1
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Giraud L, Marsan O, Dague E, Ben-Neji M, Cougoule C, Meunier E, Soueid S, Galibert AM, Tourrette A, Flahaut E. Surface-anchored carbon nanomaterials for antimicrobial surfaces. NANOSCALE 2024; 16:16517-16534. [PMID: 39171440 DOI: 10.1039/d4nr02810d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
Abstract
Carbon nanomaterials (CNMs) are known for their antimicrobial (antibacterial and antiviral) activity when dispersed in a liquid, but whether this can be transferred to the surface of common materials has rarely been investigated. We have compared two typical CNMs (double-walled carbon nanotubes and few-layer graphene) in their non-oxidised and oxidised forms in terms of their antibacterial (Pseudomonas aeruginosa and Staphylococcus aureus) and antiviral (SARS-CoV2) activities after anchoring them onto the surface of silicone. We propose a very simple and effective protocol using the air-brush spray deposition method to entrap CNMs on the surfaces of two different silicone materials and demonstrate that the nanomaterials are anchored within the polymer while still being in contact with bacteria. We also investigated their antiviral activity against SARS-COV2 after deposition on standard surgical respiratory masks. Our results show that while suspensions of double-walled carbon nanotubes had a moderate effect on P. aeruginosa, this was not transferred after anchoring them to the surface of silicone. In contrast, graphene oxide showed a very strong antibacterial effect on P. aeruginosa and oxidised double-walled carbon nanotubes on S. aureus only when anchored to the surface. No significant antiviral activity was observed. This work paves the way for new antibacterial surfaces based on CNMs.
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Affiliation(s)
- L Giraud
- CIRIMAT, Université Toulouse 3 Paul Sabatier, CNRS, INP Toulouse, Toulouse, France.
| | - O Marsan
- CIRIMAT, Université Toulouse 3 Paul Sabatier, CNRS, INP Toulouse, Toulouse, France.
| | - E Dague
- LAAS-CNRS, Université de Toulouse, CNRS, Toulouse, France
| | - M Ben-Neji
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
| | - C Cougoule
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
| | - E Meunier
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
| | - S Soueid
- CIRIMAT, Université Toulouse 3 Paul Sabatier, CNRS, INP Toulouse, Toulouse, France.
| | - A M Galibert
- CIRIMAT, Université Toulouse 3 Paul Sabatier, CNRS, INP Toulouse, Toulouse, France.
| | - A Tourrette
- CIRIMAT, Université Toulouse 3 Paul Sabatier, CNRS, INP Toulouse, Toulouse, France.
| | - E Flahaut
- CIRIMAT, Université Toulouse 3 Paul Sabatier, CNRS, INP Toulouse, Toulouse, France.
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2
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Ireddy ATS, Ghorabe FDE, Shishatskaya EI, Ryltseva GA, Dudaev AE, Kozodaev DA, Nosonovsky M, Skorb EV, Zun PS. Benchmarking Unsupervised Clustering Algorithms for Atomic Force Microscopy Data on Polyhydroxyalkanoate Films. ACS OMEGA 2024; 9:21595-21611. [PMID: 38764678 PMCID: PMC11097174 DOI: 10.1021/acsomega.4c02502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/11/2024] [Accepted: 04/12/2024] [Indexed: 05/21/2024]
Abstract
Surface of polyhydroxyalkanoate (PHA) films of varying monomer compositions are analyzed using atomic force microscopy (AFM) and unsupervised machine learning (ML) algorithms to investigate and classify films based on global attributes such as the scan size, film thickness, and monomer type. The experiment provides benchmarked results for 12 of the most widely used clustering algorithms via a hybrid investigation approach while highlighting the impact of using the Fourier transform (FT) on high-dimensional vectorized data for classification on various pools of data. Our findings indicate that the use of a one-dimensional (1D) FT of vectorized data produces the most accurate outcome. The experiment also provides insights into case-by-case investigations of algorithm performances and the impact of various data pools. Lastly, we show an early version of our tool aimed at investigating surfaces using ML approaches and discuss the results of our current experiment to configure future improvements.
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Affiliation(s)
- Ashish T. S. Ireddy
- Infochemistry
Scientific Centre, ITMO University, 9 Lomonosova St., 191002 St. Petersburg, Russia
| | - Fares D. E. Ghorabe
- Infochemistry
Scientific Centre, ITMO University, 9 Lomonosova St., 191002 St. Petersburg, Russia
| | | | - Galina A. Ryltseva
- Siberian
Federal University, 79 Svobodnyi Av., 660041 Krasnoyarsk, Russia
| | - Alexey E. Dudaev
- Siberian
Federal University, 79 Svobodnyi Av., 660041 Krasnoyarsk, Russia
| | | | - Michael Nosonovsky
- Infochemistry
Scientific Centre, ITMO University, 9 Lomonosova St., 191002 St. Petersburg, Russia
- University
of Wisconsin-Milwaukee, Milwaukee, Wisconsin 53217, United States
| | - Ekaterina V. Skorb
- Infochemistry
Scientific Centre, ITMO University, 9 Lomonosova St., 191002 St. Petersburg, Russia
| | - Pavel S. Zun
- Infochemistry
Scientific Centre, ITMO University, 9 Lomonosova St., 191002 St. Petersburg, Russia
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3
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Juković M, Ratkaj I, Kalafatovic D, Bradshaw NJ. Amyloids, amorphous aggregates and assemblies of peptides - Assessing aggregation. Biophys Chem 2024; 308:107202. [PMID: 38382283 DOI: 10.1016/j.bpc.2024.107202] [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: 11/29/2023] [Revised: 01/31/2024] [Accepted: 02/14/2024] [Indexed: 02/23/2024]
Abstract
Amyloid and amorphous aggregates represent the two major categories of aggregates associated with diseases, and although exhibiting distinct features, researchers often treat them as equivalent, which demonstrates the need for more thorough characterization. Here, we compare amyloid and amorphous aggregates based on their biochemical properties, kinetics, and morphological features. To further decipher this issue, we propose the use of peptide self-assemblies as minimalistic models for understanding the aggregation process. Peptide building blocks are significantly smaller than proteins that participate in aggregation, however, they make a plausible means to bridge the gap in discerning the aggregation process at the more complex, protein level. Additionally, we explore the potential use of peptide-inspired models to research the liquid-liquid phase separation as a feasible mechanism preceding amyloid formation. Connecting these concepts can help clarify our understanding of aggregation-related disorders and potentially provide novel drug targets to impede and reverse these serious illnesses.
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Affiliation(s)
- Maja Juković
- Faculty of Biotechnology and Drug Development, University of Rijeka, 51000 Rijeka, Croatia
| | - Ivana Ratkaj
- Faculty of Biotechnology and Drug Development, University of Rijeka, 51000 Rijeka, Croatia
| | - Daniela Kalafatovic
- Faculty of Biotechnology and Drug Development, University of Rijeka, 51000 Rijeka, Croatia.
| | - Nicholas J Bradshaw
- Faculty of Biotechnology and Drug Development, University of Rijeka, 51000 Rijeka, Croatia.
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4
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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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5
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Feng Y, Liu M, Li X, Li M, Xing X, Liu L. Nanomechanical Signatures of Extracellular Vesicles from Hematologic Cancer Patients Unraveled by Atomic Force Microscopy for Liquid Biopsy. NANO LETTERS 2023; 23:1591-1599. [PMID: 36723485 DOI: 10.1021/acs.nanolett.3c00093] [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: 06/18/2023]
Abstract
Cells release extracellular vesicles (EVs) as the carriers for intercellular communications to regulate life activities. Particularly, it is increasingly apparent that mechanical forces play an essential role in biological systems. The nanomechanical properties of EVs and their dynamics in cancer development are still not fully understood. Herein, with the use of atomic force microscopy (AFM), the nanomechanical signatures of EVs from the liquid biopsies of hematologic cancer patients were unraveled. Single native EVs were probed by AFM under aqueous conditions. The elastic and viscous properties of EVs were measured and visualized to correlate EV mechanics with EV geometry. Experimental results remarkably reveal the significant differences in EV mechanics among multiple myeloma patients, lymphoma patients, and healthy volunteers. The study unveils the unique nanomechanical signatures of EVs in hematologic cancers, which will benefit the studies of liquid biopsies for cancer diagnosis and prognosis with translational significance.
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Affiliation(s)
- Yaqi Feng
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang 110016, People's Republic of China
- Institutes for Robotics and Intelligent Manufacturing, Chinese Academy of Sciences, Shenyang 110169, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Meichen Liu
- Cancer Hospital of China Medical University, Shenyang 110042, People's Republic of China
- Liaoning Cancer Hospital & Institute, Shenyang 110042, People's Republic of China
| | - Xinxin Li
- Cancer Hospital of China Medical University, Shenyang 110042, People's Republic of China
- Liaoning Cancer Hospital & Institute, Shenyang 110042, People's Republic of China
| | - Mi Li
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang 110016, People's Republic of China
- Institutes for Robotics and Intelligent Manufacturing, Chinese Academy of Sciences, Shenyang 110169, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Xiaojing Xing
- Cancer Hospital of China Medical University, Shenyang 110042, People's Republic of China
- Liaoning Cancer Hospital & Institute, Shenyang 110042, People's Republic of China
| | - Lianqing Liu
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang 110016, People's Republic of China
- Institutes for Robotics and Intelligent Manufacturing, Chinese Academy of Sciences, Shenyang 110169, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
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6
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Simpson J, Ray A, Marcon C, dos Santos Natividade R, Dorrazehi GM, Durlet K, Koehler M, Alsteens D. Single-Molecule Analysis of SARS-CoV-2 Binding to C-Type Lectin Receptors. NANO LETTERS 2023; 23:1496-1504. [PMID: 36758952 PMCID: PMC9924085 DOI: 10.1021/acs.nanolett.2c04931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/27/2023] [Indexed: 06/18/2023]
Abstract
Despite intense scrutiny throughout the pandemic, development of efficacious drugs against SARS-CoV-2 spread remains hindered. Understanding the underlying mechanisms of viral infection is fundamental for developing novel treatments. While angiotensin converting enzyme 2 (ACE2) is accepted as the key entry receptor of the virus, other infection mechanisms exist. Dendritic cell-specific intercellular adhesion molecule-3 grabbing non-integrin (DC-SIGN) and its counterpart DC-SIGN-related (DC-SIGNR, also known as L-SIGN) have been recognized as possessing functional roles in COVID-19 disease and binding to SARS-CoV-2 has been demonstrated previously with ensemble and qualitative techniques. Here we examine the thermodynamic and kinetic parameters of the ligand-receptor interaction between these C-type lectins and the SARS-CoV-2 S1 protein using force-distance curve-based AFM and biolayer interferometry. We evidence that the S1 receptor binding domain is likely involved in this bond formation. Further, we employed deglycosidases and examined a nonglycosylated S1 variant to confirm the significance of glycosylation in this interaction. We demonstrate that the high affinity interactions observed occur through a mechanism distinct from that of ACE2.
