51
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Yu M, Zhang K, Guo X, Qian L. Effects of the Degree of Deacetylation on the Single-Molecule Mechanics of Chitosans. J Phys Chem B 2023; 127:4261-4267. [PMID: 37141100 DOI: 10.1021/acs.jpcb.3c01661] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Chitosan is one of the most prevalent biomass materials, and its physicochemical and biological characteristics, such as solubility, crystallinity, flocculation ability, biodegradability, and amino-related chemical processes, are directly connected to the degree of deacetylation (DD). However, the specifics about the effects of the DD on the characteristics of chitosan are still unclear up to now. In this work, atomic force microscopy-based single-molecule force spectroscopy was used to study the role of the DD in the single-molecule mechanics of chitosan. Even though the DD varies largely (17% ≤ DD ≤ 95%), the experimental results demonstrate that the chitosans exhibit the same natural (in nonane) and backbone (in dimethyl sulfoxide (DMSO)) single-chain elasticity. This suggests that chitosans have the same intra-chain hydrogen bond (H-bond) state in nonane and to which these H-bonds can be eliminated in DMSO. However, when the experiments are carried out in ethylene glycol (EG) and water, the single-chain mechanics are increased with the increases of the DD. The energy consumed to stretch chitosans in water is larger than that in EG, indicating that amino can form a strong interaction with water and induce the formation of the binding water around the sugar rings. The strong interaction between water and amino may be the key factor for the well solubility and chemical activity of chitosan. The results of this work are anticipated to provide fresh light on the significant role played by the DD and water in the structures and functions of chitosan at the single molecular level.
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Affiliation(s)
- Miao Yu
- School of Mechanical Engineering, Sichuan University, Chengdu 610065, China
- Yibin Industrial Technology Research Institute of Sichuan University, Yibin 644000, China
| | - Kai Zhang
- School of Mechanical Engineering, Sichuan University, Chengdu 610065, China
- Yibin Industrial Technology Research Institute of Sichuan University, Yibin 644000, China
| | - Xin Guo
- School of Mechanical Engineering, Sichuan University, Chengdu 610065, China
- Yibin Industrial Technology Research Institute of Sichuan University, Yibin 644000, China
| | - Lu Qian
- School of Materials Science and Engineering, South China University of Technology, Guangzhou 510641, China
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52
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Shan M, Wang H, Li S, Zhang X, Yang G, Shan Y. Distinguishing the Cellular Transport of Folic Acid Conjugated Nano-Drugs among Different Cell Lines by Using Force Tracing Technique. Mol Pharm 2023. [PMID: 37083400 DOI: 10.1021/acs.molpharmaceut.2c01035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
Folic acid (FA) is a ligand that has been renowned for its strong binding to FA receptor (FR), and the robustness of the specific interaction has led to the generation of multitudinous tumor-targeted nano-drug delivery systems. However, selecting the appropriate FA targeted nano-drugs according to types of cancerous cells to achieve a high effect is critical. Understanding of how the drug is transported through the cell membrane and is delivered intracellularly is very important in screening ideal targeted nano-drugs for cancerous changes in different organs. Herein, by using a force tracing technique based on atomic force microscopy (AFM), the dynamic process of FA-polyamidoamine-Doxorubicin (FA-PAMAM-DOX) entry into different tumor cells (HeLa and A549) and normal cells (Vero) was monitored in real time. The cell membrane transport efficacy of FA-PAMAM-DOX in tumor cells with an FR high overexpression level (HeLa) and FR low overexpression level (A549) is analyzed, which is significantly higher than that in normal cells (Vero), especially for HeLa cells. Subsequently, the intracellular delivery efficiency of FA-PAMAM-DOX in different cell lines was measured by using fluorescence imaging and AFM-based nanoindentation techniques. This report will help to discover the cellular transport mechanism of nano-drugs and screen out optimal therapeutic nano-drugs for different types of tumors.
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Affiliation(s)
- Meirong Shan
- School of Chemistry and Life Science, Advanced Institute of Materials Science, Changchun University of Technology, Changchun 130012, China
| | - Hui Wang
- School of Chemistry and Life Science, Advanced Institute of Materials Science, Changchun University of Technology, Changchun 130012, China
| | - Siying Li
- School of Chemistry and Life Science, Advanced Institute of Materials Science, Changchun University of Technology, Changchun 130012, China
| | - Xiaowan Zhang
- School of Chemistry and Life Science, Advanced Institute of Materials Science, Changchun University of Technology, Changchun 130012, China
| | - Guocheng Yang
- School of Chemistry and Life Science, Advanced Institute of Materials Science, Changchun University of Technology, Changchun 130012, China
| | - Yuping Shan
- School of Chemistry and Life Science, Advanced Institute of Materials Science, Changchun University of Technology, Changchun 130012, China
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53
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Lostao A, Lim K, Pallarés MC, Ptak A, Marcuello C. Recent advances in sensing the inter-biomolecular interactions at the nanoscale - A comprehensive review of AFM-based force spectroscopy. Int J Biol Macromol 2023; 238:124089. [PMID: 36948336 DOI: 10.1016/j.ijbiomac.2023.124089] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/13/2023] [Accepted: 03/15/2023] [Indexed: 03/24/2023]
Abstract
Biomolecular interactions underpin most processes inside the cell. Hence, a precise and quantitative understanding of molecular association and dissociation events is crucial, not only from a fundamental perspective, but also for the rational design of biomolecular platforms for state-of-the-art biomedical and industrial applications. In this context, atomic force microscopy (AFM) appears as an invaluable experimental technique, allowing the measurement of the mechanical strength of biomolecular complexes to provide a quantitative characterization of their interaction properties from a single molecule perspective. In the present review, the most recent methodological advances in this field are presented with special focus on bioconjugation, immobilization and AFM tip functionalization, dynamic force spectroscopy measurements, molecular recognition imaging and theoretical modeling. We expect this work to significantly aid in grasping the principles of AFM-based force spectroscopy (AFM-FS) technique and provide the necessary tools to acquaint the type of data that can be achieved from this type of experiments. Furthermore, a critical assessment is done with other nanotechnology techniques to better visualize the future prospects of AFM-FS.
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Affiliation(s)
- Anabel Lostao
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, Zaragoza 50009, Spain; Laboratorio de Microscopias Avanzadas (LMA), Universidad de Zaragoza, Zaragoza 50018, Spain; Fundación ARAID, Aragón, Spain.
| | - KeeSiang Lim
- WPI-Nano Life Science Institute, Kanazawa University, Ishikawa 920-1192, Japan
| | - María Carmen Pallarés
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, Zaragoza 50009, Spain; Laboratorio de Microscopias Avanzadas (LMA), Universidad de Zaragoza, Zaragoza 50018, Spain
| | - Arkadiusz Ptak
- Institute of Physics, Faculty of Materials Engineering and Technical Physics, Poznan University of Technology, Poznan 60-925, Poland
| | - Carlos Marcuello
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, Zaragoza 50009, Spain; Laboratorio de Microscopias Avanzadas (LMA), Universidad de Zaragoza, Zaragoza 50018, Spain.
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54
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Marcuello C, Chabbert B, Berzin F, Bercu NB, Molinari M, Aguié-Béghin V. Influence of Surface Chemistry of Fiber and Lignocellulosic Materials on Adhesion Properties with Polybutylene Succinate at Nanoscale. MATERIALS (BASEL, SWITZERLAND) 2023; 16:ma16062440. [PMID: 36984320 PMCID: PMC10056059 DOI: 10.3390/ma16062440] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/13/2023] [Accepted: 03/14/2023] [Indexed: 06/01/2023]
Abstract
The production of bio-based composites with enhanced characteristics constitutes a strategic action to minimize the use of fossil fuel resources. The mechanical performances of these materials are related to the specific properties of their components, as well as to the quality of the interface between the matrix and the fibers. In a previous research study, it was shown that the polarity of the matrix played a key role in the mechanisms of fiber breakage during processing, as well as on the final properties of the composite. However, some key questions remained unanswered, and new investigations were necessary to improve the knowledge of the interactions between a lignocellulosic material and a polar matrix. In this work, for the first time, atomic force microscopy based on force spectroscopy measurements was carried out using functionalized tips to characterize the intermolecular interactions at the single molecule level, taking place between poly(butylene succinate) and four different plant fibers. The efficiency of the tip functionalization was checked out by scanning electron microscopy and energy-dispersive X-ray spectroscopy, whereas the fibers chemistry was characterized by Fourier-transform infrared spectroscopy. Larger interactions at the nanoscale level were found between the matrix and hypolignified fibers compared to lignified ones, as in control experiments on single lignocellulosic polymer films. These results could significantly aid in the design of the most appropriate composite composition depending on its final use.
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Affiliation(s)
- Carlos Marcuello
- Université de Reims Champagne Ardenne, INRAE, FARE, 51097 Reims, France
| | - Brigitte Chabbert
- Université de Reims Champagne Ardenne, INRAE, FARE, 51097 Reims, France
| | - Françoise Berzin
- Université de Reims Champagne Ardenne, INRAE, FARE, 51097 Reims, France
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55
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Magazzù A, Marcuello C. Investigation of Soft Matter Nanomechanics by Atomic Force Microscopy and Optical Tweezers: A Comprehensive Review. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:963. [PMID: 36985857 PMCID: PMC10053849 DOI: 10.3390/nano13060963] [Citation(s) in RCA: 59] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 02/28/2023] [Accepted: 03/02/2023] [Indexed: 05/17/2023]
Abstract
Soft matter exhibits a multitude of intrinsic physico-chemical attributes. Their mechanical properties are crucial characteristics to define their performance. In this context, the rigidity of these systems under exerted load forces is covered by the field of biomechanics. Moreover, cellular transduction processes which are involved in health and disease conditions are significantly affected by exogenous biomechanical actions. In this framework, atomic force microscopy (AFM) and optical tweezers (OT) can play an important role to determine the biomechanical parameters of the investigated systems at the single-molecule level. This review aims to fully comprehend the interplay between mechanical forces and soft matter systems. In particular, we outline the capabilities of AFM and OT compared to other classical bulk techniques to determine nanomechanical parameters such as Young's modulus. We also provide some recent examples of nanomechanical measurements performed using AFM and OT in hydrogels, biopolymers and cellular systems, among others. We expect the present manuscript will aid potential readers and stakeholders to fully understand the potential applications of AFM and OT to soft matter systems.
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Affiliation(s)
- Alessandro Magazzù
- CNR-IPCF, Istituto per i Processi Chimico-Fisici, 98158 Mesina, Italy
- NLHT-Lab, Department of Physics, University of Calabria, 87036 Rende, Italy
| | - Carlos Marcuello
- Instituto de Nanociencia y Materiales de Aragón (INMA), CSIC-Universidad de Zaragoza, 50009 Zaragoza, Spain
- Laboratorio de Microscopias Avanzadas (LMA), Universidad de Zaragoza, 50018 Zaragoza, Spain
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56
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Yu L, Zhang M, Chen H, Xiao B, Chang S. Measurements of single-molecule electromechanical properties based on atomic force microscopy fixed-junction technique. NANOSCALE 2023; 15:4277-4281. [PMID: 36751974 DOI: 10.1039/d2nr06074d] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
A hybrid technique combining atomic force microscopy and the fixed-junction technique is developed to simultaneously probe the electrical and mechanical characteristics of a single-molecule junction.
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Affiliation(s)
- Lei Yu
- The State Key Laboratory of Refractories and Metallurgy, Wuhan University of Science and Technology, Wuhan, Hubei 430081, China.
- The Institute of Advanced Materials and Nanotechnology, Wuhan University of Science and Technology, Wuhan, Hubei 430081, China
| | - Mingyang Zhang
- The State Key Laboratory of Refractories and Metallurgy, Wuhan University of Science and Technology, Wuhan, Hubei 430081, China.
