsive receptor tyrosine kinases (RTKs) to sense user-defined force cues, enabling de novo-designed mechanotransduction. AMR is a modular DNA-protein chimera comprising a mechanosensing-and-transmitting DNA nanodevice grafted on natural RTKs via aptameric anchors. AMR senses intercellular tensile force via an allosteric DNA mechano-switch with tunable piconewton-sensitive force tolerance, actuating a force-triggered dynamic DNA assembly to manipulate RTK dimerization and activate intracellular signaling. By swapping the force-reception ligands, we demonstrate the AMR-mediated activation of c-Met, a representative RTK, in response to the cellular tensile forces mediated by cell-adhesion proteins (integrin, E-cadherin) or membrane protein endocytosis (CI-M6PR). Moreover, AMR also allows the reprogramming of FGFR1, another RTK, to customize mechanobiological function, for example, adhesion-mediated neural stem cell maintenance.
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Affiliation(s)
- Sihui Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, College of Chemistry and Chemical Engineering, College of Biology, Hunan University, Changsha, China
| | - Miao Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, College of Chemistry and Chemical Engineering, College of Biology, Hunan University, Changsha, China
| | - Dawei Tian
- Center of Biomechanics and Bioengineering, Key Laboratory of Microgravity (National Microgravity Laboratory), Beijing Key Laboratory of Engineered Construction and Mechanobiology, Institute of Mechanics, Chinese Academy of Sciences, Beijing, China
- School of Engineering Science, University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoyu Zhang
- Center of Biomechanics and Bioengineering, Key Laboratory of Microgravity (National Microgravity Laboratory), Beijing Key Laboratory of Engineered Construction and Mechanobiology, Institute of Mechanics, Chinese Academy of Sciences, Beijing, China
- School of Engineering Science, University of Chinese Academy of Sciences, Beijing, China
| | - Kaiqing Cui
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, College of Chemistry and Chemical Engineering, College of Biology, Hunan University, Changsha, China
| | - Shouqin Lü
- Center of Biomechanics and Bioengineering, Key Laboratory of Microgravity (National Microgravity Laboratory), Beijing Key Laboratory of Engineered Construction and Mechanobiology, Institute of Mechanics, Chinese Academy of Sciences, Beijing, China
- School of Engineering Science, University of Chinese Academy of Sciences, Beijing, China
| | - Hong-Hui Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, College of Chemistry and Chemical Engineering, College of Biology, Hunan University, Changsha, China
| | - Mian Long
- Center of Biomechanics and Bioengineering, Key Laboratory of Microgravity (National Microgravity Laboratory), Beijing Key Laboratory of Engineered Construction and Mechanobiology, Institute of Mechanics, Chinese Academy of Sciences, Beijing, China
- School of Engineering Science, University of Chinese Academy of Sciences, Beijing, China
| | - Zhou Nie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, College of Chemistry and Chemical Engineering, College of Biology, Hunan University, Changsha, China.
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25
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Gong L, Zhu J, Yang Y, Qiao S, Ma L, Wang H, Zhang Y. Effect of polyethylene glycol on polysaccharides: From molecular modification, composite matrixes, synergetic properties to embeddable application in food fields. Carbohydr Polym 2024; 327:121647. [PMID: 38171672 DOI: 10.1016/j.carbpol.2023.121647] [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: 09/20/2023] [Revised: 11/21/2023] [Accepted: 11/25/2023] [Indexed: 01/05/2024]
Abstract
Polyethylene glycol (PEG) is a flexible, water-soluble, non-immunogenic, as well as biocompatible polymer, and it could synergize with polysaccharides for food applications. The molecular modification strategies, including covalent bond interactions (amino groups, carboxyl groups, aldehyde groups, tosylate groups, etc.), and non-covalent bond interactions (hydrogen bonding, electrostatic interactions, etc.) on PEG molecular chains are discussed. Its versatile structure, group modifiability, and amphiphilic block buildability could improve the functions of polysaccharides (e.g., chitosan, cellulose, starch, alginate, etc.) and adjust the properties of combined PEG/polysaccharides with outstanding chain tunability and matrix processability owing to plasticizing effects, compatibilizing effects, steric stabilizing effects and excluded volume effects by PEG, for achieving the diverse performance targets. The synergetic properties of PEG/polysaccharides with remarkable architecture were summarized, including mechanical properties, antibacterial activity, antioxidant performance, self-healing properties, carrier and delivery characteristics. The PEG/polysaccharides with excellent combined properties and embeddable merits illustrate potential applications including food packaging, food intelligent indication/detection, food 3D printing and nutraceutical food absorption. Additionally, prospects (like food innovation and preferable nutrient utilization) and key challenges (like structure-effectiveness-applicability relationship) for PEG/polysaccharides are proposed and addressed for food fields.
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Affiliation(s)
- Linshan Gong
- College of Food Science, Southwest University, Chongqing 400715, PR China
| | - Juncheng Zhu
- College of Food Science, Southwest University, Chongqing 400715, PR China
| | - Yuxin Yang
- College of Food Science, Southwest University, Chongqing 400715, PR China
| | - Shihao Qiao
- College of Food Science, Southwest University, Chongqing 400715, PR China
| | - Liang Ma
- College of Food Science, Southwest University, Chongqing 400715, PR China
| | - Hongxia Wang
- College of Food Science, Southwest University, Chongqing 400715, PR China; Chongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, Chongqing 400715, PR China; Key Laboratory of Quality and Safety Control of Citrus Fruits, Ministry of Agriculture and Rural Affairs, Southwest University, Chongqing, 400712, PR China; Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, Chongqing 400715, PR China; Key Laboratory of Condiment Supervision Technology for State Market Regulation, Chongqing 401121, PR China.
| | - Yuhao Zhang
- College of Food Science, Southwest University, Chongqing 400715, PR China; Chongqing Key Laboratory of Speciality Food Co-Built by Sichuan and Chongqing, Chongqing 400715, PR China; Key Laboratory of Quality and Safety Control of Citrus Fruits, Ministry of Agriculture and Rural Affairs, Southwest University, Chongqing, 400712, PR China; Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, Chongqing 400715, PR China; Key Laboratory of Condiment Supervision Technology for State Market Regulation, Chongqing 401121, PR China.
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26
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Li Y, Xue B, Yang J, Jiang J, Liu J, Zhou Y, Zhang J, Wu M, Yuan Y, Zhu Z, Wang ZJ, Chen Y, Harabuchi Y, Nakajima T, Wang W, Maeda S, Gong JP, Cao Y. Azobenzene as a photoswitchable mechanophore. Nat Chem 2024; 16:446-455. [PMID: 38052946 DOI: 10.1038/s41557-023-01389-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 10/27/2023] [Indexed: 12/07/2023]
Abstract
Azobenzene has been widely explored as a photoresponsive element in materials science. Although some studies have investigated the force-induced isomerization of azobenzene, the effect of force on the rupture of azobenzene has not been explored. Here we show that the light-induced structural change of azobenzene can also alter its rupture forces, making it an ideal light-responsive mechanophore. Using single-molecule force spectroscopy and ultrasonication, we found that cis and trans para-azobenzene isomers possess contrasting mechanical properties. Dynamic force spectroscopy experiments and quantum-chemical calculations in which azobenzene regioisomers were pulled from different directions revealed that the distinct rupture forces of the two isomers are due to the pulling direction rather than the energetic difference between the two isomers. These mechanical features of azobenzene can be used to rationally control the macroscopic fracture behaviours of polymer networks by photoillumination. The use of light-induced conformational changes to alter the mechanical response of mechanophores provides an attractive way to engineer polymer networks of light-regulatable mechanical properties.