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Affiliation(s)
- Joshua
D. Simpson
- Louvain
Institute of Biomolecular Science and Technology, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Ankita Ray
- Louvain
Institute of Biomolecular Science and Technology, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Claire Marcon
- Louvain
Institute of Biomolecular Science and Technology, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Rita dos Santos Natividade
- Louvain
Institute of Biomolecular Science and Technology, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Gol Mohammad Dorrazehi
- Louvain
Institute of Biomolecular Science and Technology, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Kimberly Durlet
- Louvain
Institute of Biomolecular Science and Technology, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Melanie Koehler
- Louvain
Institute of Biomolecular Science and Technology, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - David Alsteens
- Louvain
Institute of Biomolecular Science and Technology, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
- Walloon
Excellence in Life Sciences and Biotechnology (WELBIO), 1300 Wavre, Belgium
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7
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Venugopal A, Ruiz-Perez L, Swamynathan K, Kulkarni C, Calò A, Kumar M. Caught in Action: Visualizing Dynamic Nanostructures Within Supramolecular Systems Chemistry. Angew Chem Int Ed Engl 2023; 62:e202208681. [PMID: 36469792 DOI: 10.1002/anie.202208681] [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: 06/14/2022] [Revised: 11/30/2022] [Accepted: 12/05/2022] [Indexed: 12/12/2022]
Abstract
Supramolecular systems chemistry has been an area of active research to develop nanomaterials with life-like functions. Progress in systems chemistry relies on our ability to probe the nanostructure formation in solution. Often visualizing the dynamics of nanostructures which transform over time is a formidable challenge. This necessitates a paradigm shift from dry sample imaging towards solution-based techniques. We review the application of state-of-the-art techniques for real-time, in situ visualization of dynamic self-assembly processes. We present how solution-based techniques namely optical super-resolution microscopy, solution-state atomic force microscopy, liquid-phase transmission electron microscopy, molecular dynamics simulations and other emerging techniques are revolutionizing our understanding of active and adaptive nanomaterials with life-like functions. This Review provides the visualization toolbox and futuristic vision to tap the potential of dynamic nanomaterials.
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Affiliation(s)
- Akhil Venugopal
- Institute for Bioengineering of Catalonia (IBEC), Calle Baldiri Reixac 10-12, 08028, Barcelona, Spain
| | - Lorena Ruiz-Perez
- Institute for Bioengineering of Catalonia (IBEC), Calle Baldiri Reixac 10-12, 08028, Barcelona, Spain
| | - K Swamynathan
- Soft Condensed Matter, Raman Research Institute, C. V. Raman Avenue, Sadashivanagar, Bangalore-560080, India.,Department of Chemistry, NITTE Meenakshi Institute of Technology, Yelahanka, Bengaluru 560064, India
| | - Chidambar Kulkarni
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai-400076, India
| | - Annalisa Calò
- Institute for Bioengineering of Catalonia (IBEC), Calle Baldiri Reixac 10-12, 08028, Barcelona, Spain.,Department of Electronic and Biomedical Engineering, University of Barcelona, Calle Marti i Fraquès 1-11, 08028, Barcelona, Spain
| | - Mohit Kumar
- Institute for Bioengineering of Catalonia (IBEC), Calle Baldiri Reixac 10-12, 08028, Barcelona, Spain.,Department of Organic Chemistry, University of Barcelona, Calle Marti i Fraquès 1-11, 08028, Barcelona, Spain
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8
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Baccouch R, Shi Y, Vernay E, Mathelié-Guinlet M, Taib-Maamar N, Villette S, Feuillie C, Rascol E, Nuss P, Lecomte S, Molinari M, Staneva G, Alves ID. The impact of lipid polyunsaturation on the physical and mechanical properties of lipid membranes. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2023; 1865:184084. [PMID: 36368636 DOI: 10.1016/j.bbamem.2022.184084] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 10/21/2022] [Accepted: 10/25/2022] [Indexed: 11/09/2022]
Abstract
The lipid composition of cellular membranes and the balance between the different lipid components can be impacted by aging, certain pathologies, specific diets and other factors. This is the case in a subgroup of individuals with psychiatric disorders, such as schizophrenia, where cell membranes of patients have been shown to be deprived in polyunsaturated fatty acids (PUFAs), not only in brain areas where the target receptors are expressed but also in peripheral tissues. This PUFA deprivation thus represents a biomarker of such disorders that might impact not only the interaction of antipsychotic medications with these membranes but also the activation and signaling of the targeted receptors embedded in the lipid membrane. Therefore, it is crucial to understand how PUFAs levels alterations modulate the different physical properties of membranes. In this paper, several biophysical approaches were combined (Laurdan fluorescence spectroscopy, atomic force microscopy, differential scanning calorimetry, molecular modeling) to characterize membrane properties such as fluidity, elasticity and thickness in PUFA-enriched cell membranes and lipid model systems reflecting the PUFA imbalance observed in some diseases. The impact of both the number of unsaturations and their position along the chain on the above properties was investigated. Briefly, data revealed that PUFA presence in membranes increases membrane fluidity, elasticity and flexibility and decreases its thickness and order parameter. Both the level of unsaturation and their position affect these membrane properties.
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Affiliation(s)
- Rim Baccouch
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, Bat B14, allée Geoffroy St. Hilaire, F-33600 Pessac, France
| | - Yarong Shi
- Laboratoire de Recherche en Nanosciences, LRN EA4682, University of Reims Champagne Ardenne, France
| | - Emilie Vernay
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, Bat B14, allée Geoffroy St. Hilaire, F-33600 Pessac, France
| | - Marion Mathelié-Guinlet
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, Bat B14, allée Geoffroy St. Hilaire, F-33600 Pessac, France
| | - Nada Taib-Maamar
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, Bat B14, allée Geoffroy St. Hilaire, F-33600 Pessac, France
| | - Sandrine Villette
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, Bat B14, allée Geoffroy St. Hilaire, F-33600 Pessac, France
| | - Cécile Feuillie
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, Bat B14, allée Geoffroy St. Hilaire, F-33600 Pessac, France
| | - Estelle Rascol
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, Bat B14, allée Geoffroy St. Hilaire, F-33600 Pessac, France
| | - Philippe Nuss
- Centre de Recherche Saint-Antoine, INSERM UMRS 938, Sorbonne Université, Paris, France; Service de psychiatrie et de psychologie médicale, Sorbonne Université, Hôpital Saint-Antoine, AP-HP, Paris, France
| | - Sophie Lecomte
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, Bat B14, allée Geoffroy St. Hilaire, F-33600 Pessac, France
| | - Michael Molinari
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, Bat B14, allée Geoffroy St. Hilaire, F-33600 Pessac, France
| | - Galya Staneva
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Bl.21, 1113 Sofia, Bulgaria
| | - Isabel D Alves
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, Bat B14, allée Geoffroy St. Hilaire, F-33600 Pessac, France.
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9
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Liu J, Fan S, Xiang Y, Xia J, Jin H, Xu JF, Yang F, Cai J, Pi J. Nanoscale Features of Gambogic Acid Induced ROS-Dependent Apoptosis in Esophageal Cancer Cells Imaged by Atomic Force Microscopy. SCANNING 2022; 2022:1422185. [PMID: 35937670 PMCID: PMC9337977 DOI: 10.1155/2022/1422185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 06/07/2022] [Accepted: 07/05/2022] [Indexed: 06/15/2023]
Abstract
Gambogic acid (GA), a kind of polyprenylated xanthone derived from Garcinia hanburyi tree, has showed spectrum anticancer effects both in vitro and in vivo with low toxicity. However, up to now, there is little information about the effects of GA on esophageal cancer. In this study, we aim to test the anticancer effects of GA on esophageal cancer EC9706 cells. We established a nanoscale imaging method based on AFM to evaluate the reactive oxygen species- (ROS-) mediated anticancer effects of GA on esophageal cancer regarding the morphological and ultrastructural changes of esophageal cancer cells. The obtained results demonstrated that GA could inhibit cell proliferation, induce apoptosis, induce cell cycle arrest, and induce mitochondria membrane potential disruption in a ROS-dependent way. And using AFM imaging, we also found that GA could induce the damage of cellular morphology and increase of membrane height distribution and membrane roughness in EC9706 cells, which could be reversed by the removal of GA-induced excessive intracellular ROS. Our results not only demonstrated the anticancer effects of GA on EC9706 cells in ROS-dependent mechanism but also strongly suggested AFM as a powerful tool for the detection of ROS-mediated cancer cell apoptosis on the basis of imaging.