- The Institute of Advanced Materials and Nanotechnology, Wuhan University of Science and Technology, Wuhan, Hubei 430081, China
| | - Haijian Chen
- The State Key Laboratory of Refractories and Metallurgy, Wuhan University of Science and Technology, Wuhan, Hubei 430081, China.
- The Institute of Advanced Materials and Nanotechnology, Wuhan University of Science and Technology, Wuhan, Hubei 430081, China
| | - Bohuai Xiao
- The State Key Laboratory of Refractories and Metallurgy, Wuhan University of Science and Technology, Wuhan, Hubei 430081, China.
- The Institute of Advanced Materials and Nanotechnology, Wuhan University of Science and Technology, Wuhan, Hubei 430081, China
| | - Shuai Chang
- The State Key Laboratory of Refractories and Metallurgy, Wuhan University of Science and Technology, Wuhan, Hubei 430081, China.
- The Institute of Advanced Materials and Nanotechnology, Wuhan University of Science and Technology, Wuhan, Hubei 430081, China
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57
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Ma L, Li X, Petersen RB, Peng A, Huang K. Probing the interactions between amyloidogenic proteins and bio-membranes. Biophys Chem 2023; 296:106984. [PMID: 36889133 DOI: 10.1016/j.bpc.2023.106984] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/11/2023] [Accepted: 02/22/2023] [Indexed: 03/01/2023]
Abstract
Protein misfolding diseases (PMDs) in humans are characterized by the deposition of protein aggregates in tissues, including Alzheimer's disease, Parkinson's disease, type 2 diabetes, and amyotrophic lateral sclerosis. Misfolding and aggregation of amyloidogenic proteins play a central role in the onset and progression of PMDs, and these processes are regulated by multiple factors, especially the interaction between proteins and bio-membranes. Bio-membranes induce conformational changes in amyloidogenic proteins and affect their aggregation; on the other hand, the aggregates of amyloidogenic proteins may cause membrane damage or dysfunction leading to cytotoxicity. In this review, we summarize the factors that affect the binding of amyloidogenic proteins and membranes, the effects of bio-membranes on the aggregation of amyloidogenic proteins, mechanisms of membrane disruption by amyloidogenic aggregates, technical approaches for detecting these interactions, and finally therapeutic strategies targeting membrane damage caused by amyloidogenic proteins.
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Affiliation(s)
- Liang Ma
- Department of Pharmacy, Wuhan Mental Health Center, Wuhan, China; Department of Pharmacy, Wuhan Hospital for Psychotherapy, Wuhan, China
| | - Xi Li
- Tongji School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Robert B Petersen
- Foundational Sciences, Central Michigan University College of Medicine, Mount Pleasant, MI, USA
| | - Anlin Peng
- Department of Pharmacy, The Third Hospital of Wuhan, Tongren Hospital of Wuhan University, Wuhan, China.
| | - Kun Huang
- Tongji School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
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58
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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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59
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Kolbeck P, Dass M, Martynenko IV, van Dijk-Moes RJA, Brouwer KJH, van Blaaderen A, Vanderlinden W, Liedl T, Lipfert J. DNA Origami Fiducial for Accurate 3D Atomic Force Microscopy Imaging. NANO LETTERS 2023; 23:1236-1243. [PMID: 36745573 PMCID: PMC9951250 DOI: 10.1021/acs.nanolett.2c04299] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/25/2022] [Indexed: 06/01/2023]
Abstract
Atomic force microscopy (AFM) is a powerful technique for imaging molecules, macromolecular complexes, and nanoparticles with nanometer resolution. However, AFM images are distorted by the shape of the tip used. These distortions can be corrected if the tip shape can be determined by scanning a sample with features sharper than the tip and higher than the object of interest. Here we present a 3D DNA origami structure as fiducial for tip reconstruction and image correction. Our fiducial is stable under a broad range of conditions and has sharp steps at different heights that enable reliable tip reconstruction from as few as ten fiducials. The DNA origami is readily codeposited with biological and nonbiological samples, achieves higher precision for the tip apex than polycrystalline samples, and dramatically improves the accuracy of the lateral dimensions determined from the images. Our fiducial thus enables accurate and precise AFM imaging for a broad range of applications.
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Affiliation(s)
- Pauline
J. Kolbeck
- Department
of Physics and Center for NanoScience, LMU
Munich, Amalienstrasse 54, 80799Munich, Germany
- Department
of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CCUtrecht, The Netherlands
| | - Mihir Dass
- Department
of Physics and Center for NanoScience, LMU
Munich, Amalienstrasse 54, 80799Munich, Germany
| | - Irina V. Martynenko
- Department
of Physics and Center for NanoScience, LMU
Munich, Amalienstrasse 54, 80799Munich, Germany
| | - Relinde J. A. van Dijk-Moes
- Department
of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CCUtrecht, The Netherlands
| | - Kelly J. H. Brouwer
- Department
of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CCUtrecht, The Netherlands
| | - Alfons van Blaaderen
- Department
of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CCUtrecht, The Netherlands
| | - Willem Vanderlinden
- Department
of Physics and Center for NanoScience, LMU
Munich, Amalienstrasse 54, 80799Munich, Germany
- Department
of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CCUtrecht, The Netherlands
| | - Tim Liedl
- Department
of Physics and Center for NanoScience, LMU
Munich, Amalienstrasse 54, 80799Munich, Germany
| | - Jan Lipfert
- Department
of Physics and Center for NanoScience, LMU
Munich, Amalienstrasse 54, 80799Munich, Germany
- Department
of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CCUtrecht, The Netherlands
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60
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Ogorodnik E, Karsai A, Liu YX, Di Lucente J, Huang Y, Keel T, Haudenschild DR, Jin LW, Liu GY. Mechanical Cues for Triggering and Regulating Cellular Movement Selectively at the Single-Cell Level. J Phys Chem B 2023; 127:866-873. [PMID: 36652348 DOI: 10.1021/acs.jpcb.2c06461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Cell motility plays important roles in many biophysical and physiological processes ranging from in vitro biomechanics, wound healing, to cancer metastasis. This work introduces a new means to trigger and regulate motility individually using transient mechanical stimulus applied to designated cells. Using BV2 microglial cells, our investigations indicate that motility can be reproducibly and reliably initiated using mechanical compression of the cells. The location and magnitude of the applied force impact the movement of the cell. Based on observations from this investigation and current knowledge of BV2 cellular motility, new physical insights are revealed into the underlying mechanism of force-induced single cellular movement. The process involves high degrees of myosin activation to repair actin cortex breakages induced by the initial mechanical compression, which leads to focal adhesion degradation, lamellipodium detachment, and finally, cell polarization and movement. Modern technology enables accurate control over force magnitude and location of force delivery, thus bringing us closer to programming cellular movement at the single-cell level. This approach is of generic importance to other cell types beyond BV2 cells and has the intrinsic advantages of being transient, non-toxic, and non-destructive, thus exhibiting high translational potentials including mechano-based therapy.
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Affiliation(s)
- Evgeny Ogorodnik
- Biophysics Graduate Group, University of California, Davis, California 95616, United States
| | - Arpad Karsai
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - Ying X Liu
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - Jacopo Di Lucente
- M.I.N.D. Institute, Department of Pathology and Laboratory Medicine, University of California Davis Medical Center, Sacramento, California 95817, United States
| | - Yuqi Huang
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - Terell Keel
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - Dominik R Haudenschild
- Department of Orthopedic Surgery, University of California Davis School of Medicine, Sacramento, California 95817, United States
| | - Lee-Way Jin
- M.I.N.D. Institute, Department of Pathology and Laboratory Medicine, University of California Davis Medical Center, Sacramento, California 95817, United States
| | - Gang-Yu Liu
- Biophysics Graduate Group, University of California, Davis, California 95616, United States.,Department of Chemistry, University of California, Davis, California 95616, United States
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61
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Yang K, Wang L, Zhang D, Yan Y, Ji XJ, Cao M, Shi ZZ, Wang LN. Nanomechanical probing of bacterial adhesion to biodegradable Zn alloys. BIOMATERIALS ADVANCES 2023; 145:213243. [PMID: 36566645 DOI: 10.1016/j.bioadv.2022.213243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 11/13/2022] [Accepted: 12/09/2022] [Indexed: 12/15/2022]
Abstract
Bacterial infections on implants cause an inflammatory response and even implant failure. Bacterial adhesion is an initial and critical step during implant infection. The prevention of bacterial adhesion to implant materials has attracted much attention, especially for biodegradable metals. A deep understanding of the mechanisms of bacterial adhesion to biodegradable metals is urgently needed. In this work, a bacterial probe based on atomic force spectroscopy was employed to determine the bacterial adhesion to Zn alloy, which depended on surface charge, roughness, and wettability. Negative surface charges of Zn, Zn-0.5Li, and 316L generated electrostatic repulsion force towards bacteria. The surface roughness of Zn-0.5Li was significantly increased by localized corrosion. Bacterial adhesion forces on Zn, Zn-0.5Li, and 316L were 325.2 pN, 519.1 pN, and 727.7 pN, respectively. The density of attached bacteria (early-stage bacterial adhesion) on these samples exhibited a positive correlation with the bacterial adhesion force. The bacterial adhesion force and adhesion work provide a quantitative determination of the interactions between bacteria and biodegradable alloys. These results provide a deeper understanding of early bacterial adhesion on Zn alloys, which can further guide the antibacterial surface design of biodegradable materials for clinical application.
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Affiliation(s)
- Kun Yang
- Beijing Advanced Innovation Center for Materials Genome Engineering, School of Materials Science and Engineering, University of Science and Technology Beijing, Beijing 100083, PR China
| | - Lei Wang
- Beijing Advanced Innovation Center for Materials Genome Engineering, School of Materials Science and Engineering, University of Science and Technology Beijing, Beijing 100083, PR China.
| | - Dawei Zhang
- Beijing Advanced Innovation Center for Materials Genome Engineering, School of Materials Science and Engineering, University of Science and Technology Beijing, Beijing 100083, PR China; Institute for Advanced Materials and Technology, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, PR China
| | - Yu Yan
- Beijing Advanced Innovation Center for Materials Genome Engineering, School of Materials Science and Engineering, University of Science and Technology Beijing, Beijing 100083, PR China; Institute for Advanced Materials and Technology, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, PR China
| | - Xiao-Jing Ji
- Beijing Advanced Innovation Center for Materials Genome Engineering, School of Materials Science and Engineering, University of Science and Technology Beijing, Beijing 100083, PR China
| | - Meng Cao
- Beijing Advanced Innovation Center for Materials Genome Engineering, School of Materials Science and Engineering, University of Science and Technology Beijing, Beijing 100083, PR China
| | - Zhang-Zhi Shi
- Beijing Advanced Innovation Center for Materials Genome Engineering, School of Materials Science and Engineering, University of Science and Technology Beijing, Beijing 100083, PR China
| | - Lu-Ning Wang
- Beijing Advanced Innovation Center for Materials Genome Engineering, School of Materials Science and Engineering, University of Science and Technology Beijing, Beijing 100083, PR China.
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62
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Sun H, Wang J. Novel perspective for protein-drug interaction analysis: atomic force microscope. Analyst 2023; 148:454-474. [PMID: 36398684 DOI: 10.1039/d2an01591a] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Proteins are major drug targets, and drug-target interaction identification and analysis are important factors for drug discovery. Atomic force microscopy (AFM) is a powerful tool making it possible to image proteins with nanometric resolution and probe intermolecular forces under physiological conditions. We review recent studies conducted in the field of target protein drug discovery using AFM-based analysis technology, including drug-driven changes in nanomechanical properties of protein morphology and interactions. Underlying mechanisms (including thermodynamic and kinetic parameters) of the drug-target interaction and drug-modulating protein-protein interaction (PPI) on the surfaces of models or living cells are discussed. Furthermore, challenges and the outlook for the field are likewise discussed. Overall, this insight into the mechanical properties of protein-drug interactions provides an unprecedented information framework for rational drug discovery in the pharmaceutical field.