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Affiliation(s)
- Yiran Li
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid-State Microstructure, Key Laboratory of Intelligent Optical Sensing and Manipulation, Ministry of Education, Department of Physics, Nanjing University, Nanjing, China
- Medical School, Nanjing University, Nanjing, China
| | - Bin Xue
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid-State Microstructure, Key Laboratory of Intelligent Optical Sensing and Manipulation, Ministry of Education, Department of Physics, Nanjing University, Nanjing, China
| | - Jiahui Yang
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid-State Microstructure, Key Laboratory of Intelligent Optical Sensing and Manipulation, Ministry of Education, Department of Physics, Nanjing University, Nanjing, China
| | | | - Jing Liu
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid-State Microstructure, Key Laboratory of Intelligent Optical Sensing and Manipulation, Ministry of Education, Department of Physics, Nanjing University, Nanjing, China
| | - Yanyan Zhou
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid-State Microstructure, Key Laboratory of Intelligent Optical Sensing and Manipulation, Ministry of Education, Department of Physics, Nanjing University, Nanjing, China
| | - Junsheng Zhang
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid-State Microstructure, Key Laboratory of Intelligent Optical Sensing and Manipulation, Ministry of Education, Department of Physics, Nanjing University, Nanjing, China
| | - Mengjiao Wu
- College of Chemistry, Jilin University, Changchun, China
| | - Yuan Yuan
- Tianjin Key Laboratory of Molecular Optoelectronic Science, Department of Chemistry, Tianjin University, Tianjin, China
| | - Zhenshu Zhu
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid-State Microstructure, Key Laboratory of Intelligent Optical Sensing and Manipulation, Ministry of Education, Department of Physics, Nanjing University, Nanjing, China
| | - Zhi Jian Wang
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan
| | - Yulan Chen
- College of Chemistry, Jilin University, Changchun, China
| | - Yu Harabuchi
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan
| | - Tasuku Nakajima
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan
| | - Wei Wang
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid-State Microstructure, Key Laboratory of Intelligent Optical Sensing and Manipulation, Ministry of Education, Department of Physics, Nanjing University, Nanjing, China.
| | - Satoshi Maeda
- Hokkaido University, Sapporo, Japan.
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan.
| | - Jian Ping Gong
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan.
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan.
| | - Yi Cao
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid-State Microstructure, Key Laboratory of Intelligent Optical Sensing and Manipulation, Ministry of Education, Department of Physics, Nanjing University, Nanjing, China.
- Institute for Brain Sciences, Nanjing University, Nanjing, China.
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, China.
- Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing, China.
- MOE Key Laboratory of High Performance Polymer Materials and Technology, Nanjing University, Nanjing, China.
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27
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Sun H, Liao F, Tian Y, Lei Y, Fu Y, Wang J. Molecular-Scale Investigations Reveal the Effect of Natural Polyphenols on BAX/Bcl-2 Interactions. Int J Mol Sci 2024; 25:2474. [PMID: 38473728 DOI: 10.3390/ijms25052474] [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: 01/11/2024] [Revised: 02/14/2024] [Accepted: 02/16/2024] [Indexed: 03/14/2024] Open
Abstract
Apoptosis signaling controls the cell cycle through the protein-protein interactions (PPIs) of its major B-cell lymphoma 2-associated x protein (BAX) and B-cell lymphoma 2 protein (Bcl-2). Due to the antagonistic function of both proteins, apoptosis depends on a properly tuned balance of the kinetics of BAX and Bcl-2 activities. The utilization of natural polyphenols to regulate the binding process of PPIs is feasible. However, the mechanism of this modulation has not been studied in detail. Here, we utilized atomic force microscopy (AFM) to evaluate the effects of polyphenols (kaempferol, quercetin, dihydromyricetin, baicalin, curcumin, rutin, epigallocatechin gallate, and gossypol) on the BAX/Bcl-2 binding mechanism. We demonstrated at the molecular scale that polyphenols quantitatively affect the interaction forces, kinetics, thermodynamics, and structural properties of BAX/Bcl-2 complex formation. We observed that rutin, epigallocatechin gallate, and baicalin reduced the binding affinity of BAX/Bcl-2 by an order of magnitude. Combined with surface free energy and molecular docking, the results revealed that polyphenols are driven by multiple forces that affect the orientation freedom of PPIs, with hydrogen bonding, hydrophobic interactions, and van der Waals forces being the major contributors. Overall, our work provides valuable insights into how molecules tune PPIs to modulate their function.
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Affiliation(s)
- Heng Sun
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China
| | - Fenghui Liao
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China
| | - Yichen Tian
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China
| | - Yongrong Lei
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China
| | - Yuna Fu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China
| | - Jianhua Wang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China
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28
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Rodríguez-López R, Wang Z, Oda H, Erdi M, Kofinas P, Fytas G, Scarcelli G. Network Viscoelasticity from Brillouin Spectroscopy. Biomacromolecules 2024; 25:955-963. [PMID: 38156622 PMCID: PMC10865340 DOI: 10.1021/acs.biomac.3c01073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 12/02/2023] [Accepted: 12/04/2023] [Indexed: 01/03/2024]
Abstract
Even though the physical nature of shear and longitudinal moduli are different, empirical correlations between them have been reported in several biological systems. This correlation is of fundamental interest and immense practical value in biomedicine due to the importance of the shear modulus and the possibility to map the longitudinal modulus at high-resolution with all-optical spectroscopy. We investigate the origin of such a correlation in hydrogels. We hypothesize that both moduli are influenced in the same direction by underlying physicochemical properties, which leads to the observed material-dependent correlation. Matching theoretical models with experimental data, we quantify the scenarios in which the correlation holds. For polymerized hydrogels, a correlation was found across different hydrogels through a common dependence on the effective polymer volume fraction. For hydrogels swollen to equilibrium, the correlation is valid only within a given hydrogel system, as the moduli are found to have different scalings on the swelling ratio. The observed correlation allows one to extract one modulus from another in relevant scenarios.
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Affiliation(s)
- Raymundo Rodríguez-López
- Fischell
Department of Bioengineering, University
of Maryland, College
Park, Maryland 20742, United States
| | - Zuyuan Wang
- School
of Mechanical and Electrical Engineering, University of Electronic Science and Technology of China, Chengdu, Sichuan 611731, China
| | - Haruka Oda
- School
of Information Science and Technology, The
University of Tokyo, Tokyo 113-8656,Japan
| | - Metecan Erdi
- Department
of Chemical and Biomolecular Engineering, University of Maryland, College
Park, Maryland 20742, United States
| | - Peter Kofinas
- Department
of Chemical and Biomolecular Engineering, University of Maryland, College
Park, Maryland 20742, United States
| | - George Fytas
- Max
Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- Institute
of Electronic Structure and Laser, FO.R.T.H, N. Plastira 10, Heraklion, 70013, Greece
| | - Giuliano Scarcelli
- Fischell
Department of Bioengineering, University
of Maryland, College
Park, Maryland 20742, United States
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29
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Matos RS, Pinto EP, Pires MA, Ramos GQ, Ţălu Ş, Lima LS, da Fonseca Filho HD. Evaluating the roughness dynamics of kefir biofilms grown on Amazon cupuaçu juice: a monofractal and multifractal approach. Microscopy (Oxf) 2024; 73:55-65. [PMID: 37540558 DOI: 10.1093/jmicro/dfad040] [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: 03/03/2023] [Revised: 05/22/2023] [Accepted: 07/17/2023] [Indexed: 08/05/2023] Open
Abstract
We conducted a comprehensive analysis of the surface microtexture of kefir biofilms grown on Theobroma grandiflorum Shum (cupuaçu) juice using atomic force microscopy. Our goal was to investigate the unique monofractal and multifractal spatial patterns of these biofilms to complement the existing limited literature. The biofilms were prepared dispersing four different concentrations of kefir grains in cupuaçu juice. Our morphological analysis showed that the surface of the obtained biofilms is essentially formed by the presence of cupuaçu fibers and microorganisms like lactobacilli and yeast. The topographic height-based parameter analysis reveals that there is a dependence between surface roughness and the concentration of kefir grains used. The strongly anisotropic well-centralized topographical height distribution of the biofilms also exhibited a quasi-symmetrical and platykurtic pattern. The biofilms exhibit comparable levels of spatial complexity, surface percolation and surface homogeneity, which can be attributed to their similar topographic uniformity. This aspect was further supported by the presence of similar multifractality in the biofilms, suggesting that despite their varying topographic roughness, their vertical growth dynamics follow a similar pattern. Our findings demonstrate that the surface roughness of kefir biofilms cultivated on cupuaçu juice is influenced by the concentration of kefir grains in the precursor solution. However, this dependence follows a consistent pattern across different concentrations. Graphical Abstract.