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Affiliation(s)
- Jianxin Liu
- Hunan Provincial Key Laboratory of Dong Medicine, Hunan Province Key Laboratory for Antibody-Based Drug and Intelligent Delivery System, Hunan Provincial Key Laboratory for Synthetic Biology of Traditional Chinese Medicine, School of Pharmaceutical Sciences, Hunan University of Medicine, Huaihua, China
| | - Shuhao Fan
- Institute of Laboratory Medicine, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, School of Medical Technology, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, China
| | - Yinhong Xiang
- School of Basic Medical Sciences, Hunan University of Medicine, Huaihua, China
| | - Jiaojiao Xia
- Institute of Laboratory Medicine, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, School of Medical Technology, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, China
| | - Hua Jin
- Institute of Laboratory Medicine, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, School of Medical Technology, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, China
| | - Jun-fa Xu
- Institute of Laboratory Medicine, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, School of Medical Technology, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, China
| | - Fen Yang
- Institute of Laboratory Medicine, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, School of Medical Technology, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, China
| | - Jiye Cai
- Department of Chemistry, Jinan University, Guangzhou, China
| | - Jiang Pi
- Institute of Laboratory Medicine, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, School of Medical Technology, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, China
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10
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Cho DH, Xie T, Mulcahey PJ, Kelleher NP, Hahm JI. Distinctive Adsorption Mechanism and Kinetics of Immunoglobulin G on a Nanoscale Polymer Surface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:1458-1470. [PMID: 35037456 DOI: 10.1021/acs.langmuir.1c02710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Elucidation of protein adsorption beyond simple polymer surfaces to those presenting greater chemical complexity and nanoscopic features is critical to developing well-controlled nanobiomaterials and nanobiosensors. In this study, we repeatedly and faithfully track individual proteins on the same nanodomain areas of a block copolymer (BCP) surface and monitor the adsorption and assembly behavior of a model protein, immunoglobulin G (IgG), over time into a tight surface-packed structure. With discrete protein adsorption events unambiguously visualized at the biomolecular level, the detailed assembly and packing states of IgG on the BCP nanodomain surface are subsequently correlated to various regimes of IgG adsorption kinetic plots. Intriguing features, entirely different from those observed from macroscopic homopolymer templates, are identified from the IgG adsorption isotherms on the nanoscale, chemically varying BCP surface. They include the presence of two Langmuir-like adsorption segments and a nonmonotonic regime in the adsorption plot. Via correlation to time-corresponding topographic data, the unique isotherm features are explained with single biomolecule level details of the IgG adsorption pathway on the BCP. This work not only provides much needed, direct experimental evidence for time-resolved, single protein level, adsorption events on nanoscale polymer surfaces but also signifies mutual linking between specific topographic states of protein adsorption and assembly to particular segments of adsorption isotherms. From the fundamental research viewpoint, the correlative ability to examine the nanoscopic surface organizations of individual proteins and their local as well as global adsorption kinetic profiles will be highly valuable for accurately determining protein assembly mechanisms and interpreting protein adsorption kinetics on nanoscale surfaces. Application-wise, such knowledge will also be important for fundamentally guiding the design and development of biomaterials and biomedical devices that exploit nanoscale polymer architectures.
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Affiliation(s)
- David H Cho
- Department of Chemistry, Georgetown University, 37th & O Sts. NW., Washington, D.C. 20057, United States
| | - Tian Xie
- Department of Chemistry, Georgetown University, 37th & O Sts. NW., Washington, D.C. 20057, United States
| | - Patrick J Mulcahey
- Department of Chemistry, Georgetown University, 37th & O Sts. NW., Washington, D.C. 20057, United States
| | - Noah P Kelleher
- Department of Chemistry, Georgetown University, 37th & O Sts. NW., Washington, D.C. 20057, United States
| | - Jong-In Hahm
- Department of Chemistry, Georgetown University, 37th & O Sts. NW., Washington, D.C. 20057, United States
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11
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Tang X, Fan G, Zhang H, Dai X, Hu Y, Zhang Z, Li Y. An integrated optical waveguide micro-cantilever system for chip-based AFM. J Microsc 2021; 285:112-116. [PMID: 34866187 DOI: 10.1111/jmi.13080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 11/19/2021] [Accepted: 12/02/2021] [Indexed: 11/25/2022]
Abstract
An optical waveguide cantilever system with a tip is introduced as the displacement detection system of chip-based atomic force microscopy (AFM) system. A chip-based AFM on optical waveguide is demonstrated with sensitivity of up to 4.0 × 10-2 nm-1 , which is mainly constructed by a 210 nm thick optical waveguide cantilever with a nano-tip. The nano-tip is a height of 1.2 μm and diameter of 140 nm. This integrated on-chip system provides a displacement range of approximately ±0.4 μm, which makes it possible for the device to be used for AFM imaging and pays the way for further performance improvement.
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Affiliation(s)
- Xinxin Tang
- Key Laboratory of All Optical Network and Advanced Telecommunication Network, Ministry of Education, Institute of Lightwave Technology, Beijing Jiaotong University, Beijing, China
| | - Guofang Fan
- Key Laboratory of All Optical Network and Advanced Telecommunication Network, Ministry of Education, Institute of Lightwave Technology, Beijing Jiaotong University, Beijing, China
| | - Hongru Zhang
- Key Laboratory of All Optical Network and Advanced Telecommunication Network, Ministry of Education, Institute of Lightwave Technology, Beijing Jiaotong University, Beijing, China
| | - Xingang Dai
- Key Laboratory of All Optical Network and Advanced Telecommunication Network, Ministry of Education, Institute of Lightwave Technology, Beijing Jiaotong University, Beijing, China
| | - Yanjun Hu
- Key Laboratory of All Optical Network and Advanced Telecommunication Network, Ministry of Education, Institute of Lightwave Technology, Beijing Jiaotong University, Beijing, China
| | - Zhiping Zhang
- Academy for Engineering & Technology, Fudan University, Shanghai, China
| | - Yuan Li
- National Center of Measurement and Testing for East China, Shanghai Institute of Measurement and Testing Technology, National Center of Testing Technology, Shanghai, China
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12
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Pan J, Kmieciak T, Liu YT, Wildenradt M, Chen YS, Zhao Y. Quantifying molecular- to cellular-level forces in living cells. JOURNAL OF PHYSICS D: APPLIED PHYSICS 2021; 54:483001. [PMID: 34866655 PMCID: PMC8635116 DOI: 10.1088/1361-6463/ac2170] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Mechanical cues have been suggested to play an important role in cell functions and cell fate determination, however, such physical quantities are challenging to directly measure in living cells with single molecule sensitivity and resolution. In this review, we focus on two main technologies that are promising in probing forces at the single molecule level. We review their theoretical fundamentals, recent technical advancements, and future directions, tailored specifically for interrogating mechanosensitive molecules in live cells.
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Affiliation(s)
- Jason Pan
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States of America
| | - Tommy Kmieciak
- Department of Engineering Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States of America
| | - Yen-Ting Liu
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States of America
| | - Matthew Wildenradt
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States of America
| | - Yun-Sheng Chen
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States of America
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States of America
| | - Yang Zhao
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States of America
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, 208 N. Wright Street, Urbana, IL 61801, United States of America
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13
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Andryukov BG, Karpenko AA, Lyapun IN. Learning from Nature: Bacterial Spores as a Target for Current Technologies in Medicine (Review). Sovrem Tekhnologii Med 2021; 12:105-122. [PMID: 34795986 PMCID: PMC8596247 DOI: 10.17691/stm2020.12.3.13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Indexed: 01/05/2023] Open
Abstract
The capability of some representatives of Clostridium spp. and Bacillus spp. genera to form spores in extreme external conditions long ago became a subject of medico-biological investigations. Bacterial spores represent dormant cellular forms of gram-positive bacteria possessing a high potential of stability and the capability to endure extreme conditions of their habitat. Owing to these properties, bacterial spores are recognized as the most stable systems on the planet, and spore-forming microorganisms became widely spread in various ecosystems. Spore-forming bacteria have been attracted increased interest for years due to their epidemiological danger. Bacterial spores may be in the quiescent state for dozens or hundreds of years but after they appear in the favorable conditions of a human or animal organism, they turn into vegetative forms causing an infectious process. The greatest threat among the pathogenic spore-forming bacteria is posed by the causative agents of anthrax (B. anthracis), food toxicoinfection (B. cereus), pseudomembranous colitis (C. difficile), botulism (C. botulinum), gas gangrene (C. perfringens). For the effective prevention of severe infectious diseases first of all it is necessary to study the molecular structure of bacterial spores and the biochemical mechanisms of sporulation and to develop innovative methods of detection and disinfection of dormant cells. There is another side of the problem: the necessity to investigate exo- and endospores from the standpoint of obtaining similar artificially synthesized models in order to use them in the latest medical technologies for the development of thermostable vaccines, delivery of biologically active substances to the tissues and intracellular structures. In recent years, bacterial spores have become an interesting object for the exploration from the point of view of a new paradigm of unicellular microbiology in order to study microbial heterogeneity by means of the modern analytical tools.
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Affiliation(s)
- B G Andryukov
- Leading Researcher, Laboratory of Molecular Microbiology; G.P. Somov Institute of Epidemiology and Microbiology, 1 Selskaya St., Vladivostok, 690087, Russia; Professor, Department of Fundamental Sciences; Far Eastern Federal University, 10 Village Ayaks, Island Russkiy, Vladivostok, 690922, Russia
| | - A A Karpenko
- Senior Researcher, Laboratory of Cell Biophysics; A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch of the Russian Academy of Sciences, 17 Palchevskogo St., Vladivostok, 690041, Russia
| | - I N Lyapun
- Researcher, Laboratory of Molecular Microbiology G.P. Somov Institute of Epidemiology and Microbiology, 1 Selskaya St., Vladivostok, 690087, Russia
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14
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Beadell BA, Chieng A, Parducho KR, Dai Z, Ho SO, Fujii G, Wang Y, Porter E. Nano- and Macroscale Imaging of Cholesterol Linoleate and Human Beta Defensin 2-Induced Changes in Pseudomonas aeruginosa Biofilms. Antibiotics (Basel) 2021; 10:antibiotics10111279. [PMID: 34827217 PMCID: PMC8615053 DOI: 10.3390/antibiotics10111279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/13/2021] [Accepted: 10/16/2021] [Indexed: 11/16/2022] Open
Abstract
The biofilm production of Pseudomonas aeruginosa (PA) is central to establishing chronic infection in the airways in cystic fibrosis. Epithelial cells secrete an array of innate immune factors, including antimicrobial proteins and lipids, such as human beta defensin 2 (HBD2) and cholesteryl lineolate (CL), respectively, to combat colonization by pathogens. We have recently shown that HBD2 inhibits biofilm production by PA, possibly linked to interference with the transport of biofilm precursors. Considering that both HBD2 and CL are increased in airway fluids during infection, we hypothesized that CL synergizes with HBD2 in biofilm inhibition. CL was formulated in phospholipid-based liposomes (CL-PL). As measured by atomic force microscopy of single bacteria, CL-PL alone and in combination with HBD2 significantly increased bacterial surface roughness. Additionally, extracellular structures emanated from untreated bacterial cells, but not from cells treated with CL-PL and HBD2 alone and in combination. Crystal violet staining of the biofilm revealed that CL-PL combined with HBD2 effected a significant decrease of biofilm mass and increased the number of larger biofilm particles consistent with altered cohesion of formed biofilms. These data suggest that CL and HBD2 affect PA biofilm formation at the single cell and community-wide level and that the community-wide effects of CL are enhanced by HBD2. This research may inform future novel treatments for recalcitrant infections in the airways of CF patients.