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Affiliation(s)
- Heng Sun
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, China.
| | - Jianhua Wang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, China.
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Li H. Single Molecule Force Spectroscopy Studies on Metalloproteins: Opportunities and Challenges. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:1345-1353. [PMID: 36647634 DOI: 10.1021/acs.langmuir.2c03332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Metalloproteins play important roles in a wide range of biological processes. Elucidating the mechanisms via which metalloproteins fold and constitute their metal centers is critical to the understanding of the functions and dynamics of metalloproteins. Owing to its superior force and length resolution, single-molecule force spectroscopy (SMFS) has evolved into a powerful tool to probe the unfolding and folding mechanisms of metalloproteins at the single level by forcing metalloproteins to unfold and then refold along a reaction coordinate defined by the applied stretching force. The folding of metalloproteins is complex and involves two interwound processes, the folding of the polypeptide chain and the constitution of the metal center. Experimental studies of the folding of metalloproteins are challenging. SMFS studies have allowed researchers to directly probe the folding and unfolding of metalloproteins at the single-molecule level and the effect of metal centers on the folding-unfolding energy landscape of metalloproteins. New mechanistic insights on the folding and unfolding of some metalloproteins have been obtained, demonstrating the power and unique advantages that SMFS techniques may offer. In this Perspective, using calcium-binding proteins and small iron-sulfur proteins as examples, I provide a concise overview of the information and insights that SMFS studies have provided to understand the folding and unfolding of metalloproteins. I also discuss the opportunities and challenges that are present in this fast-progressing area of research.
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Affiliation(s)
- Hongbin Li
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
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64
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Incaviglia I, Herzog S, Fläschner G, Strohmeyer N, Tosoratti E, Müller DJ. Tailoring the Sensitivity of Microcantilevers To Monitor the Mass of Single Adherent Living Cells. NANO LETTERS 2023; 23:588-596. [PMID: 36607826 PMCID: PMC9881155 DOI: 10.1021/acs.nanolett.2c04198] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/19/2022] [Indexed: 06/17/2023]
Abstract
Microcantilevers are widely employed as mass sensors for biological samples, from single molecules to single cells. However, the accurate mass quantification of living adherent cells is impaired by the microcantilever's mass sensitivity and cell migration, both of which can lead to detect masses mismatching by ≫50%. Here, we design photothermally actuated microcantilevers to optimize the accuracy of cell mass measurements. By reducing the inertial mass of the microcantilever using a focused ion beam, we considerably increase its mass sensitivity, which is validated by finite element analysis and experimentally by gelatin microbeads. The improved microcantilevers allow us to instantly monitor at much improved accuracy the mass of both living HeLa cells and mouse fibroblasts adhering to different substrates. Finally, we show that the improved cantilever design favorably restricts cell migration and thus reduces the large measurement errors associated with this effect.
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Affiliation(s)
- Ilaria Incaviglia
- Department
of Biosystems Science and Engineering, Swiss
Federal Institute of Technology Zurich (ETH), Basel4058, Switzerland
| | - Sophie Herzog
- Department
of Biosystems Science and Engineering, Swiss
Federal Institute of Technology Zurich (ETH), Basel4058, Switzerland
| | - Gotthold Fläschner
- Department
of Biosystems Science and Engineering, Swiss
Federal Institute of Technology Zurich (ETH), Basel4058, Switzerland
- Nanosurf
AG, Liestal4410, Switzerland
| | - Nico Strohmeyer
- Department
of Biosystems Science and Engineering, Swiss
Federal Institute of Technology Zurich (ETH), Basel4058, Switzerland
| | - Enrico Tosoratti
- Department
of Mechanical and Process Engineering, Swiss
Federal Institute of Technology Zurich (ETH), Zürich8092, Switzerland
| | - Daniel J. Müller
- Department
of Biosystems Science and Engineering, Swiss
Federal Institute of Technology Zurich (ETH), Basel4058, Switzerland
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65
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Qian L, Zhang K, Guo X, Yu M. What happens when chitin becomes chitosan? A single-molecule study. RSC Adv 2023; 13:2294-2300. [PMID: 36741137 PMCID: PMC9841443 DOI: 10.1039/d2ra07303j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 01/09/2023] [Indexed: 01/19/2023] Open
Abstract
Chitin and chitosan are important support structures for many organisms and are important renewable macromolecular biomass resources. Structurally, with the removal of acetyl group, the solubility of chitosan is improved. However, the specific mechanism of solubility enhancement from chitin to chitosan is still unclear. In this study, the atomic force microscopy (AFM)-based single molecule force spectroscopy (SMFS) was used to obtain the single-chain mechanical behavior of chitin and chitosan. The results show that the hydrogen (H)-bonds' state, which can be influenced by the solvent, determines the degree of binding water (solubility) of polysaccharides, and that the binding water energy of a single chitosan chain is 6 times higher than that of chitin in water. Thus, H-bonding is the key to solubility enhancement and can be used to modulate the solubility properties of chitosan. It is expected that our studies can help to understand the structural and functional properties of chitin and chitosan at the single molecule level.
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Affiliation(s)
- Lu Qian
- School of Materials Science and Engineering, South China University of TechnologyGuangzhou 510641China
| | - Kai Zhang
- School of Mechanical Engineering, Sichuan UniversityChengdu 610065China
| | - Xin Guo
- School of Mechanical Engineering, Sichuan UniversityChengdu 610065China
| | - Miao Yu
- School of Mechanical Engineering, Sichuan UniversityChengdu 610065China
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66
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67
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Iida S, Tomoshi K. Free energy and kinetic rate calculation via non-equilibrium molecular simulation: application to biomolecules. Biophys Rev 2022; 14:1303-1314. [PMID: 36659997 PMCID: PMC9842846 DOI: 10.1007/s12551-022-01036-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 11/26/2022] [Indexed: 12/30/2022] Open
Abstract
Non-equilibrium molecular dynamics (NEMD) simulation has been recognized as a powerful tool for examining biomolecules and provides fruitful insights into not only non-equilibrium but also equilibrium processes. We review recent advances in NEMD simulation and relevant, fundamental results of non-equilibrium statistical mechanics. We first introduce Crooks fluctuation theorem and Jarzynski equality that relate free energy difference to work done on a physical system during a non-equilibrium process. The theorems are beneficial for the analysis of NEMD trajectories. We then describe rate theory, a framework to calculate molecular kinetics from a non-equilibrium process; this theoretical framework enables us to calculate a reaction time-mean-first passage time-from NEMD trajectories. We, in turn, present recent NEMD techniques that apply an external force to a system to enhance molecular dissociation and introduce their application to biomolecules. Lastly, we show the current status of an appropriate selection of reaction coordinates for NEMD simulation.
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Affiliation(s)
- Shinji Iida
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-Ku, Tokyo, 135-0064 Japan
| | - Kameda Tomoshi
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-Ku, Tokyo, 135-0064 Japan
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68
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Peyronnet R, Desai A, Edelmann JC, Cameron BA, Emig R, Kohl P, Dean D. Simultaneous assessment of radial and axial myocyte mechanics by combining atomic force microscopy and carbon fibre techniques. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210326. [PMID: 36189808 PMCID: PMC9527909 DOI: 10.1098/rstb.2021.0326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 07/21/2022] [Indexed: 11/12/2022] Open
Abstract
Cardiomyocytes sense and shape their mechanical environment, contributing to its dynamics by their passive and active mechanical properties. While axial forces generated by contracting cardiomyocytes have been amply investigated, the corresponding radial mechanics remain poorly characterized. Our aim is to simultaneously monitor passive and active forces, both axially and radially, in cardiomyocytes freshly isolated from adult mouse ventricles. To do so, we combine a carbon fibre (CF) set-up with a custom-made atomic force microscope (AFM). CF allows us to apply stretch and to record passive and active forces in the axial direction. The AFM, modified for frontal access to fit in CF, is used to characterize radial cell mechanics. We show that stretch increases the radial elastic modulus of cardiomyocytes. We further find that during contraction, cardiomyocytes generate radial forces that are reduced, but not abolished, when cells are forced to contract near isometrically. Radial forces may contribute to ventricular wall thickening during contraction, together with the dynamic re-orientation of cells and sheetlets in the myocardium. This new approach for characterizing cell mechanics allows one to obtain a more detailed picture of the balance of axial and radial mechanics in cardiomyocytes at rest, during stretch, and during contraction. This article is part of the theme issue 'The cardiomyocyte: new revelations on the interplay between architecture and function in growth, health, and disease'.
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Affiliation(s)
- Rémi Peyronnet
- Institute for Experimental Cardiovascular Medicine, University Heart Center Freiburg – Bad Krozingen, University of Freiburg, 79110 Freiburg, Germany
- Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany
- National Heart and Lung Institute, Imperial College London, London, UK
| | | | | | - Breanne A. Cameron
- Institute for Experimental Cardiovascular Medicine, University Heart Center Freiburg – Bad Krozingen, University of Freiburg, 79110 Freiburg, Germany
- Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany
| | - Ramona Emig
- Institute for Experimental Cardiovascular Medicine, University Heart Center Freiburg – Bad Krozingen, University of Freiburg, 79110 Freiburg, Germany
- Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany
- CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Peter Kohl
- Institute for Experimental Cardiovascular Medicine, University Heart Center Freiburg – Bad Krozingen, University of Freiburg, 79110 Freiburg, Germany
- Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany
- National Heart and Lung Institute, Imperial College London, London, UK
- CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
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69
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Ding X, Wang Z, Zheng B, Shi S, Deng Y, Yu H, Zheng P. One-step asparaginyl endopeptidase ( OaAEP1)-based protein immobilization for single-molecule force spectroscopy. RSC Chem Biol 2022; 3:1276-1281. [PMID: 36320890 PMCID: PMC9533667 DOI: 10.1039/d2cb00135g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 08/18/2022] [Indexed: 11/22/2022] Open
Abstract
Enzymatic protein ligation has become the most powerful and widely used method for high-precision atomic force microscopy single-molecule force spectroscopy (AFM-SMFS) study of protein mechanics. However, this methodology typically requires the functionalization of the glass surface with a corresponding peptide sequence/tag for enzymatic recognition and multiple steps are needed. Thus, it is time-consuming and a high level of experience is needed for reliable results. To solve this problem, we simplified the procedure using two strategies both based on asparaginyl endopeptidase (AEP). First, we designed a heterobifunctional peptide-based crosslinker, GL-peptide-propargylglycine, which links to an N 3-functionalized surface via the click reaction. Then, the target protein with a C-terminal NGL sequence can be immobilized via the AEP-mediated ligation. Furthermore, we took advantage of the direct ligation between primary amino in a small molecule and protein with C-terminal NGL by AEP. Thus, the target protein can be immobilized on an amino-functionalized surface via AEP in one step. Both approaches were successfully applied to the AFM-SMFS study of eGFP, showing consistent single-molecule results.