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Affiliation(s)
- Robert S Matos
- Amazonian Materials Group, Department of Physics, Federal University of Amapá-UNIFAP, Rod. Juscelino Kubitscheck, km 02 - Jardim Marco Zero, Macapá, Amapá 68.903-419, Brazil
| | - Erveton P Pinto
- Amazonian Materials Group, Department of Physics, Federal University of Amapá-UNIFAP, Rod. Juscelino Kubitscheck, km 02 - Jardim Marco Zero, Macapá, Amapá 68.903-419, Brazil
| | - Marcelo A Pires
- Department of Physiscs, Federal University of Alagoas-UFAL, Rodovia AL 145, Km 3, 3849 - Cidade Universitária, Delmiro Gouveia, Alagoas 57.480-000, Brazil
| | - Glenda Q Ramos
- Centro Multiusuário para Análise de Fenômenos Biomédicos da Universidade do Estado do Amazonas, Universidade do Estado do Amazonas-UEA, Av. Carvalho Leal, 1777 - Cachoeirinha, Amazonas 69.065-001, Brazil
| | - Ştefan Ţălu
- Technical University of Cluj-Napoca, The Directorate of Research, Development and Innovation Management (DMCDI), Constantin Daicoviciu St., no. 15, Cluj-Napoca, Cluj County 400020, Romania
| | - Lucas S Lima
- Laboratory of Corrosion and Nanotechnology (LCNT), Federal University of Sergipe-UFS, Cidade Universitária Prof. "José Aloísio de Campos" Av. Marechal Rondom, S/N - Jardim Rosa Elze, São Cristovão, Sergipe 49.100-000, Brazil
| | - Henrique D da Fonseca Filho
- Laboratory of Synthesis of Nanomaterials and Nanoscopy, Department of Physics, Federal University of Amazonas-UFAM, Av. General Rodrigo Octavio Jordão Ramos, 1200 - Coroado I, Manaus, Amazonas 69.067-005, Brazil
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Yu M, Guo X, Zhang K, Kang X, Zhang S, Qian L. Hyaluronic Acid Unveiled: Exploring the Nanomechanics and Water Retention Properties at the Single-Molecule Level. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:2616-2623. [PMID: 38251884 DOI: 10.1021/acs.langmuir.3c02961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Abstract
Hyaluronic acid (HA), a vital glycosaminoglycan in living organisms, possesses remarkable mechanical and viscoelastic properties that have garnered significant attention in therapeutic, biomedical, and cosmetic applications. However, a comprehensive picture of the physicochemical and biocharacterization of HA at the single-molecule level remains elusive. In this work, atomic force microscopy (AFM)-based single-molecule force spectroscopy (SMFS) and molecular dynamics (MD) simulation were used to investigate the nanomechanics and water retention properties of HA at the single-molecule level. The present study aims to unravel the intricate details of the influence of molecular structure on HA behavior and shed light on its unique attributes. According to the force measurements, the energy used to stretch a HA chain in water is 8.45 kJ/mol, significantly surpassing that of Curdlan (3.45 kJ/mol) and chitin (2.23 kJ/mol), both of which possess molecular structures partially similar to that of HA. Intriguingly, the strength of the intrachain interaction of HA (5.54 kJ/mol) was considerably weaker compared to Curdlan (11.06 kJ/mol) and chitin (or cellulose, 10.76 kJ/mol). This result indicates that HA exhibits a preference for interacting with water rather than with itself, thereby showing enhanced water affinity. Moreover, the force measurements demonstrated that changing the glycosidic bond from β-(1-3) (Curdlan) or β-(1-4) (chitin or cellulose) to β-(1-3) + β-(1-4) (HA) resulted in polysaccharides displaying improved water affinity and more extended conformation. These conclusions were further verified by molecular dynamics (MD) simulations. Overall, our work sheds new light on the nanomechanics and water retention properties of HA at the single-molecule level, offering valuable insights for future research in this field.
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Affiliation(s)
- Miao Yu
- School of Mechanical Engineering, Sichuan University, Chengdu 610065, China
- Yibin Industrial Technology Research Institute of Sichuan University, Yibin 644000, China
| | - Xin Guo
- School of Mechanical Engineering, Sichuan University, Chengdu 610065, China
- Yibin Industrial Technology Research Institute of Sichuan University, Yibin 644000, China
| | - Kai Zhang
- School of Mechanical Engineering, Sichuan University, Chengdu 610065, China
- Yibin Industrial Technology Research Institute of Sichuan University, Yibin 644000, China
| | - Xiaomin Kang
- School of Mechanical Engineering, University of South China, Hengyang 421001, China
| | - Song Zhang
- Department of Food Science and Engineering, Moutai Institute, Renhuai 564502, Guizhou, China
| | - Lu Qian
- School of Materials Science and Engineering, South China University of Technology, Guangzhou 510641, China
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31
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Yang X, Yang Y, Zhang Z, Li M. Deep Learning Image Recognition-Assisted Atomic Force Microscopy for Single-Cell Efficient Mechanics in Co-culture Environments. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:837-852. [PMID: 38154137 DOI: 10.1021/acs.langmuir.3c03046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2023]
Abstract
Atomic force microscopy (AFM)-based force spectroscopy assay has become an important method for characterizing the mechanical properties of single living cells under aqueous conditions, but a disadvantage is its reliance on manual operation and experience as well as the resulting low throughput. Particularly, providing a capacity to accurately identify the type of the cell grown in co-culture environments without the need of fluorescent labeling will further facilitate the applications of AFM in life sciences. Here, we present a study of deep learning image recognition-assisted AFM, which not only enables fluorescence-independent recognition of the identity of single co-cultured cells but also allows efficient downstream AFM force measurements of the identified cells. With the use of the deep learning-based image recognition model, the viability and type of individual cells grown in co-culture environments were identified directly from the optical bright-field images, which were confirmed by the following cell growth and fluorescent labeling results. Based on the image recognition results, the positional relationship between the AFM probe and the targeted cell was automatically determined, allowing the precise movement of the AFM probe to the target cell to perform force measurements. The experimental results show that the presented method was applicable not only to the conventional (microsphere-modified) AFM probe used in AFM indentation assay for measuring the Young's modulus of single co-cultured cells but also to the single-cell probe used in AFM-based single-cell force spectroscopy (SCFS) assay for measuring the adhesion forces of single co-cultured cells. The study illustrates deep learning imaging recognition-assisted AFM as a promising approach for label-free and high-throughput detection of single-cell mechanics under co-culture conditions, which will facilitate unraveling the mechanical cues involved in cell-cell interactions in their native states at the single-cell level and will benefit the field of mechanobiology.