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Affiliation(s)
- Brent A. Beadell
- Department of Biological Sciences, California State University Los Angeles, Los Angeles, CA 90032, USA; (B.A.B.); (K.R.P.)
| | - Andy Chieng
- Department of Chemistry and Biochemistry, California State University Los Angeles, Los Angeles, CA 90032, USA; (A.C.); (Y.W.)
| | - Kevin R. Parducho
- Department of Biological Sciences, California State University Los Angeles, Los Angeles, CA 90032, USA; (B.A.B.); (K.R.P.)
| | - Zhipeng Dai
- Molecular Express, Inc., Rancho Dominguez, CA 90220, USA; (Z.D.); (S.O.H.); (G.F.)
| | - Sam On Ho
- Molecular Express, Inc., Rancho Dominguez, CA 90220, USA; (Z.D.); (S.O.H.); (G.F.)
| | - Gary Fujii
- Molecular Express, Inc., Rancho Dominguez, CA 90220, USA; (Z.D.); (S.O.H.); (G.F.)
| | - Yixian Wang
- Department of Chemistry and Biochemistry, California State University Los Angeles, Los Angeles, CA 90032, USA; (A.C.); (Y.W.)
| | - Edith Porter
- Department of Biological Sciences, California State University Los Angeles, Los Angeles, CA 90032, USA; (B.A.B.); (K.R.P.)
- Correspondence: ; Tel.: +1-323-343-6353
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15
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Ferraz L, Sauer M, Sousa MJ, Branduardi P. The Plasma Membrane at the Cornerstone Between Flexibility and Adaptability: Implications for Saccharomyces cerevisiae as a Cell Factory. Front Microbiol 2021; 12:715891. [PMID: 34434179 PMCID: PMC8381377 DOI: 10.3389/fmicb.2021.715891] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 07/19/2021] [Indexed: 11/23/2022] Open
Abstract
In the last decade, microbial-based biotechnological processes are paving the way toward sustainability as they implemented the use of renewable feedstocks. Nonetheless, the viability and competitiveness of these processes are often limited due to harsh conditions such as: the presence of feedstock-derived inhibitors including weak acids, non-uniform nature of the substrates, osmotic pressure, high temperature, extreme pH. These factors are detrimental for microbial cell factories as a whole, but more specifically the impact on the cell’s membrane is often overlooked. The plasma membrane is a complex system involved in major biological processes, including establishing and maintaining transmembrane gradients, controlling uptake and secretion, intercellular and intracellular communication, cell to cell recognition and cell’s physical protection. Therefore, when designing strategies for the development of versatile, robust and efficient cell factories ready to tackle the harshness of industrial processes while delivering high values of yield, titer and productivity, the plasma membrane has to be considered. Plasma membrane composition comprises diverse macromolecules and it is not constant, as cells adapt it according to the surrounding environment. Remarkably, membrane-specific traits are emerging properties of the system and therefore it is not trivial to predict which membrane composition is advantageous under certain conditions. This review includes an overview of membrane engineering strategies applied to Saccharomyces cerevisiae to enhance its fitness under industrially relevant conditions as well as strategies to increase microbial production of the metabolites of interest.
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Affiliation(s)
- Luís Ferraz
- Center of Molecular and Environmental Biology, University of Minho, Braga, Portugal.,Department of Biotechnology and Biosciences, University of Milano Bicocca, Milan, Italy
| | - Michael Sauer
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, BOKU University of Natural Resources and Life Sciences, Vienna, Austria
| | - Maria João Sousa
- Center of Molecular and Environmental Biology, University of Minho, Braga, Portugal
| | - Paola Branduardi
- Department of Biotechnology and Biosciences, University of Milano Bicocca, Milan, Italy
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16
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Mittal R, Bencie N, Langlie J, Mittal J, Eshraghi AA. Exosomes as drug delivery vehicles and biomarkers for neurological and auditory systems. J Cell Physiol 2021; 236:8035-8049. [PMID: 34224589 DOI: 10.1002/jcp.30484] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 05/19/2021] [Accepted: 06/14/2021] [Indexed: 12/14/2022]
Abstract
Exosomes are small extracellular membrane particles that play a crucial role in intracellular signaling. Research shows that exosomes have the potential to be used as biomarkers or drug delivery systems in specific organs, such as the neurological system and the inner ear. Exosomes in neurological and auditory systems release different molecules when under stress versus in healthy states, highlighting their potential use as biomarkers in the identification of diseased states. Studies have suggested that exosomes can be harnessed for drug delivery to hard-to-reach organs, such as cochlear sensory hair cells and the brain due to their ability to cross the blood-labyrinth and blood-brain barriers. In this article, we describe the biogenesis, classification, and characterization methods of exosomes. We then discuss recent studies that indicate their potential usage as biomarkers and drug delivery systems to help treat inner ear and neurological disorders.
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Affiliation(s)
- Rahul Mittal
- Department of Otolaryngology, Cochlear Implant and Hearing Research Laboratory, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Nicole Bencie
- Department of Otolaryngology, Cochlear Implant and Hearing Research Laboratory, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Jake Langlie
- Department of Otolaryngology, Cochlear Implant and Hearing Research Laboratory, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Jeenu Mittal
- Department of Otolaryngology, Cochlear Implant and Hearing Research Laboratory, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Adrien A Eshraghi
- Department of Otolaryngology, Cochlear Implant and Hearing Research Laboratory, University of Miami Miller School of Medicine, Miami, Florida, USA.,Department of Neurological Surgery, University of Miami Miller School of Medicine, Miami, Florida, USA.,Department of Biomedical Engineering, University of Miami, Coral Gables, Florida, USA.,Department of Pediatrics, University of Miami Miller School of Medicine, Miami, Florida, USA
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17
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Li M, Xi N, Liu L. Peak force tapping atomic force microscopy for advancing cell and molecular biology. NANOSCALE 2021; 13:8358-8375. [PMID: 33913463 DOI: 10.1039/d1nr01303c] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The advent of atomic force microscopy (AFM) provides an exciting tool to detect molecular and cellular behaviors under aqueous conditions. AFM is able to not only visualize the surface topography of the specimens, but also can quantify the mechanical properties of the specimens by force spectroscopy assay. Nevertheless, integrating AFM topographic imaging with force spectroscopy assay has long been limited due to the low spatiotemporal resolution. In recent years, the appearance of a new AFM imaging mode called peak force tapping (PFT) has shattered this limit. PFT allows AFM to simultaneously acquire the topography and mechanical properties of biological samples with unprecedented spatiotemporal resolution. The practical applications of PFT in the field of life sciences in the past decade have demonstrated the excellent capabilities of PFT in characterizing the fine structures and mechanics of living biological systems in their native states, offering novel possibilities to reveal the underlying mechanisms guiding physiological/pathological activities. In this paper, the recent progress in cell and molecular biology that has been made with the utilization of PFT is summarized, and future perspectives for further progression and biomedical applications of PFT are provided.
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Affiliation(s)
- Mi Li
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang 110016, China and Institutes for Robotics and Intelligent Manufacturing, Chinese Academy of Sciences, Shenyang 110169, China and University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Ning Xi
- Department of Industrial and Manufacturing Systems Engineering, The University of Hong Kong, Hong Kong 999077, China
| | - Lianqing Liu
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang 110016, China and Institutes for Robotics and Intelligent Manufacturing, Chinese Academy of Sciences, Shenyang 110169, China and University of Chinese Academy of Sciences, Beijing 100049, China.
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18
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Kubota R, Tanaka W, Hamachi I. Microscopic Imaging Techniques for Molecular Assemblies: Electron, Atomic Force, and Confocal Microscopies. Chem Rev 2021; 121:14281-14347. [DOI: 10.1021/acs.chemrev.0c01334] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Ryou Kubota
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Wataru Tanaka
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
- JST-ERATO, Hamachi Innovative Molecular Technology for Neuroscience, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8530, Japan
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19
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Abstract
Mycobacteria have unique cell envelopes, surface properties, and growth dynamics, which all play a part in the ability of these important pathogens to infect, evade host immunity, disseminate, and resist antibiotic challenges. Recent atomic force microscopy (AFM) studies have brought new insights into the nanometer-scale ultrastructural, adhesive, and mechanical properties of mycobacteria. The molecular forces with which mycobacterial adhesins bind to host factors, like heparin and fibronectin, and the hydrophobic properties of the mycomembrane have been unraveled by AFM force spectroscopy studies. Real-time correlative AFM and fluorescence imaging have delineated a complex interplay between surface ultrastructure, tensile stresses within the cell envelope, and cellular processes leading to division. The unique capabilities of AFM, which include subdiffraction-limit topographic imaging and piconewton force sensitivity, have great potential to resolve important questions that remain unanswered on the molecular interactions, surface properties, and growth dynamics of this important class of pathogens.