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Affiliation(s)
- Xuan Ding
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University 163 Xianlin Road Nanjing Jiangsu 210023 P. R. China
- State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University Nanjing Jiangsu 210023 P. R. China
| | - Ziyi Wang
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University Nanjing Jiangsu 210023 P. R. China
| | - Bin Zheng
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University Nanjing Jiangsu 210023 P. R. China
| | - Shengchao Shi
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University Nanjing Jiangsu 210023 P. R. China
| | - Yibing Deng
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University Nanjing Jiangsu 210023 P. R. China
| | - Hanyang Yu
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University 163 Xianlin Road Nanjing Jiangsu 210023 P. R. China
| | - Peng Zheng
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University Nanjing Jiangsu 210023 P. R. China
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70
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Hirschi S, Ward TR, Meier WP, Müller DJ, Fotiadis D. Synthetic Biology: Bottom-Up Assembly of Molecular Systems. Chem Rev 2022; 122:16294-16328. [PMID: 36179355 DOI: 10.1021/acs.chemrev.2c00339] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The bottom-up assembly of biological and chemical components opens exciting opportunities to engineer artificial vesicular systems for applications with previously unmet requirements. The modular combination of scaffolds and functional building blocks enables the engineering of complex systems with biomimetic or new-to-nature functionalities. Inspired by the compartmentalized organization of cells and organelles, lipid or polymer vesicles are widely used as model membrane systems to investigate the translocation of solutes and the transduction of signals by membrane proteins. The bottom-up assembly and functionalization of such artificial compartments enables full control over their composition and can thus provide specifically optimized environments for synthetic biological processes. This review aims to inspire future endeavors by providing a diverse toolbox of molecular modules, engineering methodologies, and different approaches to assemble artificial vesicular systems. Important technical and practical aspects are addressed and selected applications are presented, highlighting particular achievements and limitations of the bottom-up approach. Complementing the cutting-edge technological achievements, fundamental aspects are also discussed to cater to the inherently diverse background of the target audience, which results from the interdisciplinary nature of synthetic biology. The engineering of proteins as functional modules and the use of lipids and block copolymers as scaffold modules for the assembly of functionalized vesicular systems are explored in detail. Particular emphasis is placed on ensuring the controlled assembly of these components into increasingly complex vesicular systems. Finally, all descriptions are presented in the greater context of engineering valuable synthetic biological systems for applications in biocatalysis, biosensing, bioremediation, or targeted drug delivery.
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Affiliation(s)
- Stephan Hirschi
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland.,Molecular Systems Engineering, National Centre of Competence in Research (NCCR), 4002 Basel, Switzerland
| | - Thomas R Ward
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland.,Molecular Systems Engineering, National Centre of Competence in Research (NCCR), 4002 Basel, Switzerland
| | - Wolfgang P Meier
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland.,Molecular Systems Engineering, National Centre of Competence in Research (NCCR), 4002 Basel, Switzerland
| | - Daniel J Müller
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland.,Molecular Systems Engineering, National Centre of Competence in Research (NCCR), 4002 Basel, Switzerland
| | - Dimitrios Fotiadis
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland.,Molecular Systems Engineering, National Centre of Competence in Research (NCCR), 4002 Basel, Switzerland
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71
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Lei H, Zhang J, Li Y, Wang X, Qin M, Wang W, Cao Y. Histidine-Specific Bioconjugation for Single-Molecule Force Spectroscopy. ACS NANO 2022; 16:15440-15449. [PMID: 35980082 DOI: 10.1021/acsnano.2c07298] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Atomic force microscopy (AFM) based single-molecule force spectroscopy (SMFS) is a powerful tool to study the mechanical properties of proteins. In these experiments, site-specific immobilization of proteins is critical, as the tether determines the direction and amplitude of forces applied to the protein of interest. However, existing methods are mainly based on thiol chemistry or specific protein tags, which cannot meet the need of many challenging experiments. Here, we developed a histidine-specific phosphorylation strategy to covalently anchor proteins to an AFM cantilever tip or the substrate via their histidine tag or surface-exposed histidine residues. The formed covalent linkage was mechanically stable with rupture forces of over 1.3 nN. This protein immobilization method considerably improved the pickup rate and data quality of SMFS experiments. We further demonstrated the use of this method to explore the pulling-direction-dependent mechanical stability of green fluorescent protein and the unfolding of the membrane protein archaerhodopsin-3.
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Affiliation(s)
- Hai Lei
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University 22 Hankou Road, Nanjing 210093, People's Republic of China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University 163 Xianlin Road, Nanjing 210023, People's Republic of China
| | - Junsheng Zhang
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University 22 Hankou Road, Nanjing 210093, People's Republic of China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325001, People's Republic of China
| | - Ying Li
- Institute of Advanced Materials and Flexible Electronics (IAMFE), School of Chemistry and Materials Science, Nanjing University of Information Science & Technology 219 Ningliu Road, Nanjing, 210044, People's Republic of China
| | - Xin Wang
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325001, People's Republic of China
| | - Meng Qin
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University 22 Hankou Road, Nanjing 210093, People's Republic of China
| | - Wei Wang
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University 22 Hankou Road, Nanjing 210093, People's Republic of China
| | - Yi Cao
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University 22 Hankou Road, Nanjing 210093, People's Republic of China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University 163 Xianlin Road, Nanjing 210023, People's Republic of China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325001, People's Republic of China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan 250021, People's Republic of China
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72
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Alkhalde A, Seferovic H, Abri A, Simbrunner A, Hinterdorfer P, Oh YJ. Assessment of Efficacy of a Novel Crosslinking Protocol with Intracameral Oxygen (Bubble-CXL) in Increasing the Corneal Stiffness Using Atomic Force Microscopy. NANOMATERIALS (BASEL, SWITZERLAND) 2022; 12:nano12183185. [PMID: 36144973 PMCID: PMC9504955 DOI: 10.3390/nano12183185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/05/2022] [Accepted: 09/12/2022] [Indexed: 05/04/2023]
Abstract
The environmental oxygen level plays a critical role in corneal crosslinking (CXL), a treatment method to increase corneal biomechanical stability. In this study, we introduce a new CXL method (Bubble-CXL), in which intracameral oxygen serves as an additional oxygen source during eye treatment. The efficiency of this new method was compared with the efficiency of the standard CXL method. Three fresh porcine eye pairs were included in this study. One eye of each pair was treated with standard CXL, whereas in the partner eye, intracameral oxygen was injected prior to CXL and removed at the end of the procedure. The Young's modulus of each cornea was measured using atomic force microscopy. All analyzed corneas treated with intracameral oxygen showed significantly higher Young's modulus and thus an increased stiffness compared to the cornea of the partner eye treated with the standard protocol. Using intracameral oxygen in CXL therapy may increase crosslinking efficiency and improve biomechanical corneal properties.
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Affiliation(s)
- Ammar Alkhalde
- Department of Ophthalmology, Hospital Wels-Grieskirchen, 4600 Wels, Austria
| | - Hannah Seferovic
- Institute of Biophysics, Johannes Kepler University, 4020 Linz, Austria
- Correspondence: (H.S.); (Y.J.O.)
| | - Ali Abri
- Department of Ophthalmology, Hospital Wels-Grieskirchen, 4600 Wels, Austria
| | - Alvana Simbrunner
- Department of Ophthalmology, Hospital Wels-Grieskirchen, 4600 Wels, Austria
| | | | - Yoo Jin Oh
- Institute of Biophysics, Johannes Kepler University, 4020 Linz, Austria
- Correspondence: (H.S.); (Y.J.O.)
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73
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Cai M, Wang H, Zhao G, Li H, Gao J, Wang H. Cell membrane sample preparation method of combined AFM and dSTORM analysis. BIOPHYSICS REPORTS 2022; 8:183-192. [PMID: 37288003 PMCID: PMC10185485 DOI: 10.52601/bpr.2022.220004] [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: 01/31/2022] [Accepted: 04/06/2022] [Indexed: 11/05/2022] Open
Abstract
A major role of cell membranes is to provide an ideal environment for the constituent proteins to perform their biological functions. A deep understanding of the membrane proteins assembly process under physiological conditions is quite important to elucidate both the structure and the function of the cell membranes. Along these lines, in this work, a complete workflow of the cell membrane sample preparation and the correlated AFM and dSTORM imaging analysis methods are presented. A specially designed, angle-controlled sample preparation device was used to prepare the cell membrane samples. The correlated distributions of the specific membrane proteins with the topography of the cytoplasmic side of the cell membranes can be obtained by performing correlative AFM and dSTORM measurements. These methods are ideal for systematically studying the structure of the cell membranes. The proposed method of the sample characterization was not only limited to the measurement of the cell membrane but also can be applied for both biological tissue section analysis and detection.
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Affiliation(s)
- Mingjun Cai
- University of Science and Technology of China, Hefei 230027, China
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Huili Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Guanfang Zhao
- University of Science and Technology of China, Hefei 230027, China
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Hongru Li
- University of Science and Technology of China, Hefei 230027, China
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Jing Gao
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Hongda Wang
- University of Science and Technology of China, Hefei 230027, China
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, Shandong, China
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74
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Yin Y, Shen H. Common methods in mitochondrial research (Review). Int J Mol Med 2022; 50:126. [PMID: 36004457 PMCID: PMC9448300 DOI: 10.3892/ijmm.2022.5182] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 08/09/2022] [Indexed: 01/18/2023] Open
Affiliation(s)
- Yiyuan Yin
- Department of Emergency Medicine, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Haitao Shen
- Department of Emergency Medicine, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
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75
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Harris NJ, Pellowe GA, Blackholly LR, Gulaidi-Breen S, Findlay HE, Booth PJ. Methods to study folding of alpha-helical membrane proteins in lipids. Open Biol 2022; 12:220054. [PMID: 35855589 PMCID: PMC9297032 DOI: 10.1098/rsob.220054] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
How alpha-helical membrane proteins fold correctly in the highly hydrophobic membrane interior is not well understood. Their folding is known to be highly influenced by the lipids within the surrounding bilayer, but the majority of folding studies have focused on detergent-solubilized protein rather than protein in a lipid environment. There are different ways to study folding in lipid bilayers, and each method has its own advantages and disadvantages. This review will discuss folding methods which can be used to study alpha-helical membrane proteins in bicelles, liposomes, nanodiscs or native membranes. These folding methods include in vitro folding methods in liposomes such as denaturant unfolding studies, and single-molecule force spectroscopy studies in bicelles, liposomes and native membranes. This review will also discuss recent advances in co-translational folding studies, which use cell-free expression with liposomes or nanodiscs or are performed in vivo with native membranes.
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Affiliation(s)
- Nicola J. Harris
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London, SE1 1DB, UK
| | - Grant A. Pellowe
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London, SE1 1DB, UK
| | - Laura R. Blackholly
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London, SE1 1DB, UK
| | | | - Heather E. Findlay
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London, SE1 1DB, UK,The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Paula J. Booth
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London, SE1 1DB, UK,The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
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76
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Petitjean SJL, Chen W, Koehler M, Jimmidi R, Yang J, Mohammed D, Juniku B, Stanifer ML, Boulant S, Vincent SP, Alsteens D. Multivalent 9-O-Acetylated-sialic acid glycoclusters as potent inhibitors for SARS-CoV-2 infection. Nat Commun 2022; 13:2564. [PMID: 35538121 PMCID: PMC9091252 DOI: 10.1038/s41467-022-30313-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 04/25/2022] [Indexed: 01/08/2023] Open
Abstract
The recent emergence of highly transmissible SARS-CoV-2 variants illustrates the urgent need to better understand the molecular details of the virus binding to its host cell and to develop anti-viral strategies. While many studies focused on the role of the angiotensin-converting enzyme 2 receptor in the infection, others suggest the important role of cell attachment factors such as glycans. Here, we use atomic force microscopy to study these early binding events with the focus on the role of sialic acids (SA). We show that SARS-CoV-2 binds specifically to 9-O-acetylated-SA with a moderate affinity, supporting its role as an attachment factor during virus landing to cell host surfaces. For therapeutic purposes and based on this finding, we have designed novel blocking molecules with various topologies and carrying a controlled number of SA residues, enhancing affinity through a multivalent effect. Inhibition assays show that the AcSA-derived glycoclusters are potent inhibitors of cell binding and infectivity, offering new perspectives in the treatment of SARS-CoV-2 infection. Cell surface attachment factors, such as glycans, play an important role in viral infection. Here, Petitjean et al. show that SARS-CoV-2 specifically binds to 9-Oacetylated sialic acid and have designed novel inhibitors based on multivalent derivatives.