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Affiliation(s)
- Xuliang Yang
- School of Artificial Intelligence, Shenyang University of Technology, Shenyang 110870, China
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang 110016, China
| | - Yanqi Yang
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang 110016, China
- Institutes for Robotics and Intelligent Manufacturing, Chinese Academy of Sciences, Shenyang 110169, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhihui Zhang
- School of Artificial Intelligence, Shenyang University of Technology, Shenyang 110870, China
| | - Mi Li
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang 110016, China
- Institutes for Robotics and Intelligent Manufacturing, Chinese Academy of Sciences, Shenyang 110169, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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32
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Feng Y, Roos WH. Atomic Force Microscopy: An Introduction. Methods Mol Biol 2024; 2694:295-316. [PMID: 37824010 DOI: 10.1007/978-1-0716-3377-9_14] [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] [Indexed: 10/13/2023]
Abstract
Imaging of nano-sized particles and sample features is crucial in a variety of research fields, for instance, in biological sciences, where it is paramount to investigate structures at the single particle level. Often, two-dimensional images are not sufficient, and further information such as topography and mechanical properties are required. Furthermore, to increase the biological relevance, it is desired to perform the imaging in close to physiological environments. Atomic force microscopy (AFM) meets these demands in an all-in-one instrument. It provides high-resolution images including surface height information leading to three-dimensional information on sample morphology. AFM can be operated both in air and in buffer solutions. Moreover, it has the capacity to determine protein and membrane material properties via the force spectroscopy mode. Here we discuss the principles of AFM operation and provide examples of how biomolecules can be studied. New developments in AFM are discussed, and by including approaches such as bimodal AFM and high-speed AFM (HS-AFM), we show how AFM can be used to study a variety of static and dynamic single biomolecules and biomolecular assemblies.
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Affiliation(s)
- Yuzhen Feng
- Moleculaire Biofysica, Zernike instituut, Rijksuniversiteit Groningen, Groningen, the Netherlands
| | - Wouter H Roos
- Moleculaire Biofysica, Zernike instituut, Rijksuniversiteit Groningen, Groningen, the Netherlands.
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33
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Petitjean SJL, Eeckhout S, Delguste M, Zhang Q, Durlet K, Alsteens D. Heparin-Induced Allosteric Changes in SARS-CoV-2 Spike Protein Facilitate ACE2 Binding and Viral Entry. NANO LETTERS 2023; 23:11678-11684. [PMID: 38055954 DOI: 10.1021/acs.nanolett.3c03550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
Understanding the entry of severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) into host cells is crucial in the battle against COVID-19. Using atomic force microscopy (AFM), we probed the interaction between the virus's spike protein and heparan sulfate (HS) as a potential attachment factor. Our AFM studies revealed a moderate-affinity interaction between the spike protein and HS on both model surfaces and living cells, highlighting HS's role in early viral attachment. Remarkably, we observed an interplay between HS and the host cell receptor angiotensin-converting enzyme 2 (ACE2), with HS engagement resulting in enhanced ACE2 binding and subsequent viral entry. Our research furthers our understanding of SARS-CoV-2 infection mechanisms and reveals potential interventions targeting viral entry. These insights are valuable as we navigate the evolving landscape of viral threats and seek effective strategies to combat emerging infectious diseases.
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Affiliation(s)
- Simon J L Petitjean
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Walloon Brabant 1348, Belgium
| | - Savannah Eeckhout
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Walloon Brabant 1348, Belgium
| | - Martin Delguste
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Walloon Brabant 1348, Belgium
| | - Qingrong Zhang
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Walloon Brabant 1348, Belgium
| | - Kimberley Durlet
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Walloon Brabant 1348, Belgium
| | - David Alsteens
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Walloon Brabant 1348, Belgium
- WELBIO Department, WEL Research Institute, Wavre, Walloon Brabant 1300, Belgium
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34
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Song P, Li X, Cui J, Chen K, Chu Y. Investigation on the Impact of Excitation Amplitude on AFM-TM Microcantilever Beam System's Dynamic Characteristics and Implementation of an Equivalent Circuit. SENSORS (BASEL, SWITZERLAND) 2023; 24:107. [PMID: 38202969 PMCID: PMC10781406 DOI: 10.3390/s24010107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 12/18/2023] [Accepted: 12/23/2023] [Indexed: 01/12/2024]
Abstract
Alterations in the dynamical properties of an atomic force microscope microcantilever beam system in tapping mode can appreciably impact its measurement precision. Understanding the influence mechanism of dynamic parameter changes on the system's motion characteristics is vital to improve the accuracy of the atomic force microscope in tapping mode (AFM-TM). In this study, we categorize the mathematical model of the AFM-TM microcantilever beam system into systems 1 and 2 based on actual working conditions. Then, we analyze the alterations in the dynamic properties of both systems due to external excitation variations using bifurcation diagrams, phase trajectories, Lyapunov indices, and attraction domains. The numerical simulation results show that when the dimensionless external excitation g < 0.183, the motion state of system 2 is period 1. When g < 0.9, the motion state of system 1 is period 1 motion. Finally, we develop the equivalent circuit model of the AFM-TM microcantilever beam and perform related software simulations, along with practical circuit experiments. Our experimental results indicate that the constructed equivalent circuit can effectively analyze the dynamic characteristics of the AFM-TM microcantilever beam system in the presence of complex external environmental factors. It is observed that the practical circuit simulation attenuates high-frequency signals, resulting in a 31.4% reduction in excitation amplitude compared to numerical simulation results. This provides an essential theoretical foundation for selecting external excitation parameters for AFM-TM cantilever beams and offers a novel method for analyzing the dynamics of micro- and nanomechanical systems, as well as other nonlinear systems.
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Affiliation(s)
- Peijie Song
- School of Electrical Engineering. Lanzhou Jiaotong University, Lanzhou 730070, China;
- Gansu Institute of Metrology, Lanzhou 730050, China
| | - Xiaojuan Li
- Gansu Institute of Metrology, Lanzhou 730050, China
| | - Jianjun Cui
- Geometric Sciences Institute, National Institute of Metrology, Beijing 100013, China; (J.C.)
| | - Kai Chen
- Geometric Sciences Institute, National Institute of Metrology, Beijing 100013, China; (J.C.)
| | - Yandong Chu
- School of Electrical Engineering. Lanzhou Jiaotong University, Lanzhou 730070, China;
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35
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Sun H, Tian Y, Fu Y, Lei Y, Wang Y, Yan X, Wang J. Single-molecule scale quantification reveals interactions underlying protein-protein interface: from forces to non-covalent bonds. Phys Chem Chem Phys 2023; 25:31791-31803. [PMID: 37966041 DOI: 10.1039/d3cp04351g] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Protein-protein interactions (PPIs) between the B-cell lymphoma 2 (Bcl-2) family are considered a major driving force in cell cycle regulation and signaling. However, how this interfacial noncovalent interaction is achieved molecularly remains poorly understood. Herein, anti-apoptotic protein (Bcl-2) and pro-apoptotic protein (BAX) were used as models and their PPIs were explored for the first time using atomic force microscopy-based single-molecule force spectroscopy (SMFS) and in silico approaches. In addition, we used advanced analytical models, including multiple kinetic models, thermodynamic models, Poisson distributions, and contact angle molecular recognition to fully reveal the complexity of the BAX/Bcl-2 interaction interfaces. We propose that the binding kinetics between BAX/Bcl-2 are mainly mediated by specific (hydrogen bonding) and non-specific forces (hydrophobic interactions and electrostatic interactions) and show that the complicated multivalent binding interaction induces stable BAX/Bcl-2 complexes. This study enriches our understanding of the molecular mechanisms by which BAX interacts with Bcl-2. It provides valuable insights into the physical factors that need to be considered when designing PPI inhibitors.
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Affiliation(s)
- Heng Sun
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, China.
| | - Yichen Tian
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, China.
| | - Yuna Fu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, China.
| | - Yongrong Lei
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, China.
| | - Yani Wang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, China.
| | - Xinrui Yan
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, China.
| | - Jianhua Wang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, China.