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20
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Dufrêne YF, Viljoen A, Mignolet J, Mathelié-Guinlet M. AFM in cellular and molecular microbiology. Cell Microbiol 2021; 23:e13324. [PMID: 33710716 DOI: 10.1111/cmi.13324] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/22/2021] [Accepted: 02/23/2021] [Indexed: 12/14/2022]
Abstract
The unique capabilities of the atomic force microscope (AFM), including super-resolution imaging, piconewton force-sensitivity, nanomanipulation and ability to work under physiological conditions, have offered exciting avenues for cellular and molecular biology research. AFM imaging has helped unravel the fine architectures of microbial cell envelopes at the nanoscale, and how these are altered by antimicrobial treatment. Nanomechanical measurements have shed new light on the elasticity, tensile strength and turgor pressure of single cells. Single-molecule and single-cell force spectroscopy experiments have revealed the forces and dynamics of receptor-ligand interactions, the nanoscale distribution of receptors on the cell surface and the elasticity and adhesiveness of bacterial pili. Importantly, recent force spectroscopy studies have demonstrated that extremely stable bonds are formed between bacterial adhesins and their cognate ligands, originating from a catch bond behaviour allowing the pathogen to reinforce adhesion under shear or tensile stress. Here, we survey how the versatility of AFM has enabled addressing crucial questions in microbiology, with emphasis on bacterial pathogens. TAKE AWAYS: AFM topographic imaging unravels the ultrastructure of bacterial envelopes. Nanomechanical mapping shows what makes cell envelopes stiff and resistant to drugs. Force spectroscopy characterises the molecular forces in pathogen adhesion. Stretching pili reveals a wealth of mechanical and adhesive responses.
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Affiliation(s)
- Yves F Dufrêne
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Albertus Viljoen
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Johann Mignolet
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Marion Mathelié-Guinlet
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
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21
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Morozov IA. Atomic force microscopy nanoindentation kinetics and subsurface visualization of soft inhomogeneous polymer. Microsc Res Tech 2021; 84:1959-1966. [PMID: 33713508 DOI: 10.1002/jemt.23751] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 02/10/2021] [Accepted: 02/27/2021] [Indexed: 11/11/2022]
Abstract
Modern techniques of nanoindentation by atomic force microscopy (AFM) produce maps of topography and physical-mechanical properties of the material. Analysis of the interaction rate of the AFM tip with the soft surface reveals the surface and subsurface structure and expands standard analysis of the material behavior. Phase-separated polymer (polyurethane, elastic modulus-6 MPa) is studied. Reversible inelastic changes of the surface at different stages of indentation were established in dependence on peculiarities of velocity and position of the AFM-tip in the material: uniform soft nanofilm covering the outer surface gradually passes into fibrillar heterogeneous structure of the polymer. The point of stable mechanical contact is defined, and the elastic moduli of soft and hard blocks of the polymer are estimated using certain intervals of the indentation. The presented methods of surface analysis are useful in the study of a wide class of soft heterogeneous materials.
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Affiliation(s)
- Ilya A Morozov
- Institute of Continuous Media Mechanics UB RAS, Perm, Russia
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22
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Li M, Xi N, Wang YC, Liu LQ. Atomic force microscopy for revealing micro/nanoscale mechanics in tumor metastasis: from single cells to microenvironmental cues. Acta Pharmacol Sin 2021; 42:323-339. [PMID: 32807839 PMCID: PMC8027022 DOI: 10.1038/s41401-020-0494-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 07/27/2020] [Indexed: 02/06/2023] Open
Abstract
Mechanics are intrinsic properties which appears throughout the formation, development, and aging processes of biological systems. Mechanics have been shown to play important roles in regulating the development and metastasis of tumors, and understanding tumor mechanics has emerged as a promising way to reveal the underlying mechanisms guiding tumor behaviors. In particular, tumors are highly complex diseases associated with multifaceted factors, including alterations in cancerous cells, tissues, and organs as well as microenvironmental cues, indicating that investigating tumor mechanics on multiple levels is significantly helpful for comprehensively understanding the effects of mechanics on tumor progression. Recently, diverse techniques have been developed for probing the mechanics of tumors, among which atomic force microscopy (AFM) has appeared as an excellent platform enabling simultaneously characterizing the structures and mechanical properties of living biological systems ranging from individual molecules and cells to tissue samples with unprecedented spatiotemporal resolution, offering novel possibilities for understanding tumor physics and contributing much to the studies of cancer. In this review, we survey the recent progress that has been achieved with the use of AFM for revealing micro/nanoscale mechanics in tumor development and metastasis. Challenges and future progress are also discussed.
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Affiliation(s)
- 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.
| | - Ning Xi
- Department of Industrial and Manufacturing Systems Engineering, The University of Hong Kong, Hong Kong, China
| | - Yue-Chao Wang
- 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
| | - Lian-Qing Liu
- 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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23
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Abdelsattar AS, Mansour Y, Aboul-Ela F. The Perturbed Free-Energy Landscape: Linking Ligand Binding to Biomolecular Folding. Chembiochem 2021; 22:1499-1516. [PMID: 33351206 DOI: 10.1002/cbic.202000695] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 12/19/2020] [Indexed: 12/24/2022]
Abstract
The effects of ligand binding on biomolecular conformation are crucial in drug design, enzyme mechanisms, the regulation of gene expression, and other biological processes. Descriptive models such as "lock and key", "induced fit", and "conformation selection" are common ways to interpret such interactions. Another historical model, linked equilibria, proposes that the free-energy landscape (FEL) is perturbed by the addition of ligand binding energy for the bound population of biomolecules. This principle leads to a unified, quantitative theory of ligand-induced conformation change, building upon the FEL concept. We call the map of binding free energy over biomolecular conformational space the "binding affinity landscape" (BAL). The perturbed FEL predicts/explains ligand-induced conformational changes conforming to all common descriptive models. We review recent experimental and computational studies that exemplify the perturbed FEL, with emphasis on RNA. This way of understanding ligand-induced conformation dynamics motivates new experimental and theoretical approaches to ligand design, structural biology and systems biology.
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Affiliation(s)
- Abdallah S Abdelsattar
- Center for X-Ray Determination of the Structure of Matter, Zewail City of Science and Technology, Ahmed Zewail Road, October Gardens, 12578, Giza, Egypt
| | - Youssef Mansour
- Center for X-Ray Determination of the Structure of Matter, Zewail City of Science and Technology, Ahmed Zewail Road, October Gardens, 12578, Giza, Egypt
| | - Fareed Aboul-Ela
- Center for X-Ray Determination of the Structure of Matter, Zewail City of Science and Technology, Ahmed Zewail Road, October Gardens, 12578, Giza, Egypt
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24
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Beaussart A, Feuillie C, El-Kirat-Chatel S. The microbial adhesive arsenal deciphered by atomic force microscopy. NANOSCALE 2020; 12:23885-23896. [PMID: 33289756 DOI: 10.1039/d0nr07492f] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Microbes employ a variety of strategies to adhere to abiotic and biotic surfaces, as well as host cells. In addition to their surface physicochemical properties (e.g. charge, hydrophobic balance), microbes produce appendages (e.g. pili, fimbriae, flagella) and express adhesion proteins embedded in the cell wall or cell membrane, with adhesive domains targeting specific ligands or chemical properties. Atomic force microscopy (AFM) is perfectly suited to deciphering the adhesive properties of microbial cells. Notably, AFM imaging has revealed the cell wall topographical organization of live cells at unprecedented resolution, and AFM has a dual capability to probe adhesion at the single-cell and single-molecule levels. AFM is thus a powerful tool for unravelling the molecular mechanisms of microbial adhesion at scales ranging from individual molecular interactions to the behaviours of entire cells. In this review, we cover some of the major breakthroughs facilitated by AFM in deciphering the microbial adhesive arsenal, including the exciting development of anti-adhesive strategies.
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3D-printed cellular tips for tuning fork atomic force microscopy in shear mode. Nat Commun 2020; 11:5732. [PMID: 33184281 PMCID: PMC7661501 DOI: 10.1038/s41467-020-19536-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 10/12/2020] [Indexed: 12/21/2022] Open
Abstract
Conventional atomic force microscopy (AFM) tips have remained largely unchanged in nanomachining processes, constituent materials, and microstructural constructions for decades, which limits the measurement performance based on force-sensing feedbacks. In order to save the scanning images from distortions due to excessive mechanical interactions in the intermittent shear-mode contact between scanning tips and sample, we propose the application of controlled microstructural architectured material to construct AFM tips by exploiting material-related energy-absorbing behavior in response to the tip–sample impact, leading to visual promotions of imaging quality. Evidenced by numerical analysis of compressive responses and practical scanning tests on various samples, the essential scanning functionality and the unique contribution of the cellular buffer layer to imaging optimization are strongly proved. This approach opens new avenues towards the specific applications of cellular solids in the energy-absorption field and sheds light on novel AFM studies based on 3D-printed tips possessing exotic properties. The authors investigate 3D-printed tips, based on controlled microstructural architectured materials, as probes for shear-mode atomic force microscopy. They demonstrate that the tailored stiffness and energy-absorbing behaviour of the material are beneficial for improving image quality.
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Hammond K, Ryadnov MG, Hoogenboom BW. Atomic force microscopy to elucidate how peptides disrupt membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1863:183447. [PMID: 32835656 DOI: 10.1016/j.bbamem.2020.183447] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/30/2020] [Accepted: 08/13/2020] [Indexed: 12/24/2022]
Abstract
Atomic force microscopy is an increasingly attractive tool to study how peptides disrupt membranes. Often performed on reconstituted lipid bilayers, it provides access to time and length scales that allow dynamic investigations with nanometre resolution. Over the last decade, AFM studies have enabled visualisation of membrane disruption mechanisms by antimicrobial or host defence peptides, including peptides that target malignant cells and biofilms. Moreover, the emergence of high-speed modalities of the technique broadens the scope of investigations to antimicrobial kinetics as well as the imaging of peptide action on live cells in real time. This review describes how methodological advances in AFM facilitate new insights into membrane disruption mechanisms.
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Affiliation(s)
- Katharine Hammond
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, UK; London Centre for Nanotechnology, University College London, London WC1H 0AH, UK; Department of Physics & Astronomy, University College London, London WC1E 6BT, UK.
| | - Maxim G Ryadnov
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, UK; Department of Physics, King's College London, Strand Lane, London WC2R 2LS, UK.
| | - Bart W Hoogenboom
- London Centre for Nanotechnology, University College London, London WC1H 0AH, UK; Department of Physics & Astronomy, University College London, London WC1E 6BT, UK.
