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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: 0] [Impact Index Per Article: 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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Cheng H, Yu J, Wang Z, Ma P, Guo C, Wang B, Zhong W, Xu B. Details of Single-Molecule Force Spectroscopy Data Decoded by a Network-Based Automatic Clustering Algorithm. J Phys Chem B 2021; 125:9660-9667. [PMID: 34425052 DOI: 10.1021/acs.jpcb.1c03552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Atomic force microscopy-single-molecule force spectroscopy (AFM-SMFS) is a powerful methodology to probe intermolecular and intramolecular interactions in biological systems because of its operability in physiological conditions, facile and rapid sample preparation, versatile molecular manipulation, and combined functionality with high-resolution imaging. Since a huge number of AFM-SMFS force-distance curves are collected to avoid human bias and errors and to save time, numerous algorithms have been developed to analyze the AFM-SMFS curves. Nevertheless, there is still a need to develop new algorithms for the analysis of AFM-SMFS data since the current algorithms cannot specify an unbinding force to a corresponding/each binding site due to the lack of networking functionality to model the relationship between the unbinding forces. To address this challenge, herein, we develop an unsupervised method, i.e., a network-based automatic clustering algorithm (NASA), to decode the details of specific molecules, e.g., the unbinding force of each binding site, given the input of AFM-SMFS curves. Using the interaction of heparan sulfate (HS)-antithrombin (AT) on different endothelial cell surfaces as a model system, we demonstrate that NASA is able to automatically detect the peak and calculate the unbinding force. More importantly, NASA successfully identifies three unbinding force clusters, which could belong to three different binding sites, for both Ext1f/f and Ndst1f/f cell lines. NASA has great potential to be applied either readily or slightly modified to other AFM-based SMFS measurements that result in "saw-tooth"-shaped force-distance curves showing jumps related to the force unbinding, such as antibody-antigen interaction and DNA-protein interaction.
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Affiliation(s)
- Huimin Cheng
- Big Data Analytics Lab, Department of Statistics, University of Georgia, Athens, Georgia 30602, United States
| | - Jun Yu
- School of Mathematics and Statistics, Beijing Institute of Technology, Beijing 100081, P. R. China
| | - Zhen Wang
- Big Data Analytics Lab, Department of Statistics, University of Georgia, Athens, Georgia 30602, United States
| | - Ping Ma
- Big Data Analytics Lab, Department of Statistics, University of Georgia, Athens, Georgia 30602, United States
| | - Cunlan Guo
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China.,Single Molecule Study Laboratory, College of Engineering, University of Georgia, Athens, Georgia 30602, United States
| | - Bin Wang
- Single Molecule Study Laboratory, College of Engineering, University of Georgia, Athens, Georgia 30602, United States
| | - Wenxuan Zhong
- Big Data Analytics Lab, Department of Statistics, University of Georgia, Athens, Georgia 30602, United States
| | - Bingqian Xu
- Single Molecule Study Laboratory, College of Engineering, University of Georgia, Athens, Georgia 30602, United States
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Liu J, Ren X, Yan W, Li C, Zhang H, Jia Y, Zeng X, Chen W, Gao X, Liu D, Tan X, Zhang X, Ni T, Zhang H, Zuo W, Su Y, Wen W. Descent trajectory reconstruction and landing site positioning of Chang'E-4 on the lunar farside. Nat Commun 2019; 10:4229. [PMID: 31551413 PMCID: PMC6760200 DOI: 10.1038/s41467-019-12278-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 08/23/2019] [Indexed: 12/02/2022] Open
Abstract
Chang'E-4 (CE-4) was the first mission to accomplish the goal of a successful soft landing on the lunar farside. The landing trajectory and the location of the landing site can be effectively reconstructed and determined using series of images obtained during descent when there were no Earth-based radio tracking and the telemetry data. Here we reconstructed the powered descent trajectory of CE-4 using photogrammetrically processed images of the CE-4 landing camera, navigation camera, and terrain data of Chang'E-2. We confirmed that the precise location of the landing site is 177.5991°E, 45.4446°S with an elevation of -5935 m. The landing location was accurately identified with lunar imagery and terrain data with spatial resolutions of 7 m/p, 5 m/p, 1 m/p, 10 cm/p and 5 cm/p. These results will provide geodetic data for the study of lunar control points, high-precision lunar mapping, and subsequent lunar exploration, such as by the Yutu-2 rover.
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Affiliation(s)
- Jianjun Liu
- Key Laboratory of Lunar and Deep Space Exploration, National Astronomical Observatories, Chinese Academy of Sciences, Beijing, 100101, China
- School of Astronomy and Space Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xin Ren
- Key Laboratory of Lunar and Deep Space Exploration, National Astronomical Observatories, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wei Yan
- Key Laboratory of Lunar and Deep Space Exploration, National Astronomical Observatories, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chunlai Li
- Key Laboratory of Lunar and Deep Space Exploration, National Astronomical Observatories, Chinese Academy of Sciences, Beijing, 100101, China.