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36
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Schmid SY, Lachowski K, Chiang HT, Pozzo L, De Yoreo J, Zhang S. Mechanisms of Biomolecular Self-Assembly Investigated Through In Situ Observations of Structures and Dynamics. Angew Chem Int Ed Engl 2023; 62:e202309725. [PMID: 37702227 DOI: 10.1002/anie.202309725] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Indexed: 09/14/2023]
Abstract
Biomolecular self-assembly of hierarchical materials is a precise and adaptable bottom-up approach to synthesizing across scales with considerable energy, health, environment, sustainability, and information technology applications. To achieve desired functions in biomaterials, it is essential to directly observe assembly dynamics and structural evolutions that reflect the underlying energy landscape and the assembly mechanism. This review will summarize the current understanding of biomolecular assembly mechanisms based on in situ characterization and discuss the broader significance and achievements of newly gained insights. In addition, we will also introduce how emerging deep learning/machine learning-based approaches, multiparametric characterization, and high-throughput methods can boost the development of biomolecular self-assembly. The objective of this review is to accelerate the development of in situ characterization approaches for biomolecular self-assembly and to inspire the next generation of biomimetic materials.
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Affiliation(s)
- Sakshi Yadav Schmid
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Kacper Lachowski
- Chemical Engineering, University of Washington, Seattle, WA 98105, USA
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA 98105, USA
| | - Huat Thart Chiang
- Chemical Engineering, University of Washington, Seattle, WA 98105, USA
| | - Lilo Pozzo
- Chemical Engineering, University of Washington, Seattle, WA 98105, USA
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA 98105, USA
- Materials Science and Engineering, University of Washington, Seattle, WA 98105, USA
| | - Jim De Yoreo
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
- Materials Science and Engineering, University of Washington, Seattle, WA 98105, USA
| | - Shuai Zhang
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA 98105, USA
- Materials Science and Engineering, University of Washington, Seattle, WA 98105, USA
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37
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Li P, Hou S, Wu Q, Chen Y, Wang B, Ren H, Wang J, Zhai Z, Yu Z, Lambert CJ, Jia C, Guo X. The role of halogens in Au-S bond cleavage for energy-differentiated catalysis at the single-bond limit. Nat Commun 2023; 14:7695. [PMID: 38001141 PMCID: PMC10673828 DOI: 10.1038/s41467-023-43639-8] [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: 06/21/2023] [Accepted: 11/15/2023] [Indexed: 11/26/2023] Open
Abstract
The transformation from one compound to another involves the breaking and formation of chemical bonds at the single-bond level, especially during catalytic reactions that are of great significance in broad fields such as energy conversion, environmental science, life science and chemical synthesis. The study of the reaction process at the single-bond limit is the key to understanding the catalytic reaction mechanism and further rationally designing catalysts. Here, we develop a method to monitor the catalytic process from the perspective of the single-bond energy using high-resolution scanning tunneling microscopy single-molecule junctions. Experimental and theoretical studies consistently reveal that the attack of a halogen atom on an Au atom can reduce the breaking energy of Au-S bonds, thereby accelerating the bond cleavage reaction and shortening the plateau length during the single-molecule junction breaking. Furthermore, the distinction in catalytic activity between different halogen atoms can be compared as well. This study establishes the intrinsic relationship among the reaction activation energy, the chemical bond breaking energy and the single-molecule junction breaking process, strengthening our mastery of catalytic reactions towards precise chemistry.
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Affiliation(s)
- Peihui Li
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Micro-Scale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, 38 Tongyan Road, Jinnan District, 300350, Tianjin, People's Republic of China
| | - Songjun Hou
- Department of Physics, Lancaster University, Lancaster, LA1 4YB, UK
| | - Qingqing Wu
- Department of Physics, Lancaster University, Lancaster, LA1 4YB, UK
| | - Yijian Chen
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Micro-Scale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, 38 Tongyan Road, Jinnan District, 300350, Tianjin, People's Republic of China
| | - Boyu Wang
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Micro-Scale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, 38 Tongyan Road, Jinnan District, 300350, Tianjin, People's Republic of China
| | - Haiyang Ren
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Micro-Scale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, 38 Tongyan Road, Jinnan District, 300350, Tianjin, People's Republic of China
| | - Jinying Wang
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Micro-Scale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, 38 Tongyan Road, Jinnan District, 300350, Tianjin, People's Republic of China
| | - Zhaoyi Zhai
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, 300350, Tianjin, People's Republic of China
| | - Zhongbo Yu
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, 300350, Tianjin, People's Republic of China.
| | - Colin J Lambert
- Department of Physics, Lancaster University, Lancaster, LA1 4YB, UK.
| | - Chuancheng Jia
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Micro-Scale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, 38 Tongyan Road, Jinnan District, 300350, Tianjin, People's Republic of China.
| | - Xuefeng Guo
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, Tianjin Key Laboratory of Micro-Scale Optical Information Science and Technology, College of Electronic Information and Optical Engineering, Nankai University, 38 Tongyan Road, Jinnan District, 300350, Tianjin, People's Republic of China.
- Beijing National Laboratory for Molecular Sciences, National Biomedical Imaging Center, College of Chemistry and Molecular Engineering, Peking University, 292 Chengfu Road, Haidian District, 100871, Beijing, People's Republic of China.
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38
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Doffini V, Liu H, Liu Z, Nash MA. Iterative Machine Learning for Classification and Discovery of Single-Molecule Unfolding Trajectories from Force Spectroscopy Data. NANO LETTERS 2023; 23:10406-10413. [PMID: 37933959 DOI: 10.1021/acs.nanolett.3c03026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
We report the application of machine learning techniques to expedite classification and analysis of protein unfolding trajectories from force spectroscopy data. Using kernel methods, logistic regression, and triplet loss, we developed a workflow called Forced Unfolding and Supervised Iterative Online (FUSION) learning where a user classifies a small number of repeatable unfolding patterns encoded as images, and a machine is tasked with identifying similar images to classify the remaining data. We tested the workflow using two case studies on a multidomain XMod-Dockerin/Cohesin complex, validating the approach first using synthetic data generated with a Monte Carlo algorithm and then deploying the method on experimental atomic force spectroscopy data. FUSION efficiently separated traces that passed quality filters from unusable ones, classified curves with high accuracy, and identified unfolding pathways that were undetected by the user. This study demonstrates the potential of machine learning to accelerate data analysis and generate new insights in protein biophysics.
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Affiliation(s)
- Vanni Doffini
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
- Swiss Nanoscience Institute, 4056 Basel, Switzerland
| | - Haipei Liu
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | - Zhaowei Liu
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | - Michael A Nash
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
- Swiss Nanoscience Institute, 4056 Basel, Switzerland
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39
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Hall D. HSAFM-MIREBA - Methodology for Inferring REsolution in biological applications. Anal Biochem 2023; 681:115320. [PMID: 37717838 DOI: 10.1016/j.ab.2023.115320] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 08/22/2023] [Accepted: 09/10/2023] [Indexed: 09/19/2023]
Abstract
Due to a lack of requirement for any direct labelling of the target molecule, high speed atomic force microscopy (HS-AFM) is a potentially powerful procedure for the assessment of biological processes involving macromolecules. When the sample is static the AFM device can be purposefully setup to recover high-resolution information about the feature in question. However, when the feature to be studied moves an appreciable amount during the course of the measurement, the obtained image will be blurred. Encountering such blurred observations prompts the experimenter to sacrifice higher resolution images for higher scanning speeds by tuning available experimental parameters (such as the scanned image area, the image pixel size, the resonance frequency of the cantilever and/or the diameter of the AFM tip). The present work describes a software tool, HSAFM-MIREBA (High Speed Atomic Force Microscopy - Methodology for Inferring REsolution in Biological Applications) that allows for pre-experimental optimization of such parameters through iterative rounds of simulation of both the dynamic surface process and the HS-AFM measurement (based on the particular set of governing parameters). A representative set of five dynamic biological processes that describe a range of diffusive and directed motions (which can themselves be tuned by altering characteristic governing parameter sets) are provided.