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27
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Elie-Caille C, Lascombe I, Péchery A, Bittard H, Fauconnet S. Molecular and nanoscale evaluation of N-cadherin expression in invasive bladder cancer cells under control conditions or GW501516 exposure. Mol Cell Biochem 2020; 471:113-127. [PMID: 32519230 PMCID: PMC7370938 DOI: 10.1007/s11010-020-03771-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 05/31/2020] [Indexed: 02/06/2023]
Abstract
N-cadherin is a transmembrane glycoprotein expressed by mesenchymal origin cells and is located at the adherens junctions. It regulates also cell motility and contributes to cell signaling. In previous studies, we identified that its anomalous expression in bladder carcinoma was a tumor progression marker. A pharmacological approach to inhibit N-cadherin expression or to block its function could be relevant to prevent disease progression and metastasis development. The morphological exploration of T24 invasive bladder cancer cells by atomic force microscopy (AFM) revealed a spindle-like shape with fibrous structures. By engaging force spectroscopy with AFM tip functionalized with anti-E or anti-N-cadherin antibodies, results showed that T24 cells expressed only N-cadherin as also demonstrated by Western blotting and confocal microscopy. For the first time, we demonstrated by RTqPCR and Western blotting analyses that the peroxisome proliferator-activated receptor β/δ (PPARβ/δ) agonist GW501516 significantly decreased N-cadherin expression in T24 cells. Moreover, high non-cytotoxic doses of GW501516 inhibited confluent T24 cell wound healing closure. By using AFM, a more sensitive nanoanalytical method, we showed that the treatment modified the cellular morphology and diminished N-cadherin cell surface coverage through the decreasing of these adhesion molecule-mediated interaction forces. We observed a greater decrease of N-cadherin upon GW501516 exposure with AFM than that detected with molecular biology techniques. AFM was a complementary tool to biochemical techniques to perform measurements on living cells at the nanometer resolution level. Taken together, our data suggest that GW501516 could be an interesting therapeutic strategy to avoid bladder cancer cell spreading through N-cadherin decrease.
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Affiliation(s)
- Céline Elie-Caille
- FEMTO-ST Institute, Univ. Bourgogne Franche-Comté, CNRS, ENSMM, UTBM, Besançon, France.
| | - Isabelle Lascombe
- Univ. Bourgogne Franche-Comté, EA3181, LabEx LipSTIC ANR-11-LABX-0021, 25030, Besançon, France
| | - Adeline Péchery
- Univ. Bourgogne Franche-Comté, EA3181, LabEx LipSTIC ANR-11-LABX-0021, 25030, Besançon, France
| | - Hugues Bittard
- Service Urologie et Andrologie, CHU Besançon, 25000, Besançon, France
| | - Sylvie Fauconnet
- Univ. Bourgogne Franche-Comté, EA3181, LabEx LipSTIC ANR-11-LABX-0021, 25030, Besançon, France.
- Service Urologie et Andrologie, CHU Besançon, 25000, Besançon, France.
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Garcia R. Nanomechanical mapping of soft materials with the atomic force microscope: methods, theory and applications. Chem Soc Rev 2020; 49:5850-5884. [PMID: 32662499 DOI: 10.1039/d0cs00318b] [Citation(s) in RCA: 161] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Fast, high-resolution, non-destructive and quantitative characterization methods are needed to develop materials with tailored properties at the nanoscale or to understand the relationship between mechanical properties and cell physiology. This review introduces the state-of-the-art force microscope-based methods to map at high-spatial resolution the elastic and viscoelastic properties of soft materials. The experimental methods are explained in terms of the theories that enable the transformation of observables into material properties. Several applications in materials science, molecular biology and mechanobiology illustrate the scope, impact and potential of nanomechanical mapping methods.
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Affiliation(s)
- Ricardo Garcia
- Instituto de Ciencia de Materiales de Madrid, CSIC, c/Sor Juana Inés de la Cruz 3, 28049 Madrid, Spain.
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29
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Li M, Xi N, Wang Y, Liu L. In Situ High-Resolution AFM Imaging and Force Probing of Cell Culture Medium-Forming Nanogranular Surfaces for Cell Growth. IEEE Trans Nanobioscience 2020; 19:385-393. [DOI: 10.1109/tnb.2020.2982164] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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30
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Imaging and Force Spectroscopy of Single Transmembrane Proteins with the Atomic Force Microscope. Methods Mol Biol 2020. [PMID: 31218616 DOI: 10.1007/978-1-4939-9512-7_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The atomic force microscope (AFM) has opened avenues and provided opportunities to investigate biological soft matter and processes ranging from nanometer (nm) to millimeter (mm). The high temporal (millisecond) and spatial (nanometer) resolutions of the AFM are suited for studying many biological processes in their native conditions. The AFM cantilever-aptly termed as a "lab on a tip"-can be used as an imaging tool as well as a handle to manipulate single bonds and proteins. Recent examples have convincingly established AFM as a tool to study the mechanical properties and monitor processes of single proteins and cells with high sensitivity, thus affording insight into important mechanistic details. This chapter specifically focuses on practical and analytical protocols of single-molecule AFM methodologies related to high-resolution imaging and single-molecule force spectroscopy of transmembrane proteins in a lipid bilayer (reconstituted or native). Both these techniques are operator oriented, and require specialized working knowledge of the instrument, theory and practical skills.
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Abstract
Yeast resistance to antifungal drugs is a major public health issue. Fungal adhesion onto the host mucosal surface is still a partially unknown phenomenon that is modulated by several actors among which fibronectin plays an important role. Targeting the yeast adhesion onto the mucosal surface could lead to potentially highly efficient treatments. In this work, we explored the effect of fibronectin on the nanomotion pattern of different Candida albicans strains by atomic force microscopy (AFM)-based nanomotion detection and correlated the cellular oscillations to the yeast adhesion onto epithelial cells. Preliminary results demonstrate that strongly adhering strains reduce their nanomotion activity upon fibronectin exposure whereas low adhering Candida remain unaffected. These results open novel avenues to explore cellular reactions upon exposure to stimulating agents and possibly to monitor in a rapid and simple manner adhesive properties of C. albicans.
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32
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Offroy M, Razafitianamaharavo A, Beaussart A, Pagnout C, Duval JFL. Fast automated processing of AFM PeakForce curves to evaluate spatially resolved Young modulus and stiffness of turgescent cells. RSC Adv 2020; 10:19258-19275. [PMID: 35515432 PMCID: PMC9054095 DOI: 10.1039/d0ra00669f] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 05/08/2020] [Indexed: 01/12/2023] Open
Abstract
Atomic Force Microscopy (AFM) is a powerful technique for the measurement of mechanical properties of individual cells in two (x × y) or three (x × y × time) dimensions. The instrumental progress makes it currently possible to generate a large amount of data in a relatively short time, which is particularly true for AFM operating in so-called PeakForce tapping mode (Bruker corporation). The latter corresponds to an AFM probe that periodically hits the sample surface while the pico-newton level interaction force is recorded from cantilever deflection. The method provides unprecedented high-resolution (a few tens of nm) imaging of the mechanical features of soft biological samples (e.g. bacteria, yeasts) and of hard abiotic surfaces (e.g. minerals). The rapid conversion of up to several tens of thousands spatially resolved force curves typically collected in AFM PeakForce tapping mode over a given cell surface area into comprehensive nanomechanical information requires the development of robust data analysis methodologies and dedicated numerical tools. In this work, we report an automated algorithm for (i) a rapid and unambiguous detection of the indentation regimes corresponding to non-linear and linear deformations of bacterial surfaces upon compression by the AFM probe, (ii) the subsequent evaluation of the Young modulus and cell surface stiffness, and (iii) the generation of spatial mappings of relevant nanomechanical properties at the single cell level. The procedure involves consistent evaluation of the contact point between the AFM probe and sample biosurface and that of the threshold indentation value marking the transition between non-linear and linear deformation regimes. For comparison purposes, the former regime is here analyzed on the basis of Hertz and Sneddon models corrected or not for effects of finite sample thickness. Analysis of AFM measurements performed on a selected Escherichia coli strain is detailed to demonstrate the feasibility, rapidity and robustness of the here-proposed PeakForce data treatment process. The flexibility of the algorithm allows consideration of force curve parameterizations other than that detailed here, which may be desired for investigation of e.g. eukaryotes nanomechanics. The performance of the adopted Hertz-based and Sneddon-based contact mechanics formalisms in recovering experimental data and in identifying nanomechanical heterogeneities at the bacterium scale is further thoroughly discussed. A numerical method is proposed for the modeling of AFM PeakForce curves and the automated extraction of relevant spatially-resolved nanomechanical properties of turgescent cells.![]()
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Affiliation(s)
- Marc Offroy
- Université de Lorraine
- CNRS
- LIEC
- F-54000 Nancy
- France
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33
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Mescola A, Dauvin M, Amoroso A, Duwez AS, Joris B. Single-molecule force spectroscopy to decipher the early signalling step in membrane-bound penicillin receptors embedded into a lipid bilayer. NANOSCALE 2019; 11:12275-12284. [PMID: 31211302 DOI: 10.1039/c9nr02466b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Understanding the molecular mechanism by which the signal of the presence of an antibiotic is transduced from outside to inside the bacterial cell is of fundamental interest for the β-lactam antibiotic resistance problem, but remains difficult to accomplish. No approach has ever addressed entire penicillin receptors in a membrane environment. Here we describe a method to investigate the purified Bacillus licheniformis BlaR1 receptor -a membrane-bound penicillin receptor involved in β-lactam resistance- embedded into a lipid bilayer in absence or presence of penicillin. By selecting a mutated receptor blocked in its signal transduction pathway just after its activation by penicillin, we revealed the very first step of receptor signalling by unfolding the receptor from its C-terminal end by AFM-based single-molecule force spectroscopy. We showed that the presence of the antibiotic entails significant conformational changes within the receptor. Our approach opens an avenue to study signal-transduction pathways mediated by membrane-bound proteins in a membrane environment.