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Affiliation(s)
- Simon J L Petitjean
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Wenzhang Chen
- Laboratory of Bio-Organic Chemistry (NARILIS), UNamur, Namur, Belgium
| | - Melanie Koehler
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Ravikumar Jimmidi
- Laboratory of Bio-Organic Chemistry (NARILIS), UNamur, Namur, Belgium
| | - Jinsung Yang
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Danahe Mohammed
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Blinera Juniku
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Megan L Stanifer
- Dept. of Infectious Diseases, Medical Faculty, Center for Integrative Infectious Diseases Research (CIID), University of Heidelberg, 69120, Heidelberg, Germany.,Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, USA
| | - Steeve Boulant
- Dept. of Infectious Diseases, Medical Faculty, Center for Integrative Infectious Diseases Research (CIID), University of Heidelberg, 69120, Heidelberg, Germany.,Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, USA
| | | | - David Alsteens
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium. .,Walloon Excellence in Life sciences and Biotechnology (WELBIO), Wavre, Belgium.
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77
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Simpson JD, Ray A, Koehler M, Mohammed D, Alsteens D. Atomic force microscopy applied to interrogate nanoscale cellular chemistry and supramolecular bond dynamics for biomedical applications. Chem Commun (Camb) 2022; 58:5072-5087. [PMID: 35315846 DOI: 10.1039/d1cc07200e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Understanding biological interactions at a molecular level grants valuable information relevant to improving medical treatments and outcomes. Among the suite of technologies available, Atomic Force Microscopy (AFM) is unique in its ability to quantitatively probe forces and receptor-ligand interactions in real-time. The ability to assess the formation of supramolecular bonds and intermediates in real-time on surfaces and living cells generates important information relevant to understanding biological phenomena. Combining AFM with fluorescence-based techniques allows for an unprecedented level of insight not only concerning the formation and rupture of bonds, but understanding medically relevant interactions at a molecular level. As the ability of AFM to probe cells and more complex models improves, being able to assess binding kinetics, chemical topographies, and garner spectroscopic information will likely become key to developing further improvements in fields such as cancer, nanomaterials, and virology. The rapid response to the COVID-19 crisis, producing information regarding not just receptor affinities, but also strain-dependent efficacy of neutralizing nanobodies, demonstrates just how viable and integral to the pre-clinical development of information AFM techniques are in this era of medicine.
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Affiliation(s)
- Joshua D Simpson
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-la-Neuve 1348, Belgium.
| | - Ankita Ray
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-la-Neuve 1348, Belgium.
| | - Melanie Koehler
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-la-Neuve 1348, Belgium.
| | - Danahe Mohammed
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-la-Neuve 1348, Belgium.
| | - David Alsteens
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-la-Neuve 1348, Belgium.
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78
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Molecular Recognition of Proteins through Quantitative Force Maps at Single Molecule Level. Biomolecules 2022; 12:biom12040594. [PMID: 35454182 PMCID: PMC9024611 DOI: 10.3390/biom12040594] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 04/08/2022] [Accepted: 04/14/2022] [Indexed: 12/24/2022] Open
Abstract
Intermittent jumping force is an operational atomic-force microscopy mode that produces simultaneous topography and tip-sample maximum-adhesion images based on force spectroscopy. In this work, the operation conditions have been implemented scanning in a repulsive regime and applying very low forces, thus avoiding unspecific tip-sample forces. Remarkably, adhesion images give only specific rupture events, becoming qualitative and quantitative molecular recognition maps obtained at reasonably fast rates, which is a great advantage compared to the force–volume modes. This procedure has been used to go further in discriminating between two similar protein molecules, avidin and streptavidin, in hybrid samples. The adhesion maps generated scanning with biotinylated probes showed features identified as avidin molecules, in the range of 40–80 pN; meanwhile, streptavidin molecules rendered 120–170 pN at the selected working conditions. The gathered results evidence that repulsive jumping force mode applying very small forces allows the identification of biomolecules through the specific rupture forces of the complexes and could serve to identify receptors on membranes or samples or be applied to design ultrasensitive detection technologies.
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79
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Martin-Jimenez D, Ruppert MG, Ihle A, Ahles S, Wegner HA, Schirmeisen A, Ebeling D. Chemical bond imaging using torsional and flexural higher eigenmodes of qPlus sensors. NANOSCALE 2022; 14:5329-5339. [PMID: 35348167 DOI: 10.1039/d2nr01062c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Non-contact atomic force microscopy (AFM) with CO-functionalized tips allows visualization of the chemical structure of adsorbed molecules and identify individual inter- and intramolecular bonds. This technique enables in-depth studies of on-surface reactions and self-assembly processes. Herein, we analyze the suitability of qPlus sensors, which are commonly used for such studies, for the application of modern multifrequency AFM techniques. Two different qPlus sensors were tested for submolecular resolution imaging via actuating torsional and flexural higher eigenmodes and via bimodal AFM. The torsional eigenmode of one of our sensors is perfectly suited for performing lateral force microscopy (LFM) with single bond resolution. The obtained LFM images agree well with images from the literature, which were scanned with customized qPlus sensors that were specifically designed for LFM. The advantage of using a torsional eigenmode is that the same molecule can be imaged either with a vertically or laterally oscillating tip without replacing the sensor simply by actuating a different eigenmode. Submolecular resolution is also achieved by actuating the 2nd flexural eigenmode of our second sensor. In this case, we observe particular contrast features that only appear in the AFM images of the 2nd flexural eigenmode but not for the fundamental eigenmode. With complementary laser Doppler vibrometry measurements and AFM simulations we can rationalize that these contrast features are caused by a diagonal (i.e. in-phase vertical and lateral) oscillation of the AFM tip.
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Affiliation(s)
- Daniel Martin-Jimenez
- Institute of Applied Physics (IAP), Justus Liebig University Giessen, Heinrich-Buff-Ring 16, Giessen 35392, Germany.
- Center for Materials Research (LaMa), Justus Liebig University Giessen, Heinrich-Buff-Ring 16, Giessen 35392, Germany
| | | | - Alexander Ihle
- Institute of Applied Physics (IAP), Justus Liebig University Giessen, Heinrich-Buff-Ring 16, Giessen 35392, Germany.
- Center for Materials Research (LaMa), Justus Liebig University Giessen, Heinrich-Buff-Ring 16, Giessen 35392, Germany
| | - Sebastian Ahles
- Institute of Organic Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, Giessen 35392, Germany
- Center for Materials Research (LaMa), Justus Liebig University Giessen, Heinrich-Buff-Ring 16, Giessen 35392, Germany
| | - Hermann A Wegner
- Institute of Organic Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, Giessen 35392, Germany
- Center for Materials Research (LaMa), Justus Liebig University Giessen, Heinrich-Buff-Ring 16, Giessen 35392, Germany
| | - André Schirmeisen
- Institute of Applied Physics (IAP), Justus Liebig University Giessen, Heinrich-Buff-Ring 16, Giessen 35392, Germany.
- Center for Materials Research (LaMa), Justus Liebig University Giessen, Heinrich-Buff-Ring 16, Giessen 35392, Germany
| | - Daniel Ebeling
- Institute of Applied Physics (IAP), Justus Liebig University Giessen, Heinrich-Buff-Ring 16, Giessen 35392, Germany.
- Center for Materials Research (LaMa), Justus Liebig University Giessen, Heinrich-Buff-Ring 16, Giessen 35392, Germany
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80
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Experimental discovery of structure–property relationships in ferroelectric materials via active learning. NAT MACH INTELL 2022. [DOI: 10.1038/s42256-022-00460-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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81
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Pu J, Putnis CV, Wang L. AFM imaging and single-molecule recognition of plant cell walls. TRENDS IN PLANT SCIENCE 2022; 27:412-413. [PMID: 34916130 DOI: 10.1016/j.tplants.2021.11.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 11/15/2021] [Indexed: 06/14/2023]
Affiliation(s)
- Junbao Pu
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Christine V Putnis
- Institut für Mineralogie, University of Münster, 48149 Münster, Germany; School of Molecular and Life Sciences, Curtin University, Perth 6845, Australia
| | - Lijun Wang
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China.
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82
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Li Z, Liu Q, Zhang D, Wang Y, Zhang Y, Li Q, Dong M. Probing the hydration friction of ionic interfaces at the atomic scale. NANOSCALE HORIZONS 2022; 7:368-375. [PMID: 35195643 DOI: 10.1039/d1nh00564b] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Despite the extensive studies conducted in exploring friction in the aqueous environment, the mechanism of hydration friction remains not well understood. Herein, we directly probed hydration friction on mica-electrolyte interfaces with different hydrated alkali cations through a combination of three-dimensional atomic force microscopy and friction force microscopy. The atomic scale imaging of the hydration layers at the mica surface in different electrolyte solutions clearly revealed a correlation between the alkali cations and the structure of the hydration layers. Our detailed analysis showed that the hydration force was much higher at high ionic concentrations than that at low concentrations. The hydration friction coefficient was found to follow the trend K+< Na+< Li+< Cs+, which contrasts with the Hofmeister series, indicating that the hydration friction depends not only on the hydration strength of the alkali cations but also on the arrangement of the alkali cations at the interface. The results of this study provide deep insights into the origins of hydration friction, with potential implications for the development of new boundary lubrication in aqueous media.
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Affiliation(s)
- Zibo Li
- Key Laboratory of Colloid and Interface Chemistry of the Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China.
| | - Qian Liu
- Key Laboratory of Colloid and Interface Chemistry of the Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China.
| | - Deliang Zhang
- Key Laboratory of Colloid and Interface Chemistry of the Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China.
| | - Yin Wang
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, DK-8000, Denmark.
| | - Yuge Zhang
- Key Laboratory of Colloid and Interface Chemistry of the Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China.
| | - Qiang Li
- Key Laboratory of Colloid and Interface Chemistry of the Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, China.
| | - Mingdong Dong
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, DK-8000, Denmark.
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83
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Moraille P, Abdali Z, Ramkaran M, Polcari D, Patience GS, Dorval Courchesne N, Badia A. Experimental Methods in Chemical Engineering: Atomic force microscopy—
AFM. CAN J CHEM ENG 2022. [DOI: 10.1002/cjce.24407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
| | - Zahra Abdali
- Chemical Engineering, McGill University Québec Canada
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84
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Rousso I, Deshpande A. Applications of Atomic Force Microscopy in HIV-1 Research. Viruses 2022; 14:v14030648. [PMID: 35337055 PMCID: PMC8955997 DOI: 10.3390/v14030648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/17/2022] [Accepted: 03/18/2022] [Indexed: 12/10/2022] Open
Abstract
Obtaining an understanding of the mechanism underlying the interrelations between the structure and function of HIV-1 is of pivotal importance. In previous decades, this mechanism was addressed extensively in a variety of studies using conventional approaches. More recently, atomic force microscopy, which is a relatively new technique with unique capabilities, has been utilized to study HIV-1 biology. Atomic force microscopy can generate high-resolution images at the nanometer-scale and analyze the mechanical properties of individual HIV-1 virions, virus components (e.g., capsids), and infected live cells under near-physiological environments. This review describes the working principles and various imaging and analysis modes of atomic force microscopy, and elaborates on its distinctive contributions to HIV-1 research in areas such as mechanobiology and the physics of infection.