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Affiliation(s)
- Damien Hall
- WPI Nano Life Science Institute. Kanazawa University, Kakumamachi, Kanazawa, Ishikawa, 920-1164, Japan.
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40
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Shakibapour N, Asoodeh A, Saberi MR, Chamani J. Investigating the binding mechanism of temporin Rb with human serum albumin, holo transferrin, and hemoglobin using spectroscopic and molecular dynamics techniques. J Mol Liq 2023; 389:122833. [DOI: 10.1016/j.molliq.2023.122833] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
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41
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Zuo J, Chen H, Li H. Two molecule force spectroscopy on ligand-receptor interactions. NANOSCALE 2023; 15:16581-16589. [PMID: 37740375 DOI: 10.1039/d3nr03428c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
Many biological processes involve the rupture of multiple ligand-receptors or multivalent ligand-receptors. It is challenging to study the rupture of such parallelly arranged multiple ligand-receptors due to the difficulties in engineering such systems in a well-controlled fashion. Here we report the use of two-molecule force spectroscopy to investigate the rupture of two parallelly arranged monomeric streptavidin (mSA)-biotin complexes. By using SpyCatcher-SpyTag chemistry, we successfully engineered a molecular twin of biotin, in which two biotins are arranged in parallel. By reacting mSA with twin biotin, we constructed parallelly arranged two mSA-biotin complexes for force spectroscopy experiments. The incorporation of single molecule fingerprint domains into our mSA-biotin dimers allowed us to identify and assign the rupture events of the parallelly arranged mSA-biotin complexes without any ambiguity in the two-molecule force spectroscopy experiments. Our results revealed that the rupture force of the parallel dimer mSA-biotin is 172 pN at a pulling speed of 400 nm s-1, which is about 1.6 times of that of single mSA-biotin (105 pN). Furthermore, our findings indicate that the two mSA-biotin behave as non-interacting, independent ligand-receptors. The strategy we demonstrated here can be extended to other ligand-receptors and may open up an avenue toward rigorously testing the theoretic predictions proposed in various models regarding the rupture of multiple parallel ligand-receptors.
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Affiliation(s)
- Jiacheng Zuo
- Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada.
| | - Hui Chen
- Department of Chemical Engineering, Nanjing Forestry University, Nanjing, Jiangsu, P. R. China
| | - Hongbin Li
- Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada.
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Holuigue H, Nacci L, Di Chiaro P, Chighizola M, Locatelli I, Schulte C, Alfano M, Diaferia GR, Podestà A. Native extracellular matrix probes to target patient- and tissue-specific cell-microenvironment interactions by force spectroscopy. NANOSCALE 2023; 15:15382-15395. [PMID: 37700706 DOI: 10.1039/d3nr01568h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/14/2023]
Abstract
Atomic Force Microscopy (AFM) is successfully used for the quantitative investigation of the cellular mechanosensing of the microenvironment. To this purpose, several force spectroscopy approaches aim at measuring the adhesive forces between two living cells and also between a cell and an appropriate reproduction of the extracellular matrix (ECM), typically exploiting tips suitably functionalised with single components (e.g. collagen, fibronectin) of the ECM. However, these probes only poorly reproduce the complexity of the native cellular microenvironment and consequently of the biological interactions. We developed a novel approach to produce AFM probes that faithfully retain the structural and biochemical complexity of the ECM; this was achieved by attaching to an AFM cantilever a micrometric slice of native decellularised ECM, which was cut by laser microdissection. We demonstrate that these probes preserve the morphological, mechanical, and chemical heterogeneity of the ECM. Native ECM probes can be used in force spectroscopy experiments aimed at targeting cell-microenvironment interactions. Here, we demonstrate the feasibility of dissecting mechanotransductive cell-ECM interactions in the 10 pN range. As proof-of-principle, we tested a rat bladder ECM probe against the AY-27 rat bladder cancer cell line. On the one hand, we obtained reproducible results using different probes derived from the same ECM regions; on the other hand, we detected differences in the adhesion patterns of distinct bladder ECM regions (submucosa, detrusor, and adventitia), in line with the disparities in composition and biophysical properties of these ECM regions. Our results demonstrate that native ECM probes, produced from patient-specific regions of organs and tissues, can be used to investigate cell-microenvironment interactions and early mechanotransductive processes by force spectroscopy. This opens new possibilities in the field of personalised medicine.
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Affiliation(s)
- H Holuigue
- CIMAINA and Dipartimento di Fisica "Aldo Pontremoli", Università degli Studi di Milano, Milano, Italy.
| | - L Nacci
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, Italy.
| | - P Di Chiaro
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, Italy.
| | - M Chighizola
- CIMAINA and Dipartimento di Fisica "Aldo Pontremoli", Università degli Studi di Milano, Milano, Italy.
| | - I Locatelli
- Division of Experimental Oncology/Unit of Urology, URI, IRCCS San Raffaele Hospital, Milan, Italy.
| | - C Schulte
- CIMAINA and Dipartimento di Fisica "Aldo Pontremoli", Università degli Studi di Milano, Milano, Italy.
- Department of Biomedical and Clinical Sciences "L. Sacco", Università degli Studi di Milano, Milano, Italy
| | - M Alfano
- Division of Experimental Oncology/Unit of Urology, URI, IRCCS San Raffaele Hospital, Milan, Italy.
| | - G R Diaferia
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, Italy.
| | - A Podestà
- CIMAINA and Dipartimento di Fisica "Aldo Pontremoli", Università degli Studi di Milano, Milano, Italy.
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Nguyen H, Nguyen HL, Lan PD, Thai NQ, Sikora M, Li MS. Interaction of SARS-CoV-2 with host cells and antibodies: experiment and simulation. Chem Soc Rev 2023; 52:6497-6553. [PMID: 37650302 DOI: 10.1039/d1cs01170g] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the devastating global COVID-19 pandemic announced by WHO in March 2020. Through unprecedented scientific effort, several vaccines, drugs and antibodies have been developed, saving millions of lives, but the fight against COVID-19 continues as immune escape variants of concern such as Delta and Omicron emerge. To develop more effective treatments and to elucidate the side effects caused by vaccines and therapeutic agents, a deeper understanding of the molecular interactions of SARS-CoV-2 with them and human cells is required. With special interest in computational approaches, we will focus on the structure of SARS-CoV-2 and the interaction of its spike protein with human angiotensin-converting enzyme-2 (ACE2) as a prime entry point of the virus into host cells. In addition, other possible viral receptors will be considered. The fusion of viral and human membranes and the interaction of the spike protein with antibodies and nanobodies will be discussed, as well as the effect of SARS-CoV-2 on protein synthesis in host cells.
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Affiliation(s)
- Hung Nguyen
- Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, 02-668 Warsaw, Poland.
| | - Hoang Linh Nguyen
- Institute of Fundamental and Applied Sciences, Duy Tan University, Ho Chi Minh City 700000, Vietnam
- Faculty of Environmental and Natural Sciences, Duy Tan University, Da Nang 550000, Vietnam
| | - Pham Dang Lan
- Life Science Lab, Institute for Computational Science and Technology, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, 729110 Ho Chi Minh City, Vietnam
- Faculty of Physics and Engineering Physics, VNUHCM-University of Science, 227, Nguyen Van Cu Street, District 5, 749000 Ho Chi Minh City, Vietnam
| | - Nguyen Quoc Thai
- Dong Thap University, 783 Pham Huu Lau Street, Ward 6, Cao Lanh City, Dong Thap, Vietnam
| | - Mateusz Sikora
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, 02-668 Warsaw, Poland.