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Affiliation(s)
- Andrea Mescola
- Molecular Systems, Department of Chemistry, University of Liège, 4000 Liège, Belgium.
| | - Marjorie Dauvin
- Bacterial physiology and genetics - Centre d'Ingénierie des Protéines-Integrative Biological Sciences, Department of Life Sciences, University of Liège, 4000 Liège, Belgium
| | - Ana Amoroso
- Bacterial physiology and genetics - Centre d'Ingénierie des Protéines-Integrative Biological Sciences, Department of Life Sciences, University of Liège, 4000 Liège, Belgium
| | - Anne-Sophie Duwez
- Molecular Systems, Department of Chemistry, University of Liège, 4000 Liège, Belgium.
| | - Bernard Joris
- Bacterial physiology and genetics - Centre d'Ingénierie des Protéines-Integrative Biological Sciences, Department of Life Sciences, University of Liège, 4000 Liège, Belgium
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34
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Li M, Xi N, Wang Y, Liu L. Composite Nanostructures and Adhesion Analysis of Natural Plant Hydrogels Investigated by Atomic Force Microscopy. IEEE Trans Nanobioscience 2019; 18:448-455. [DOI: 10.1109/tnb.2019.2911044] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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35
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Janel S, Popoff M, Barois N, Werkmeister E, Divoux S, Perez F, Lafont F. Stiffness tomography of eukaryotic intracellular compartments by atomic force microscopy. NANOSCALE 2019; 11:10320-10328. [PMID: 31106790 DOI: 10.1039/c8nr08955h] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Precise localization and biophysical characterization of cellular structures is a key to the understanding of biological processes happening both inside the cell and at the cell surface. Atomic force microscopy is a powerful tool to study the cell surface - topography, elasticity, viscosity, interactions - and also the viscoelastic behavior of the underlying cytoplasm, cytoskeleton or the nucleus. Here, we demonstrate the ability of atomic force microscopy to also map and characterize organelles and microorganisms inside cells, at the nanoscale, by combining stiffness tomography with super-resolution fluorescence and electron microscopy. By using this correlative approach, we could both identify and characterize intracellular compartments. The validation of this approach was performed by monitoring the stiffening effect according to the metabolic status of the mitochondria in living cells in real-time.
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Affiliation(s)
- Sébastien Janel
- Center for Infection and Immunity of Lille, CNRS UMR 8204, INSERM U1019, CHU Lille, Institut Pasteur de Lille, Univ Lille, F-59000 Lille, France.
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36
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López-Guerra EA, Shen H, Solares SD, Shuai D. Acquisition of time-frequency localized mechanical properties of biofilms and single cells with high spatial resolution. NANOSCALE 2019; 11:8918-8929. [PMID: 31017130 DOI: 10.1039/c8nr10287b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Biofilms are a cluster of bacteria embedded in extracellular polymeric substances (EPS) that contain a complex composition of polysaccharides, proteins, and extracellular DNA (eDNA). Desirable mechanical properties of the biofilms are critical for their survival, propagation, and dispersal, and the response of mechanical properties to different treatment conditions also sheds light on biofilm control and eradication in vivo and on engineering surfaces. However, it is challenging yet important to investigate mechanical behaviors of biofilms with a high spatial resolution because biofilms are very heterogeneous. Moreover, biofilms are viscoelastic, and their time-dependent mechanical behavior is difficult to capture. Herein, we develop a powerful technique that combines the high spatial resolution of an atomic force microscope (AFM) with a rigorous history-dependent viscoelastic analysis to deliver highly spatial-localized biofilm properties within a wide time-frequency window. By exploiting the use of static force spectroscopy in combination with an appropriate viscoelastic framework, we highlight the intensive amount of time-dependent information experimentally available that has been largely overlooked. It is shown that this technique provides a detailed nanorheological signature of the biofilms even at the single-cell level. We share the computational routines that would allow any user to perform the analysis from experimental raw data. The detailed localization of mechanical properties in space and in time-frequency domain provides insights into the understanding of biofilm stability, cohesiveness, dispersal, and control.
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Affiliation(s)
- Enrique A López-Guerra
- Department of Civil and Environmental Engineering, The George Washington University, Washington, DC 20052, USA.
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37
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Automated multi-sample acquisition and analysis using atomic force microscopy for biomedical applications. PLoS One 2019; 14:e0213853. [PMID: 30875396 PMCID: PMC6420161 DOI: 10.1371/journal.pone.0213853] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Accepted: 03/03/2019] [Indexed: 11/19/2022] Open
Abstract
In the last 20 years, atomic force microscopy (AFM) has emerged as a ubiquitous technique in biological research, allowing the analysis of biological samples under near-physiological conditions from single molecules to living cells. Despite its growing use, the low process throughput remains a major drawback. Here, we propose a solution validated on a device allowing a fully automated, multi-sample analysis. Our approach is mainly designed to study samples in fluid and biological cells. As a proof of concept, we demonstrate its feasibility applied to detect and scan both fixed and living bacteria before completion of data processing. The effect of two distinct treatments (i.e. gentamicin and heating) is then evidenced on physical parameters of fixed Yersinia pseudotuberculosis bacteria. The multi-sample analysis presented allows an increase in the number of scanned samples while limiting the user's input. Importantly, cantilever cleaning and control steps are performed regularly-as part of the automated process-to ensure consistent scanning quality. We discuss how such an approach is paving the way to AFM developments in medical and clinical fields, in which statistical significance of results is a prerequisite.
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38
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Zhang M, Guan Y, Xu J, Qin J, Li C, Ma X, Zhang Z, Zhang B, Tang J. Evaluating the protective mechanism of panax notoginseng saponins against oxidative stress damage by quantifying the biomechanical properties of single cell. Anal Chim Acta 2018; 1048:186-193. [PMID: 30598149 DOI: 10.1016/j.aca.2018.10.030] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 10/09/2018] [Accepted: 10/15/2018] [Indexed: 10/28/2022]
Abstract
Panax notoginseng saponins (PNS) have shown to be the biologically active constituents responsible for the therapeutic action of panax notoginseng. PNS could help to restrain the oxidative stress, however, whether biomechanical properties of the single cell involve in the protective effect exerted by PNS against oxidative stress injury remains unclear. In this work, we investigated the protective mechanism of PNS against oxidative stress based on the PeakForce Tapping technology firstly, focusing on the biomechanical properties of single human umbilical vascular endothelium cell (HUVEC). PNS display distinct inhibition on the reduction of the young's modulus of cells caused by oxidative stress damage. Combining with immunofluorescence assay, it indicates that improving the stability of cytoskeleton is a significant way for PNS to play a protective role in HUVEC cells during oxidative damage. This work provides a new idea for exploring the functional mechanism of traditional Chinese medicine at the single cell level, and reveals great potential of the atomic force microscope in studying the drug mechanism.
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Affiliation(s)
- Miaomiao Zhang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, PR China; University of Science and Technology of China, Hefei, 230026, PR China
| | - Yanxue Guan
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, PR China; University of Science and Technology of China, Hefei, 230026, PR China
| | - Jian Xu
- The Standardized Key Project Technology Laboratory of TCM of Jilin Province, Changchun, 130012, PR China
| | - Juan Qin
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, PR China; University of Science and Technology of China, Hefei, 230026, PR China
| | - Chen Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, PR China; University of Science and Technology of China, Hefei, 230026, PR China
| | - Xingxing Ma
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, PR China; University of Science and Technology of China, Hefei, 230026, PR China
| | - Zhe Zhang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, PR China
| | - Bailin Zhang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, PR China; University of Science and Technology of China, Hefei, 230026, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China.
| | - Jilin Tang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, PR China; University of Science and Technology of China, Hefei, 230026, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China.
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39
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Zhang P, Chen YP, Qiu JH, Dai YZ, Feng B. Imaging the Microprocesses in Biofilm Matrices. Trends Biotechnol 2018; 37:214-226. [PMID: 30075862 DOI: 10.1016/j.tibtech.2018.07.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 07/07/2018] [Accepted: 07/09/2018] [Indexed: 12/22/2022]
Abstract
Biofilms, which are aggregates of microorganisms and extracellular matrices, widely colonize natural water bodies, wastewater treatment systems, and body tissues, and have vital roles in water purification, biofouling, and infectious diseases. Recently, multiple imaging modalities have been developed to visualize the morphological structure and material distribution within biofilms and to probe the microprocesses in biofilm matrices, including biofilm formation, transfer and metabolism of substrates, and cell-cell communication. These technologies have improved our understanding of biofilm control and the fates of substrates in biofilms. In this review, we describe the principles of various imaging techniques and discuss the advantages and limitations of each approach to characterizing microprocesses in biofilm matrices.
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Affiliation(s)
- Peng Zhang
- College of Environment and Resources, Xiangtan University, Xiangtan, 411105, China; Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China
| | - You-Peng Chen
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environments of MOE, Chongqing University, Chongqing 400045, China.
| | - Ju-Hui Qiu
- College of Bioengineering, Chongqing University, Chongqing 400045, China
| | - You-Zhi Dai
- College of Environment and Resources, Xiangtan University, Xiangtan, 411105, China
| | - Bo Feng
- College of Environment and Resources, Xiangtan University, Xiangtan, 411105, China.
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40
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Yang# Y, Yu# J, Esfahani AM, Seiffert-Sinha K, Xi N, Lee I, Sinha AA, Chen L, Sun Z, Yang R, Dong L. Single-cell membrane drug delivery using porous pen nanodeposition. NANOSCALE 2018; 10:12704-12712. [PMID: 29946596 PMCID: PMC6528655 DOI: 10.1039/c8nr02600a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Delivering molecules onto the plasma membrane of single cells is still a challenging task in profiling cell signaling pathways with single cell resolution. We demonstrated that a large quantity of molecules could be targeted and released onto the membrane of individual cells to trigger signaling responses. This is achieved by a porous pen nanodeposition (PPN) method, in which a multilayer porous structure, serving as a reservoir for a large amount of molecules, is formed on an atomic force microscope (AFM) tip using layer-by-layer assembly and post processing. To demonstrate its capability for single cell membrane drug delivery, PPN was employed to induce a calcium flux triggered by the binding of released antibodies to membrane antigens in an autoimmune skin disease model. This calcium signal propagates from the target cell to its neighbors in a matter of seconds, proving the theory of intercellular communication through cell-cell junctions. Collectively, these results demonstrated the effectiveness of PPN in membrane drug delivery for single cells; to the best of our knowledge, this is the first technique that can perform the targeted transport and delivery in single cell resolution, paving the way for probing complex signaling interactions in multicellular settings.