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85
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Tsuzuki T, Baassiri K, Mahmoudi Z, Perumal AS, Rajendran K, Rubies GM, Nicolau DV. Hydrophobic Recovery of PDMS Surfaces in Contact with Hydrophilic Entities: Relevance to Biomedical Devices. MATERIALS (BASEL, SWITZERLAND) 2022; 15:2313. [PMID: 35329765 PMCID: PMC8950181 DOI: 10.3390/ma15062313] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/08/2022] [Accepted: 03/16/2022] [Indexed: 11/30/2022]
Abstract
Polydimethylsiloxane (PDMS), a silicone elastomer, is increasingly being used in health and biomedical fields due to its excellent optical and mechanical properties. Its biocompatibility and resistance to biodegradation led to various applications (e.g., lung on a chip replicating blood flow, medical interventions, and diagnostics). The many advantages of PDMS are, however, partially offset by its inherent hydrophobicity, which makes it unsuitable for applications needing wetting, thus requiring the hydrophilization of its surface by exposure to UV or O2 plasma. Yet, the elastomeric state of PDMS translates in a slow, hours to days, process of reducing its surface hydrophilicity-a process denominated as hydrophobic recovery. Using Fourier transform infrared spectroscopy (FTIR) and atomic force microscopy (AFM), the present study details the dynamics of hydrophobic recovery of PDMS, on flat bare surfaces and on surfaces embedded with hydrophilic beads. It was found that a thin, stiff, hydrophilic, silica film formed on top of the PDMS material, following its hydrophilization by UV radiation. The hydrophobic recovery of bare PDMS material is the result of an overlap of various nano-mechanical, and diffusional processes, each with its own dynamics rate, which were analyzed in parallel. The hydrophobic recovery presents a hysteresis, with surface hydrophobicity recovering only partially due to a thin, but resilient top silica layer. The monitoring of hydrophobic recovery of PDMS embedded with hydrophilic beads revealed that this is delayed, and then totally stalled in the few-micrometer vicinity of the embedded hydrophilic beads. This region where the hydrophobic recovery stalls can be used as a good approximation of the depth of the resilient, moderately hydrophilic top layer on the PDMS material. The complex processes of hydrophilization and subsequent hydrophobic recovery impact the design, fabrication, and operation of PDMS materials and devices used for diagnostics and medical procedures. Consequently, especially considering the emergence of new surgical procedures using elastomers, the impact of hydrophobic recovery on the surface of PDMS warrants more comprehensive studies.
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Affiliation(s)
- Tomoo Tsuzuki
- Faculty of Engineering and Industrial Science, Industrial Research Institute Swinburne, Swinburne University of Technology, Melbourne, VIC 3122, Australia;
| | - Karine Baassiri
- Department of Bioengineering, Faculty of Engineering, McGill University, Montreal, QC H3A 0E9, Canada; (K.B.); (Z.M.); (A.S.P.); (K.R.); (G.M.R.)
| | - Zahra Mahmoudi
- Department of Bioengineering, Faculty of Engineering, McGill University, Montreal, QC H3A 0E9, Canada; (K.B.); (Z.M.); (A.S.P.); (K.R.); (G.M.R.)
| | - Ayyappasamy Sudalaiyadum Perumal
- Department of Bioengineering, Faculty of Engineering, McGill University, Montreal, QC H3A 0E9, Canada; (K.B.); (Z.M.); (A.S.P.); (K.R.); (G.M.R.)
| | - Kavya Rajendran
- Department of Bioengineering, Faculty of Engineering, McGill University, Montreal, QC H3A 0E9, Canada; (K.B.); (Z.M.); (A.S.P.); (K.R.); (G.M.R.)
| | - Gala Montiel Rubies
- Department of Bioengineering, Faculty of Engineering, McGill University, Montreal, QC H3A 0E9, Canada; (K.B.); (Z.M.); (A.S.P.); (K.R.); (G.M.R.)
| | - Dan V. Nicolau
- Faculty of Engineering and Industrial Science, Industrial Research Institute Swinburne, Swinburne University of Technology, Melbourne, VIC 3122, Australia;
- Department of Bioengineering, Faculty of Engineering, McGill University, Montreal, QC H3A 0E9, Canada; (K.B.); (Z.M.); (A.S.P.); (K.R.); (G.M.R.)
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86
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Holuigue H, Lorenc E, Chighizola M, Schulte C, Varinelli L, Deraco M, Guaglio M, Gariboldi M, Podestà A. Force Sensing on Cells and Tissues by Atomic Force Microscopy. SENSORS (BASEL, SWITZERLAND) 2022; 22:2197. [PMID: 35336366 PMCID: PMC8955449 DOI: 10.3390/s22062197] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 03/05/2022] [Accepted: 03/09/2022] [Indexed: 01/27/2023]
Abstract
Biosensors are aimed at detecting tiny physical and chemical stimuli in biological systems. Physical forces are ubiquitous, being implied in all cellular processes, including cell adhesion, migration, and differentiation. Given the strong interplay between cells and their microenvironment, the extracellular matrix (ECM) and the structural and mechanical properties of the ECM play an important role in the transmission of external stimuli to single cells within the tissue. Vice versa, cells themselves also use self-generated forces to probe the biophysical properties of the ECM. ECM mechanics influence cell fate, regulate tissue development, and show peculiar features in health and disease conditions of living organisms. Force sensing in biological systems is therefore crucial to dissecting and understanding complex biological processes, such as mechanotransduction. Atomic Force Microscopy (AFM), which can both sense and apply forces at the nanoscale, with sub-nanonewton sensitivity, represents an enabling technology and a crucial experimental tool in biophysics and mechanobiology. In this work, we report on the application of AFM to the study of biomechanical fingerprints of different components of biological systems, such as the ECM, the whole cell, and cellular components, such as the nucleus, lamellipodia and the glycocalyx. We show that physical observables such as the (spatially resolved) Young's Modulus (YM) of elasticity of ECMs or cells, and the effective thickness and stiffness of the glycocalyx, can be quantitatively characterized by AFM. Their modification can be correlated to changes in the microenvironment, physio-pathological conditions, or gene regulation.
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Affiliation(s)
- Hatice Holuigue
- CIMAINA and Dipartimento di Fisica “Aldo Pontremoli”, Università degli Studi di Milano, Via Celoria 16, 20133 Milan, Italy; (H.H.); (E.L.); (M.C.); (C.S.)
| | - Ewelina Lorenc
- CIMAINA and Dipartimento di Fisica “Aldo Pontremoli”, Università degli Studi di Milano, Via Celoria 16, 20133 Milan, Italy; (H.H.); (E.L.); (M.C.); (C.S.)
| | - Matteo Chighizola
- CIMAINA and Dipartimento di Fisica “Aldo Pontremoli”, Università degli Studi di Milano, Via Celoria 16, 20133 Milan, Italy; (H.H.); (E.L.); (M.C.); (C.S.)
| | - Carsten Schulte
- CIMAINA and Dipartimento di Fisica “Aldo Pontremoli”, Università degli Studi di Milano, Via Celoria 16, 20133 Milan, Italy; (H.H.); (E.L.); (M.C.); (C.S.)
| | - Luca Varinelli
- Department of Research, Fondazione IRCCS Istituto Nazionale Tumori, Via G. Venezian 1, 20133 Milan, Italy; (L.V.); (M.G.)
| | - Marcello Deraco
- Peritoneal Surface Malignancies Unit, Colorectal Surgery, Fondazione IRCCS Istituto Nazionale Tumori, Via G. Venezian 1, 20133 Milan, Italy; (M.D.); (M.G.)
| | - Marcello Guaglio
- Peritoneal Surface Malignancies Unit, Colorectal Surgery, Fondazione IRCCS Istituto Nazionale Tumori, Via G. Venezian 1, 20133 Milan, Italy; (M.D.); (M.G.)
| | - Manuela Gariboldi
- Department of Research, Fondazione IRCCS Istituto Nazionale Tumori, Via G. Venezian 1, 20133 Milan, Italy; (L.V.); (M.G.)
| | - Alessandro Podestà
- CIMAINA and Dipartimento di Fisica “Aldo Pontremoli”, Università degli Studi di Milano, Via Celoria 16, 20133 Milan, Italy; (H.H.); (E.L.); (M.C.); (C.S.)
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87
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Sharafeldin M, Davis JJ. Characterising the biosensing interface. Anal Chim Acta 2022; 1216:339759. [DOI: 10.1016/j.aca.2022.339759] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 02/08/2022] [Accepted: 03/22/2022] [Indexed: 12/19/2022]
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88
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Qian L, Zhang K, Guo X, Zhou J, Yu M. Single-Chain Mechanical Properties of Gelatin: A Single-Molecule Study. Polymers (Basel) 2022; 14:869. [PMID: 35267692 PMCID: PMC8912665 DOI: 10.3390/polym14050869] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 02/18/2022] [Accepted: 02/21/2022] [Indexed: 01/27/2023] Open
Abstract
Gelatin is an important natural biological resource with a wide range of applications in the pharmaceutical, industrial and food industries. We investigated the single-chain behaviors of gelatin by atomic force microscopy (AFM)-based single-molecule force spectroscopy (SMFS), and found that gelatin exists as long chains by fitting with the M-FJC model. By comparing the single-chain elasticity in a nonpolar organic solvent (nonane) and DI water, it was surprising to find that there was almost no difference in the single-chain elasticity of gelatin in nonane and DI water. Considering the specificity of gelatin solubility and the solvent size effect of nonane molecules, when a single gelatin chain is pulled into loose nonane, dehydration does not occur due to strong binding water interactions. Gelatin chains can only interact with water molecules at high temperatures; therefore, no further interaction of single gelatin chains with water molecules occurred at the experimental temperature. This eventually led to almost no difference in the single-chain F-E curves under the two conditions. It is expected that our study will enable the deep exploration of the interaction between water molecules and gelatin and provide a theoretical basis and experimental foundation for the design of gelatin-based materials with more functionalities.
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Affiliation(s)
- Lu Qian
- School of Materials Science and Engineering, South China University of Technology, Guangzhou 510000, China;
| | - Kai Zhang
- School of Mechanical Engineering, Sichuan University, Chengdu 610065, China; (K.Z.); (X.G.); (J.Z.)
| | - Xin Guo
- School of Mechanical Engineering, Sichuan University, Chengdu 610065, China; (K.Z.); (X.G.); (J.Z.)
| | - Junyu Zhou
- School of Mechanical Engineering, Sichuan University, Chengdu 610065, China; (K.Z.); (X.G.); (J.Z.)
| | - Miao Yu
- School of Mechanical Engineering, Sichuan University, Chengdu 610065, China; (K.Z.); (X.G.); (J.Z.)
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89
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Zhang Q, Yang J, Tillieux S, Guo Z, Natividade RDS, Koehler M, Petitjean S, Cui Z, Alsteens D. Stepwise Enzymatic-Dependent Mechanism of Ebola Virus Binding to Cell Surface Receptors Monitored by AFM. NANO LETTERS 2022; 22:1641-1648. [PMID: 35108019 DOI: 10.1021/acs.nanolett.1c04677] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Ebola virus (EBOV) is responsible for several outbreaks of hemorrhagic fever with high mortality, raising great public concern. Several cell surface receptors have been identified to mediate EBOV binding and internalization, including phosphatidylserine (PS) receptors (TIM-1) and C-type lectin receptors (DC-SIGNR). However, the role of TIM-1 during early cell surface binding remains elusive and in particular whether TIM-1 acts as a specific receptor for EBOV. Here, we used force-distance curve-based atomic force microscopy (FD-based AFM) to quantify the binding between TIM-1/DC-SIGNR and EBOV glycoprotein (GP) and observed that both receptors specifically bind to GP with high-affinity. Since TIM-1 can also directly interact with PS at the single-molecule level, we also confirmed that TIM-1 acts as dual-function receptors of EBOV. These results highlight the direct involvement of multiple high-affinity receptors in the first steps of binding to cell surfaces, thus offering new perspectives for the development of anti-EBOV therapeutic molecules.