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Chu J, Romero A, Taulbee J, Aran K. Development of Single Molecule Techniques for Sensing and Manipulation of CRISPR and Polymerase Enzymes. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2300328. [PMID: 37226388 PMCID: PMC10524706 DOI: 10.1002/smll.202300328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 03/20/2023] [Indexed: 05/26/2023]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) and polymerases are powerful enzymes and their diverse applications in genomics, proteomics, and transcriptomics have revolutionized the biotechnology industry today. CRISPR has been widely adopted for genomic editing applications and Polymerases can efficiently amplify genomic transcripts via polymerase chain reaction (PCR). Further investigations into these enzymes can reveal specific details about their mechanisms that greatly expand their use. Single-molecule techniques are an effective way to probe enzymatic mechanisms because they may resolve intermediary conformations and states with greater detail than ensemble or bulk biosensing techniques. This review discusses various techniques for sensing and manipulation of single biomolecules that can help facilitate and expedite these discoveries. Each platform is categorized as optical, mechanical, or electronic. The methods, operating principles, outputs, and utility of each technique are briefly introduced, followed by a discussion of their applications to monitor and control CRISPR and Polymerases at the single molecule level, and closing with a brief overview of their limitations and future prospects.
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Affiliation(s)
- Josephine Chu
- Henry E. Riggs School of Applied Life Sciences, Keck Graduate Institute, Claremont, CA, 91711, USA
| | - Andres Romero
- Henry E. Riggs School of Applied Life Sciences, Keck Graduate Institute, Claremont, CA, 91711, USA
| | - Jeffrey Taulbee
- Henry E. Riggs School of Applied Life Sciences, Keck Graduate Institute, Claremont, CA, 91711, USA
| | - Kiana Aran
- Henry E. Riggs School of Applied Life Sciences, Keck Graduate Institute, Claremont, CA, 91711, USA
- Cardea, San Diego, CA, 92121, USA
- University of California Berkeley, Berkeley, CA, 94720, USA
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45
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Feng Y, Li M. Micropipette-assisted atomic force microscopy for single-cell 3D manipulations and nanomechanical measurements. NANOSCALE 2023; 15:13346-13358. [PMID: 37526589 DOI: 10.1039/d3nr02404k] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Mechanical cues play a crucial role in regulating physiological and pathological processes, and atomic force microscopy (AFM) has become an important and standard tool for measuring the mechanical properties of single cells. In particular, providing a capability to manipulate cells in a three-dimensional (3D) space benefits enhancing the applications of AFM measurements in cell biology. Here, we present the complementary integration of AFM and micropipette micromanipulation, which allows precise 3D manipulations and nanomechanical measurements of single living cells. A micropipette micromanipulation system under the guidance of optical microscopy was established to isolate single living cells, and polydimethylsiloxane (PDMS) micropillar substrates were used to physically immobilize the isolated living cells for downstream AFM detection. The viscoelastic properties (Young's modulus, relaxation time, viscosity) of cells were quantitatively measured by AFM-based indentation assay. The effectiveness of micropipette-assisted AFM in single-cell analysis was confirmed on both living animal suspended cells and living animal adherent cells, showing dramatic changes in cell mechanics in different states and revealing the dynamics of single cells grown on micropillar arrays. The study demonstrates the great potential of a micropipette to aid AFM in single-cell manipulations for better accessing the mechanical cues involved in cellular processes, which will allow additional studies of single-cell mechanics and will benefit the field of mechanobiology.
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Affiliation(s)
- Yaqi Feng
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang 110016, China.
- Institutes for Robotics and Intelligent Manufacturing, Chinese Academy of Sciences, Shenyang 110169, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mi Li
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang 110016, China.
- Institutes for Robotics and Intelligent Manufacturing, Chinese Academy of Sciences, Shenyang 110169, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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46
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Savin N, Erofeev A, Gorelkin P. Analytical Models for Measuring the Mechanical Properties of Yeast. Cells 2023; 12:1946. [PMID: 37566025 PMCID: PMC10417110 DOI: 10.3390/cells12151946] [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: 06/05/2023] [Revised: 07/21/2023] [Accepted: 07/26/2023] [Indexed: 08/12/2023] Open
Abstract
The mechanical properties of yeast play an important role in many biological processes, such as cell division and growth, maintenance of internal pressure, and biofilm formation. In addition, the mechanical properties of cells can indicate the degree of damage caused by antifungal drugs, as the mechanical parameters of healthy and damaged cells are different. Over the past decades, atomic force microscopy (AFM) and micromanipulation have become the most widely used methods for evaluating the mechanical characteristics of microorganisms. In this case, the reliability of such an estimate depends on the choice of mathematical model. This review presents various analytical models developed in recent years for studying the mechanical properties of both cells and their individual structures. The main provisions of the applied approaches are described along with their limitations and advantages. Attention is paid to the innovative method of low-invasive nanomechanical mapping with scanning ion-conductance microscopy (SICM), which is currently starting to be successfully used in the discovery of novel drugs acting on the yeast cell wall and plasma membrane.
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Affiliation(s)
- Nikita Savin
- Research Laboratory of Biophysics, National University of Science and Technology MISiS, Moscow 119049, Russia;
| | - Alexander Erofeev
- Research Laboratory of Biophysics, National University of Science and Technology MISiS, Moscow 119049, Russia;
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Yang Z, Wang J, Yin B, Liu W, Yin D, Shen J, Wang W, Li L, Guo X. Stimuli-Induced Subconformation Transformation of the PSI-LHCI Protein at Single-Molecule Resolution. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2205945. [PMID: 37114832 PMCID: PMC10323662 DOI: 10.1002/advs.202205945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 04/11/2023] [Indexed: 06/19/2023]
Abstract
Photosynthesis is a very important process for the current biosphere which can maintain such a subtle and stable circulatory ecosystem on earth through the transformation of energy and substance. Even though been widely studied in various aspects, the physiological activities, such as intrinsic structural vibration and self-regulation process to stress of photosynthetic proteins, are still not in-depth resolved in real-time. Herein, utilizing silicon nanowire biosensors with ultrasensitive temporal and spatial resolution, real-time responses of a single photosystem I-light harvesting complex I (PSI-LHCI) supercomplex of Pisum sativum to various conditions, including gradient variations in temperature, illumination, and electric field, are recorded. Under different temperatures, there is a bi-state switch process associated with the intrinsic thermal vibration behavior. When the variations of illumination and the bias voltage are applied, two additional shoulder states, probably derived from the self-conformational adjustment, are observed. Based on real-time monitoring of the dynamic processes of the PSI-LHCI supercomplex under various conditions, it is successively testified to promising nanotechnology for protein profiling and biological functional integration in photosynthesis studies.