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Affiliation(s)
- Yongliang Yang#
- Department of Electrical and Computer Engineering, Michigan State University, East Lansing, MI 48824, USA,
| | - Jing Yu#
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI 48824, USA
| | - Amir Monemian Esfahani
- Department of Mechanical and Materials Engineering, University of Nebraska -Lincoln, Lincoln, NE 68588, USA
| | | | - Ning Xi
- Department of Electrical and Computer Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Ilsoon Lee
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI 48824, USA
| | - Animesh A. Sinha
- Department of Dermatology, University at Buffalo, Buffalo, New York 14203, USA
| | - Liangliang Chen
- Department of Electrical and Computer Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Zhiyong Sun
- Department of Electrical and Computer Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Ruiguo Yang
- Department of Mechanical and Materials Engineering, University of Nebraska -Lincoln, Lincoln, NE 68588, USA,
| | - Lixin Dong
- Department of Electrical and Computer Engineering, Michigan State University, East Lansing, MI 48824, USA,
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41
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Patel AN, Kranz C. (Multi)functional Atomic Force Microscopy Imaging. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2018; 11:329-350. [PMID: 29490193 DOI: 10.1146/annurev-anchem-061417-125716] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Incorporating functionality to atomic force microscopy (AFM) to obtain physical and chemical information has always been a strong focus in AFM research. Modifying AFM probes with specific molecules permits accessibility of chemical information via specific reactions and interactions. Fundamental understanding of molecular processes at the solid/liquid interface with high spatial resolution is essential to many emerging research areas. Nanoscale electrochemical imaging has emerged as a complementary technique to advanced AFM techniques, providing information on electrochemical interfacial processes. While this review presents a brief introduction to advanced AFM imaging modes, such as multiparametric AFM and topography recognition imaging, the main focus herein is on electrochemical imaging via hybrid AFM-scanning electrochemical microscopy. Recent applications and the challenges associated with such nanoelectrochemical imaging strategies are presented.
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Affiliation(s)
- Anisha N Patel
- Institute of Analytical and Bioanalytical Chemistry, Ulm University, Ulm 89081, Germany;
| | - Christine Kranz
- Institute of Analytical and Bioanalytical Chemistry, Ulm University, Ulm 89081, Germany;
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Nautiyal P, Alam F, Balani K, Agarwal A. The Role of Nanomechanics in Healthcare. Adv Healthc Mater 2018; 7. [PMID: 29193838 DOI: 10.1002/adhm.201700793] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 09/18/2017] [Indexed: 12/21/2022]
Abstract
Nanomechanics has played a vital role in pushing our capability to detect, probe, and manipulate the biological species, such as proteins, cells, and tissues, paving way to a deeper knowledge and superior strategies for healthcare. Nanomechanical characterization techniques, such as atomic force microscopy, nanoindentation, nanotribology, optical tweezers, and other hybrid techniques have been utilized to understand the mechanics and kinetics of biospecies. Investigation of the mechanics of cells and tissues has provided critical information about mechanical characteristics of host body environments. This information has been utilized for developing biomimetic materials and structures for tissue engineering and artificial implants. This review summarizes nanomechanical characterization techniques and their potential applications in healthcare research. The principles and examples of label-free detection of cancers and myocardial infarction by nanomechanical cantilevers are discussed. The vital importance of nanomechanics in regenerative medicine is highlighted from the perspective of material selection and design for developing biocompatible scaffolds. This review interconnects the advancements made in fundamental materials science research and biomedical technology, and therefore provides scientific insight that is of common interest to the researchers working in different disciplines of healthcare science and technology.
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Affiliation(s)
- Pranjal Nautiyal
- Nanomechanics and Nanotribology Laboratory Florida International University 10555 West Flagler Street Miami FL 33174 USA
| | - Fahad Alam
- Biomaterials Processing and Characterization Laboratory Department of Materials Science and Engineering Indian Institute of Technology Kanpur Kanpur 208016 India
| | - Kantesh Balani
- Biomaterials Processing and Characterization Laboratory Department of Materials Science and Engineering Indian Institute of Technology Kanpur Kanpur 208016 India
| | - Arvind Agarwal
- Nanomechanics and Nanotribology Laboratory Florida International University 10555 West Flagler Street Miami FL 33174 USA
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Ozkan AD, Topal AE, Dikecoglu FB, Guler MO, Dana A, Tekinay AB. Probe microscopy methods and applications in imaging of biological materials. Semin Cell Dev Biol 2018; 73:153-164. [DOI: 10.1016/j.semcdb.2017.08.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 08/04/2017] [Accepted: 08/04/2017] [Indexed: 01/21/2023]
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Li M, Dang D, Xi N, Wang Y, Liu L. Nanoscale imaging and force probing of biomolecular systems using atomic force microscopy: from single molecules to living cells. NANOSCALE 2017; 9:17643-17666. [PMID: 29135007 DOI: 10.1039/c7nr07023c] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Due to the lack of adequate tools for observation, native molecular behaviors at the nanoscale have been poorly understood. The advent of atomic force microscopy (AFM) provides an exciting instrument for investigating physiological processes on individual living cells with molecular resolution, which attracts the attention of worldwide researchers. In the past few decades, AFM has been widely utilized to investigate molecular activities on diverse biological interfaces, and the performances and functions of AFM have also been continuously improved, greatly improving our understanding of the behaviors of single molecules in action and demonstrating the important role of AFM in addressing biological issues with unprecedented spatiotemporal resolution. In this article, we review the related techniques and recent progress about applying AFM to characterize biomolecular systems in situ from single molecules to living cells. The challenges and future directions are also discussed.
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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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Murugesapillai D, Bouaziz S, Maher LJ, Israeloff NE, Cameron CE, Williams MC. Accurate nanoscale flexibility measurement of DNA and DNA-protein complexes by atomic force microscopy in liquid. NANOSCALE 2017; 9:11327-11337. [PMID: 28762410 PMCID: PMC5597049 DOI: 10.1039/c7nr04231k] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The elasticity of double-stranded DNA (dsDNA), as described by its persistence length, is critical for many biological processes, including genomic regulation. A persistence length value can be obtained using atomic force microscopy (AFM) imaging. However, most AFM studies have been done by depositing the sample on a surface using adhesive ligands and fitting the contour to a two-dimensional (2D) wormlike chain (WLC) model. This often results in a persistence length measurement that is different from the value determined using bulk and single molecule methods. We describe a method for obtaining accurate three-dimensional (3D) persistence length measurements for DNA and DNA-protein complexes by using a previously developed liquid AFM imaging method and then applying the 3D WLC model. To demonstrate the method, we image in both air and liquid several different dsDNA constructs and DNA-protein complexes that both increase (HIV-1 Vpr) and decrease (yeast HMO1) dsDNA persistence length. Fitting the liquid AFM-imaging contour to the 3D WLC model results in a value in agreement with measurements obtained in optical tweezers experiments. Because AFM also allows characterization of local DNA properties, the ability to correctly measure global flexibility will strongly increase the impact of measurements that use AFM imaging.
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Affiliation(s)
| | - Serge Bouaziz
- Laboratoire de Cristallographie et RMN Biologiques, UMR CNRS 8015, Université Paris Descartes, Sorbonne Paris Cité, Faculté de Pharmacie, 75006 Paris, France
| | - L James Maher
- Mayo Clinic College of Medicine and Science, Department of Biochemistry and Molecular Biology, Rochester, MN 55905, USA
| | | | - Craig E Cameron
- The Pennsylvania State University, Department of Biochemistry and Molecular Biology, University Park, PA 16802, USA
| | - Mark C Williams
- Department of Physics, Northeastern University, Boston, MA, USA.
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Beckwitt EC, Kong M, Van Houten B. Studying protein-DNA interactions using atomic force microscopy. Semin Cell Dev Biol 2017; 73:220-230. [PMID: 28673677 DOI: 10.1016/j.semcdb.2017.06.028] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 06/27/2017] [Accepted: 06/29/2017] [Indexed: 12/12/2022]
Abstract
Atomic force microscopy (AFM) has made significant contributions to the study of protein-DNA interactions by making it possible to topographically image biological samples. A single protein-DNA binding reaction imaged by AFM can reveal protein binding specificity and affinity, protein-induced DNA bending, and protein binding stoichiometry. Changes in DNA structure, complex conformation, and cooperativity, can also be analyzed. In this review we highlight some important examples in the literature and discuss the advantages and limitations of these measurements. We also discuss important advances in technology that will facilitate the progress of AFM in the future.
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Affiliation(s)
- Emily C Beckwitt
- Program in Molecular Biophysics and Structural Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA; The University of Pittsburgh Cancer Institute, Hillman Cancer Center, Pittsburgh, PA 15213, USA
| | - Muwen Kong
- Program in Molecular Biophysics and Structural Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA; The University of Pittsburgh Cancer Institute, Hillman Cancer Center, Pittsburgh, PA 15213, USA
| | - Bennett Van Houten
- Program in Molecular Biophysics and Structural Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA; The University of Pittsburgh Cancer Institute, Hillman Cancer Center, Pittsburgh, PA 15213, USA; Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA.
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Handschuh-Wang S, Wang T, Zhou X. Recent advances in hybrid measurement methods based on atomic force microscopy and surface sensitive measurement techniques. RSC Adv 2017. [DOI: 10.1039/c7ra08515j] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
This review summaries the recent progress of the combination of optical and non-optical surface sensitive techniques with the atomic force microscopy.
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Affiliation(s)
- Stephan Handschuh-Wang
- College of Chemistry and Environmental Engineering
- Shenzhen University
- Shenzhen 518060
- P. R. China
| | - Tao Wang
- Functional Thin Films Research Center
- Shenzhen Institutes of Advanced Technology
- Chinese Academy of Sciences
- Shenzhen 518055
- P. R. China
| | - Xuechang Zhou
- College of Chemistry and Environmental Engineering
- Shenzhen University
- Shenzhen 518060
- P. R. China
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