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Affiliation(s)
- Qingrong Zhang
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-la-Neuve 1348, Belgium
| | - Jinsung Yang
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-la-Neuve 1348, Belgium
| | - Sueli Tillieux
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-la-Neuve 1348, Belgium
| | - Zhengyuan Guo
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China
| | - Rita Dos Santos Natividade
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-la-Neuve 1348, Belgium
| | - Melanie Koehler
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-la-Neuve 1348, Belgium
| | - Simon Petitjean
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-la-Neuve 1348, Belgium
| | - Zongqiang Cui
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China
| | - David Alsteens
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-la-Neuve 1348, Belgium
- Walloon Excellence in Life sciences and Biotechnology (WELBIO), Wavre 1300, Belgium
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90
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Ge X, Zhang W, Putnis CV, Wang L. Molecular mechanisms for the humic acid-enhanced formation of the ordered secondary structure of a conserved catalytic domain in phytase. Phys Chem Chem Phys 2022; 24:4493-4503. [PMID: 35113120 DOI: 10.1039/d2cp00054g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Changes in the secondary structure of phytase, particularly the conserved active catalytic domain (ACD, SRHGVRAPHD) are extremely important for the varied catalytic activity during hydrolyzing phytate in the presence of humic acid (HA). However, little is known about the molecular-scale mechanisms of how HA influences the secondary structure of ACD found in phytase. First, in situ surface-enhanced Raman spectroscopy (SERS) results show the secondary structure transformation of ACD from the unordered random coil to the ordered β-sheet structure after treatment with HA. Then, we use an atomic force microscopy (AFM)-based single-molecule force spectroscopy (SMFS) technique that can in situ directly probe the single-molecule interaction of ACD with HA and underlying changes in ACD secondary structure in the approach-retraction cycles in real time. Based on the SMFS results, we further detect the HA-enhanced formation of H-bonding between amide groups in the ACD backbone after noncovalently interacting with HA in the absence of phytate. Following the addition of phytate, the calculated contour length (Lc) and the free energies (ΔGb) of functional groups within ACD(-1/2) binding to mica/HA collectively demonstrate the formation of the organized intermediate structural state of ACD following its covalent binding to phytate. These spectroscopic and single-molecule determinations provide the molecular-scale understanding regarding the detailed mechanisms of HA-enhancement of the ordered β-sheet secondary structure of ACD through chemical functionalities in ACD noncovalently interacting with HA. Therefore, we suggest that similar studies of the interactions of other soil enzymes and plant nutrients may reveal predominant roles of dissolved organic matter (DOM) in controlling elemental cycling and fate for sustainable agriculture development.
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Affiliation(s)
- Xinfei Ge
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China.
| | - Wenjun Zhang
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China.
| | - Christine V Putnis
- Institut für Mineralogie, University of Münster, 48149 Münster, Germany.,School of Molecular and Life Science, Curtin University, Perth 6845, Australia
| | - Lijun Wang
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China.
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91
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Sun W, Gao X, Lei H, Wang W, Cao Y. Biophysical Approaches for Applying and Measuring Biological Forces. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2105254. [PMID: 34923777 PMCID: PMC8844594 DOI: 10.1002/advs.202105254] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Indexed: 05/13/2023]
Abstract
Over the past decades, increasing evidence has indicated that mechanical loads can regulate the morphogenesis, proliferation, migration, and apoptosis of living cells. Investigations of how cells sense mechanical stimuli or the mechanotransduction mechanism is an active field of biomaterials and biophysics. Gaining a further understanding of mechanical regulation and depicting the mechanotransduction network inside cells require advanced experimental techniques and new theories. In this review, the fundamental principles of various experimental approaches that have been developed to characterize various types and magnitudes of forces experienced at the cellular and subcellular levels are summarized. The broad applications of these techniques are introduced with an emphasis on the difficulties in implementing these techniques in special biological systems. The advantages and disadvantages of each technique are discussed, which can guide readers to choose the most suitable technique for their questions. A perspective on future directions in this field is also provided. It is anticipated that technical advancement can be a driving force for the development of mechanobiology.
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Affiliation(s)
- Wenxu Sun
- School of SciencesNantong UniversityNantong226019P. R. China
| | - Xiang Gao
- Key Laboratory of Intelligent Optical Sensing and IntegrationNational Laboratory of Solid State Microstructureand Department of PhysicsCollaborative Innovation Center of Advanced MicrostructuresNanjing UniversityNanjing210023P. R. China
- Institute of Brain ScienceNanjing UniversityNanjing210023P. R. China
| | - Hai Lei
- Key Laboratory of Intelligent Optical Sensing and IntegrationNational Laboratory of Solid State Microstructureand Department of PhysicsCollaborative Innovation Center of Advanced MicrostructuresNanjing UniversityNanjing210023P. R. China
- Institute of Brain ScienceNanjing UniversityNanjing210023P. R. China
- Chemistry and Biomedicine Innovation CenterNanjing UniversityNanjing210023P. R. China
| | - Wei Wang
- Key Laboratory of Intelligent Optical Sensing and IntegrationNational Laboratory of Solid State Microstructureand Department of PhysicsCollaborative Innovation Center of Advanced MicrostructuresNanjing UniversityNanjing210023P. R. China
- Institute of Brain ScienceNanjing UniversityNanjing210023P. R. China
| | - Yi Cao
- Key Laboratory of Intelligent Optical Sensing and IntegrationNational Laboratory of Solid State Microstructureand Department of PhysicsCollaborative Innovation Center of Advanced MicrostructuresNanjing UniversityNanjing210023P. R. China
- Institute of Brain ScienceNanjing UniversityNanjing210023P. R. China
- MOE Key Laboratory of High Performance Polymer Materials and TechnologyDepartment of Polymer Science & EngineeringCollege of Chemistry & Chemical EngineeringNanjing UniversityNanjing210023P. R. China
- Chemistry and Biomedicine Innovation CenterNanjing UniversityNanjing210023P. R. China
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92
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Lo Giudice C, Yang J, Poncin MA, Adumeau L, Delguste M, Koehler M, Evers K, Dumitru AC, Dawson KA, Alsteens D. Nanophysical Mapping of Inflammasome Activation by Nanoparticles via Specific Cell Surface Recognition Events. ACS NANO 2022; 16:306-316. [PMID: 34957816 DOI: 10.1021/acsnano.1c06301] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Silica nanoparticles (SiNP) trigger a range of innate immune responses in relevant essential organs, such as the liver and the lungs. Inflammatory reactions, including NLRP3 inflammasome activation, have been linked to particulate materials; however, the molecular mechanisms and key actors remain elusive. Although many receptors, including several scavenger receptors, were suggested to participate in SiNP cellular uptake, mechanistic evidence of their role on innate immunity is lacking. Here we present an atomic force microscopy-based approach to physico-mechanically map the specific interaction occurring between nanoparticles and scavenger receptor A1 (SRA1) in vitro on living lung epithelial cells. We find that SiNP recognition by SRA1 on human macrophages plays a key role in mediating NLRP3 inflammasome activation, and we identify cellular mechanical changes as clear indicators of inflammasome activation in human macrophages, greatly advancing our knowledge on the interplay among nanomaterials and innate immunity.
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Affiliation(s)
- Cristina Lo Giudice
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve 1348, Belgium
- Max Planck Institute for Medical Research, Heidelberg D-69120, Germany
| | - Jinsung Yang
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve 1348, Belgium
| | - Mégane A Poncin
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve 1348, Belgium
| | - Laurent Adumeau
- Centre for BioNano Interactions, School of Chemistry, University College Dublin, Dublin D04 N2E5, Ireland
| | - Martin Delguste
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve 1348, Belgium
| | - Melanie Koehler
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve 1348, Belgium
| | - Koen Evers
- Centre for BioNano Interactions, School of Chemistry, University College Dublin, Dublin D04 N2E5, Ireland
| | - Andra C Dumitru
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve 1348, Belgium
| | - Kenneth A Dawson
- Centre for BioNano Interactions, School of Chemistry, University College Dublin, Dublin D04 N2E5, Ireland
- Guangdong Provincial Education Department Key Laboratory of Nano-Immunoregulation Tumour Microenvironment, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510261, China
| | - David Alsteens
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve 1348, Belgium
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93
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Qin J, Zhang M, Guan Y, Guo X, Li Z, Rankl C, Tang J. Imaging and quantifying analysis the binding behavior of PD-L1 at molecular resolution by atomic force microscopy. Anal Chim Acta 2022; 1191:339281. [PMID: 35033247 DOI: 10.1016/j.aca.2021.339281] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 10/20/2021] [Accepted: 11/11/2021] [Indexed: 11/25/2022]
Abstract
Immunotherapy has emerged as an effective treatment modality for cancer. The interaction of programmed cell death ligand-1 (PD-L1) and programmed cell death protein-1 (PD-1) plays a key role in tumor-related immune escape and has become one of the most extensive targets for immunotherapy. Herein, we investigated the interaction of PD-L1 with its antibody and PD-1 using atomic force microscopy-based single molecule force spectroscopy for the first time. It was found that the PD-L1/anti-PD-L1 antibody complex was easier to dissociate than PD-L1/PD-1. The unbinding forces of specific interaction of PD-L1 on T24 cells with its antibody and PD-1 were quantitatively measured and similar to those on substrate. In addition, the location of PD-L1 on T24 cells was mapped at the single-molecule level by force-volume mapping. The force maps revealed that PD-L1 randomly distributed on T24 cells surface. The recognition events on cells obviously increased after INF-γ treatment, which proved that INF-γ up-regulated the expression of PD-L1 on T24 cells. These findings enrich our understanding of the molecular mechanisms by which PD-L1 interacts with its antibody and PD-1. It provides useful information for the physical factors that is needed to be considered in the design of inhibitors for tumor immunology.
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Affiliation(s)
- Juan Qin
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P.R. China; University of Science and Technology of China, Hefei, 230026, P.R. China
| | - Miaomiao Zhang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P.R. China; University of Science and Technology of China, Hefei, 230026, P.R. China
| | - Yanxue Guan
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P.R. China; University of Science and Technology of China, Hefei, 230026, P.R. China
| | - Xinyue Guo
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P.R. China; University of Science and Technology of China, Hefei, 230026, P.R. China
| | - Zongjia Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P.R. China; University of Science and Technology of China, Hefei, 230026, P.R. China
| | - Christian Rankl
- Research Center for Non Destructive Testing GmbH, Science Park 2/2. OG, Altenberger Straße 69, A-4040, Linz, Austria
| | - Jilin Tang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P.R. China; University of Science and Technology of China, Hefei, 230026, P.R. China.
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94
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Nie J, Deng Y, Tian F, Shi S, Zheng P. Detection of weak non-covalent cation-π interactions in NGAL by single-molecule force spectroscopy. NANO RESEARCH 2022; 15:4251-4257. [PMID: 35574260 PMCID: PMC9077643 DOI: 10.1007/s12274-021-4065-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 11/23/2021] [Accepted: 12/09/2021] [Indexed: 05/14/2023]
Abstract
Cation-π interaction is an electrostatic interaction between a cation and an electron-rich arene. It plays an essential role in many biological systems as a vital driving force for protein folding, stability, and receptor-ligand interaction/recognition. To date, the discovery of most cation-π interactions in proteins relies on the statistical analyses of available three-dimensional (3D) protein structures and corresponding computational calculations. However, their experimental verification and quantification remain sparse at the molecular level, mainly due to the limited methods to dynamically measure such a weak non-covalent interaction in proteins. Here, we use atomic force microscopy-based single-molecule force spectroscopy (AFM-SMFS) to measure the stability of protein neutrophil gelatinase-associated lipocalin (also known as NGAL, siderocalin, lipocalin 2) that can bind iron through the cation-π interactions between its three cationic residues and the iron-binding tri-catechols. Based on a site-specific cysteine engineering and anchoring method, we first characterized the stability and unfolding pathways of apo-NGAL. Then, the same NGAL but bound with the iron-catechol complexes through the cation-π interactions as a holo-form was characterized. AFM measurements demonstrated stronger stabilities and kinetics of the holo-NGAL from two pulling sites, F122 and F133. Here, NGAL is stretched from the designed cysteine close to the cationic residues for a maximum unfolding effect. Thus, our work demonstrates high-precision detection of the weak cation-π interaction in NGAL. Electronic Supplementary Material Supplementary material (additional SDS-PAGE, UV-vis, protein sequences, and more experimental methods) is available in the online version of this article at 10.1007/s12274-021-4065-9.