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Affiliation(s)
- Zhiheng Yang
- State Key Laboratory for Advanced Metals and MaterialsSchool of Materials Science and EngineeringUniversity of Science and Technology BeijingBeijing100083P. R. China
- Beijing National Laboratory for Molecular SciencesNational Biomedical Imaging CenterCollege of Chemistry and Molecular EngineeringPeking University292 Chengfu Road, Haidian DistrictBeijing100871P. R. China
| | - Jie Wang
- Photosynthesis Research CenterKey Laboratory of PhotobiologyInstitute of BotanyChinese Academy of SciencesBeijing100093P. R. China
| | - Bing Yin
- Beijing National Laboratory for Molecular SciencesNational Biomedical Imaging CenterCollege of Chemistry and Molecular EngineeringPeking University292 Chengfu Road, Haidian DistrictBeijing100871P. R. China
| | - Wenzhe Liu
- Beijing National Laboratory for Molecular SciencesNational Biomedical Imaging CenterCollege of Chemistry and Molecular EngineeringPeking University292 Chengfu Road, Haidian DistrictBeijing100871P. R. China
| | - Dongbao Yin
- Beijing National Laboratory for Molecular SciencesNational Biomedical Imaging CenterCollege of Chemistry and Molecular EngineeringPeking University292 Chengfu Road, Haidian DistrictBeijing100871P. R. China
| | - Jianren Shen
- Photosynthesis Research CenterKey Laboratory of PhotobiologyInstitute of BotanyChinese Academy of SciencesBeijing100093P. R. China
| | - Wenda Wang
- Photosynthesis Research CenterKey Laboratory of PhotobiologyInstitute of BotanyChinese Academy of SciencesBeijing100093P. R. China
| | - Lidong Li
- State Key Laboratory for Advanced Metals and MaterialsSchool of Materials Science and EngineeringUniversity of Science and Technology BeijingBeijing100083P. R. China
| | - Xuefeng Guo
- Beijing National Laboratory for Molecular SciencesNational Biomedical Imaging CenterCollege of Chemistry and Molecular EngineeringPeking University292 Chengfu Road, Haidian DistrictBeijing100871P. R. China
- Center of Single‐Molecule SciencesInstitute of Modern OpticsFrontiers Science Center for New Organic MatterCollege of Electronic Information and Optical EngineeringNankai University38 Tongyan Road, Jinnan DistrictTianjin300350P. R. China
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48
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Fernandez M, Shkumatov AV, Liu Y, Stulemeijer C, Derclaye S, Efremov R, Hallet B, Alsteens D. AFM-based force spectroscopy unravels stepwise formation of the DNA transposition complex in the widespread Tn3 family mobile genetic elements. Nucleic Acids Res 2023; 51:4929-4941. [PMID: 37026471 PMCID: PMC10250215 DOI: 10.1093/nar/gkad241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 03/03/2023] [Accepted: 03/23/2023] [Indexed: 04/08/2023] Open
Abstract
Transposon Tn4430 belongs to a widespread family of bacterial transposons, the Tn3 family, which plays a prevalent role in the dissemination of antibiotic resistance among pathogens. Despite recent data on the structural architecture of the transposition complex, the molecular mechanisms underlying the replicative transposition of these elements are still poorly understood. Here, we use force-distance curve-based atomic force microscopy to probe the binding of the TnpA transposase of Tn4430 to DNA molecules containing one or two transposon ends and to extract the thermodynamic and kinetic parameters of transposition complex assembly. Comparing wild-type TnpA with previously isolated deregulated TnpA mutants supports a stepwise pathway for transposition complex formation and activation during which TnpA first binds as a dimer to a single transposon end and then undergoes a structural transition that enables it to bind the second end cooperatively and to become activated for transposition catalysis, the latter step occurring at a much faster rate for the TnpA mutants. Our study thus provides an unprecedented approach to probe the dynamic of a complex DNA processing machinery at the single-particle level.
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Affiliation(s)
- Maricruz Fernandez
- NanoBioPhysics lab, Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
- Biochemistry and Genetics of Microorganisms, Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Alexander V Shkumatov
- Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium
- Structural Biology Brussels, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Yun Liu
- Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium
- Structural Biology Brussels, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Claire Stulemeijer
- Biochemistry and Genetics of Microorganisms, Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Sylvie Derclaye
- NanoBioPhysics lab, Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Rouslan G Efremov
- Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium
- Structural Biology Brussels, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Bernard Hallet
- Biochemistry and Genetics of Microorganisms, Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - David Alsteens
- NanoBioPhysics lab, Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
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Rajendran AK, Sankar D, Amirthalingam S, Kim HD, Rangasamy J, Hwang NS. Trends in mechanobiology guided tissue engineering and tools to study cell-substrate interactions: a brief review. Biomater Res 2023; 27:55. [PMID: 37264479 DOI: 10.1186/s40824-023-00393-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 05/09/2023] [Indexed: 06/03/2023] Open
Abstract
Sensing the mechanical properties of the substrates or the matrix by the cells and the tissues, the subsequent downstream responses at the cellular, nuclear and epigenetic levels and the outcomes are beginning to get unraveled more recently. There have been various instances where researchers have established the underlying connection between the cellular mechanosignalling pathways and cellular physiology, cellular differentiation, and also tissue pathology. It has been now accepted that mechanosignalling, alone or in combination with classical pathways, could play a significant role in fate determination, development, and organization of cells and tissues. Furthermore, as mechanobiology is gaining traction, so do the various techniques to ponder and gain insights into the still unraveled pathways. This review would briefly discuss some of the interesting works wherein it has been shown that specific alteration of the mechanical properties of the substrates would lead to fate determination of stem cells into various differentiated cells such as osteoblasts, adipocytes, tenocytes, cardiomyocytes, and neurons, and how these properties are being utilized for the development of organoids. This review would also cover various techniques that have been developed and employed to explore the effects of mechanosignalling, including imaging of mechanosensing proteins, atomic force microscopy (AFM), quartz crystal microbalance with dissipation measurements (QCMD), traction force microscopy (TFM), microdevice arrays, Spatio-temporal image analysis, optical tweezer force measurements, mechanoscanning ion conductance microscopy (mSICM), acoustofluidic interferometric device (AID) and so forth. This review would provide insights to the researchers who work on exploiting various mechanical properties of substrates to control the cellular and tissue functions for tissue engineering and regenerative applications, and also will shed light on the advancements of various techniques that could be utilized to unravel the unknown in the field of cellular mechanobiology.
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Affiliation(s)
- Arun Kumar Rajendran
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University, Seoul, 08826, Republic of Korea
| | - Deepthi Sankar
- Polymeric Biomaterials Lab, School of Nanosciences and Molecular Medicine, Amrita Vishwa Vidyapeetham, Kochi, 682041, India
| | - Sivashanmugam Amirthalingam
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University, Seoul, 08826, Republic of Korea
- Institute of Engineering Research, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hwan D Kim
- Department of Polymer Science and Engineering, Korea National University of Transportation, Chungju, 27469, Republic of Korea
- Department of Biomedical Engineering, Korea National University of Transportation, Chungju, 27469, Republic of Korea
| | - Jayakumar Rangasamy
- Polymeric Biomaterials Lab, School of Nanosciences and Molecular Medicine, Amrita Vishwa Vidyapeetham, Kochi, 682041, India.
| | - Nathaniel S Hwang
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University, Seoul, 08826, Republic of Korea.
- Institute of Engineering Research, Seoul National University, Seoul, 08826, Republic of Korea.
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, 08826, Republic of Korea.
- Bio-MAX/N-Bio Institute, Institute of Bio-Engineering, Seoul National University, Seoul, 08826, Republic of Korea.
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50
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Iida S, Kameda T. Dissociation Rate Calculation via Constant-Force Steered Molecular Dynamics Simulation. J Chem Inf Model 2023. [PMID: 37188657 DOI: 10.1021/acs.jcim.2c01529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Steered molecular dynamics (SMD) simulations are used to study molecular dissociation events by applying a harmonic force to the molecules and pulling them at a constant velocity. Instead of constant-velocity pulling, we use a constant force: the constant-force SMD (CF-SMD) simulation. The CF-SMD simulation employs a constant force to reduce the activation barrier of molecular dissociation, thereby enhancing the dissociation event. Here, we present the capability of the CF-SMD simulation to estimate the dissociation time at equilibrium. We performed all-atom CF-SMD simulations for NaCl and protein-ligand systems, producing dissociation time at various forces. We extrapolated these values to the dissociation rate without a constant force using Bell's model or the Dudko-Hummer-Szabo model. We demonstrate that the CF-SMD simulations with the models predicted the dissociation time in equilibrium. A CF-SMD simulation is a powerful tool for estimating the dissociation rate in a direct and computationally efficient manner.
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Affiliation(s)
- Shinji Iida
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Tomoshi Kameda
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
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