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Affiliation(s)
- Jingyuan Nie
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Road, Nanjing, 210023 China
| | - Yibing Deng
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Road, Nanjing, 210023 China
| | - Fang Tian
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Road, Nanjing, 210023 China
| | - Shengchao Shi
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Road, Nanjing, 210023 China
| | - Peng Zheng
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Road, Nanjing, 210023 China
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95
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Nie J, Tian F, Zheng B, Wang Z, Zheng P. Exploration of Metal-Ligand Coordination Bonds in Proteins by Single-molecule Force Spectroscopy. CHEM LETT 2021. [DOI: 10.1246/cl.210307] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Jingyuan Nie
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Fang Tian
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Bin Zheng
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Ziyi Wang
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
| | - Peng Zheng
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, P. R. China
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96
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Pham HA, Truong DT, Li MS. Dependence of Work on the Pulling Speed in Mechanical Ligand Unbinding. J Phys Chem B 2021; 125:8325-8330. [PMID: 34292743 PMCID: PMC8389893 DOI: 10.1021/acs.jpcb.1c01818] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In single-molecule force spectroscopy, the rupture force Fmax required for mechanical unfolding of a biomolecule or for pulling a ligand out of a binding site depends on the pulling speed V and, in the linear Bell-Evans regime, Fmax ∼ ln(V). Recently, it has been found that non-equilibrium work W is better than Fmax in describing relative ligand binding affinity, but the dependence of W on V remains unknown. In this paper, we developed an analytical theory showing that in the linear regime, W ∼ c1 ln(V) + c2 ln2(V), where c1 and c2 are constants. This quadratic dependence was also confirmed by all-atom steered molecular dynamics simulations of protein-ligand complexes. Although our theory was developed for ligand unbinding, it is also applicable to other processes, such as mechanical unfolding of proteins and other biomolecules, due to its universality.
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Affiliation(s)
- Hong An Pham
- Institute for Computational Science and Technology, QuangTrung Software City, Tan Chanh, Hiep Ward, District 12, Ho Chi Minh City 700000, Vietnam
| | - Duc Toan Truong
- Institute for Computational Science and Technology, QuangTrung Software City, Tan Chanh, Hiep Ward, District 12, Ho Chi Minh City 700000, Vietnam
| | - Mai Suan Li
- Institute of Physics, Polish Academy Science, Al. Lotnikow 32/46, Warsaw 02-668, Poland
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97
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Miroshnikova YA, Manet S, Li X, Wickström SA, Faurobert E, Albiges-Rizo C. Calcium signaling mediates a biphasic mechanoadaptive response of endothelial cells to cyclic mechanical stretch. Mol Biol Cell 2021; 32:1724-1736. [PMID: 34081532 PMCID: PMC8684738 DOI: 10.1091/mbc.e21-03-0106] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The vascular system is precisely regulated to adjust blood flow to organismal demand, thereby guaranteeing adequate perfusion under varying physiological conditions. Mechanical forces, such as cyclic circumferential stretch, are among the critical stimuli that dynamically adjust vessel distribution and diameter, but the precise mechanisms of adaptation to changing forces are unclear. We find that endothelial monolayers respond to cyclic stretch by transient remodeling of the vascular endothelial cadherin–based adherens junctions and the associated actomyosin cytoskeleton. Time-resolved proteomic profiling reveals that this remodeling is driven by calcium influx through the mechanosensitive Piezo1 channel, triggering Rho activation to increase actomyosin contraction. As the mechanical stimulus persists, calcium signaling is attenuated through transient down-regulation of Piezo1 protein. At the same time, filamins are phosphorylated to increase monolayer stiffness, allowing mechanoadaptation to restore junctional integrity despite continuing exposure to stretch. Collectively, this study identifies a biphasic response to cyclic stretch, consisting of an initial calcium-driven junctional mechanoresponse, followed by mechanoadaptation facilitated by monolayer stiffening.
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Affiliation(s)
- Yekaterina A Miroshnikova
- Université Grenoble Alpes, Institute for Advanced Biosciences, Grenoble 38042, France.,INSERM U1209, Institute for Advanced Biosciences, F-38700 La Tronche, France.,CNRS UMR 5039, Institute for Advanced Biosciences, F-38700 La Tronche, France.,Max Planck Institute for Biology of Ageing, D-50931 Cologne, Germany.,Helsinki Institute of Life Science, University of Helsinki, FI-00014 Helsinki, Finland.,Wihuri Research Institute, Biomedicum Helsinki, University of Helsinki, FI-00014 Helsinki, Finland.,Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, FI-00014 Helsinki, Finland
| | - Sandra Manet
- Université Grenoble Alpes, Institute for Advanced Biosciences, Grenoble 38042, France.,INSERM U1209, Institute for Advanced Biosciences, F-38700 La Tronche, France.,CNRS UMR 5039, Institute for Advanced Biosciences, F-38700 La Tronche, France
| | - Xinping Li
- Max Planck Institute for Biology of Ageing, D-50931 Cologne, Germany
| | - Sara A Wickström
- Max Planck Institute for Biology of Ageing, D-50931 Cologne, Germany.,Helsinki Institute of Life Science, University of Helsinki, FI-00014 Helsinki, Finland.,Wihuri Research Institute, Biomedicum Helsinki, University of Helsinki, FI-00014 Helsinki, Finland.,Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, FI-00014 Helsinki, Finland
| | - Eva Faurobert
- Université Grenoble Alpes, Institute for Advanced Biosciences, Grenoble 38042, France.,INSERM U1209, Institute for Advanced Biosciences, F-38700 La Tronche, France.,CNRS UMR 5039, Institute for Advanced Biosciences, F-38700 La Tronche, France
| | - Corinne Albiges-Rizo
- Université Grenoble Alpes, Institute for Advanced Biosciences, Grenoble 38042, France.,INSERM U1209, Institute for Advanced Biosciences, F-38700 La Tronche, France.,CNRS UMR 5039, Institute for Advanced Biosciences, F-38700 La Tronche, France
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98
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Galluzzi M, Zhang B, Zhang H, Wang L, Lin Y, Yu XF, Chu Z, Li J. Unveiling a Hidden Event in Fluorescence Correlative Microscopy by AFM Nanomechanical Analysis. Front Mol Biosci 2021; 8:669361. [PMID: 34026842 PMCID: PMC8136518 DOI: 10.3389/fmolb.2021.669361] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 04/22/2021] [Indexed: 11/18/2022] Open
Abstract
Fluorescent imaging combined with atomic force microscopy (AFM), namely AFM-fluorescence correlative microscopy, is a popular technology in life science. However, the influence of involved fluorophores on obtained mechanical information is normally underestimated, and such subtle changes are still challenging to detect. Herein, we combined AFM with laser light excitation to perform a mechanical quantitative analysis of a model membrane system labeled with a commonly used fluorophore. Mechanical quantification was additionally validated by finite element simulations. Upon staining, we noticed fluorophores forming a diffuse weakly organized overlayer on phospholipid supported membrane, easily detected by AFM mechanics. The laser was found to cause a degradation of mechanical stability of the membrane synergically with presence of fluorophore. In particular, a 30 min laser irradiation, with intensity similar to that in typical confocal scanning microscopy experiment, was found to result in a ∼40% decrease in the breakthrough force of the stained phospholipid bilayer along with a ∼30% reduction in its apparent elastic modulus. The findings highlight the significance of analytical power provided by AFM, which will allow us to “see” the “unseen” in correlative microscopy, as well as the necessity to consider photothermal effects when using fluorescent dyes to investigate, for example, the deformability and permeability of phospholipid membranes.
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Affiliation(s)
- Massimiliano Galluzzi
- Materials Interfaces Center, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Bokai Zhang
- Shenzhen Key Laboratory of Nanobiomechanics, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.,DGene (Dongjin Big Health (Shenzhen)) Co., Ltd., Shenzhen, China.,BenHealth Biopharmaceutical (Shenzhen) Co., Ltd., Shenzhen, China
| | - Han Zhang
- Shenzhen Key Laboratory of Nanobiomechanics, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.,State Key Laboratory of Traction Power, Southwest Jiaotong Univerisity, Chengdu, China
| | - Lingzhi Wang
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Hong Kong
| | - Yuan Lin
- Department of Mechanical Engineering, The University of Hong Kong, Hong Kong.,Advanced Biomedical Instrumentation Centre, Shatin, Hong Kong
| | - Xue-Feng Yu
- Materials Interfaces Center, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Zhiqin Chu
- Department of Electrical and Electronic Engineering, Joint Appointment with School of Biomedical Sciences, The University of Hong Kong, Hong Kong
| | - Jiangyu Li
- Shenzhen Key Laboratory of Nanobiomechanics, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.,Department of Materials Science and Engineering, Southern University of Science and Technology, Shenzhen, China
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99
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Miranda A, Gómez-Varela AI, Stylianou A, Hirvonen LM, Sánchez H, De Beule PAA. How did correlative atomic force microscopy and super-resolution microscopy evolve in the quest for unravelling enigmas in biology? NANOSCALE 2021; 13:2082-2099. [PMID: 33346312 DOI: 10.1039/d0nr07203f] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
With the invention of the Atomic Force Microscope (AFM) in 1986 and the subsequent developments in liquid imaging and cellular imaging it became possible to study the topography of cellular specimens under nearly physiological conditions with nanometric resolution. The application of AFM to biological research was further expanded with the technological advances in imaging modes where topographical data can be combined with nanomechanical measurements, offering the possibility to retrieve the biophysical properties of tissues, cells, fibrous components and biomolecules. Meanwhile, the quest for breaking the Abbe diffraction limit restricting microscopic resolution led to the development of super-resolution fluorescence microscopy techniques that brought the resolution of the light microscope comparable to the resolution obtained by AFM. The instrumental combination of AFM and optical microscopy techniques has evolved over the last decades from integration of AFM with bright-field and phase-contrast imaging techniques at first to correlative AFM and wide-field fluorescence systems and then further to the combination of AFM and fluorescence based super-resolution microscopy modalities. Motivated by the many developments made over the last decade, we provide here a review on AFM combined with super-resolution fluorescence microscopy techniques and how they can be applied for expanding our understanding of biological processes.
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Affiliation(s)
- Adelaide Miranda
- International Iberian Nanotechnology Laboratory, Avenida Mestre José Veiga s/n, Braga, Portugal.
| | - Ana I Gómez-Varela
- International Iberian Nanotechnology Laboratory, Avenida Mestre José Veiga s/n, Braga, Portugal. and Department of Applied Physics, University of Santiago de Compostela, E-15782, Santiago de Compostela, Spain.
| | - Andreas Stylianou
- Cancer Biophysics Laboratory, University of Cyprus, Nicosia, Cyprus and School of Sciences, European University Cyprus, Nicosia, Cyprus
| | - Liisa M Hirvonen
- Centre for Microscopy, Characterisation and Analysis (CMCA), The University of Western Australia, 35 Stirling Highway, Perth, WA 6009, Australia
| | - Humberto Sánchez
- Faculty of Applied Sciences, Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ, Delft, The Netherlands
| | - Pieter A A De Beule
- International Iberian Nanotechnology Laboratory, Avenida Mestre José Veiga s/n, Braga, Portugal.
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