- School of Astronomy and Space Science, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - He Zhang
- China Academy of Space Technology, Beijing, 100094, China
| | - Yang Jia
- China Academy of Space Technology, Beijing, 100094, China
| | - Xingguo Zeng
- Key Laboratory of Lunar and Deep Space Exploration, National Astronomical Observatories, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wangli Chen
- Key Laboratory of Lunar and Deep Space Exploration, National Astronomical Observatories, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xingye Gao
- Key Laboratory of Lunar and Deep Space Exploration, National Astronomical Observatories, Chinese Academy of Sciences, Beijing, 100101, China
| | - Dawei Liu
- Key Laboratory of Lunar and Deep Space Exploration, National Astronomical Observatories, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xu Tan
- Key Laboratory of Lunar and Deep Space Exploration, National Astronomical Observatories, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaoxia Zhang
- Key Laboratory of Lunar and Deep Space Exploration, National Astronomical Observatories, Chinese Academy of Sciences, Beijing, 100101, China
| | - Tao Ni
- Key Laboratory of Lunar and Deep Space Exploration, National Astronomical Observatories, Chinese Academy of Sciences, Beijing, 100101, China
- School of Astronomy and Space Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hongbo Zhang
- Key Laboratory of Lunar and Deep Space Exploration, National Astronomical Observatories, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wei Zuo
- Key Laboratory of Lunar and Deep Space Exploration, National Astronomical Observatories, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yan Su
- Key Laboratory of Lunar and Deep Space Exploration, National Astronomical Observatories, Chinese Academy of Sciences, Beijing, 100101, China
| | - Weibin Wen
- Key Laboratory of Lunar and Deep Space Exploration, National Astronomical Observatories, Chinese Academy of Sciences, Beijing, 100101, China
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QIN GG, LI WH, XU JC, KOU XL, ZHAO R, LUO F, FANG XH. Development of Integrated Atomic Force Microscopy and Fluorescence Microscopy for Single-Molecule Analysis in Living Cells. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2017. [DOI: 10.1016/s1872-2040(17)61056-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Wei Y, Lai B, Liu H, Li Y, Zhen W, Fu L. Effect of cigarette smoke extract and nicotine on the expression of thrombomodulin and endothelial protein C receptor in cultured human umbilical vein endothelial cells. Mol Med Rep 2017; 17:1724-1730. [PMID: 29257196 PMCID: PMC5780117 DOI: 10.3892/mmr.2017.8070] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 09/28/2017] [Indexed: 01/15/2023] Open
Abstract
The present study investigated the influence of cigarette smoke extract (CSE) and nicotine on the expression of thrombomodulin (TM) and endothelial protein C receptor (EPCR) in human umbilical vein endothelial cells (HUVECs). Smoking is associated with intravascular thrombosis. As a vital anticoagulation cofactor, TM is located on the endothelial cell surface and regulates intravascular coagulation by binding to thrombin, hence activating protein C. Activated protein C is a natural anticoagulant that interacts with EPCR to enhance the function of anticoagulation system. The effects of CSE (0.5–5%) and nicotine (10-3-10-9 mol/l) on the expression of TM and EPCR in HUVECs were observed. Reverse transcription-quantitative polymerase chain reaction and flow cytometric analysis techniques were used for detecting TM and EPCR mRNA and protein expression levels, respectively. After 6-h exposure, TM protein and mRNA expression levels decreased in a dose-dependent manner. Stimulation with 5% CSE for 0, 6, 10, 12 and 24 h led to a decrease in the levels of TM mRNA and protein over time, which reached a peak at 12 h. The levels were significantly reduced compared with the control group (P<0.001). However, CSE had no effect on EPCR. Furthermore, nicotine had no influence on TM and EPCR. In conclusion, the present study supports a novel molecular mechanism of cigarette smoking-associated thrombosis by the decreased expression of TM. Further studies are required to identify specific components in CSE responsible for decreasing TM expression and its associated consequences.
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Affiliation(s)
- Yujie Wei
- Institute of Cardiology, the General Hospital of Chinese People's Armed Police Forces, Beijing 100039, P.R. China
| | - Bin Lai
- Department of Emergency, the General Hospital of Chinese People's Armed Police Forces, Beijing 100039, P.R. China
| | - Huiliang Liu
- Institute of Cardiology, the General Hospital of Chinese People's Armed Police Forces, Beijing 100039, P.R. China
| | - Yi Li
- Institute of Cardiology, the General Hospital of Chinese People's Armed Police Forces, Beijing 100039, P.R. China
| | - Wang Zhen
- Institute of Cardiology, the General Hospital of Chinese People's Armed Police Forces, Beijing 100039, P.R. China
| | - Ling Fu
- Institute of Biotechnology, Academy of Military Medical Sciences, Beijing 100071, P.R. China
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Wang Q, Liu L, Yang X, Wang K, Chen N, Zhou C, Luo B, Du S. Evaluation of medicine effects on the interaction of myoglobin and its aptamer or antibody using atomic force microscopy. Anal Chem 2015; 87:2242-8. [PMID: 25615803 DOI: 10.1021/ac503885e] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The effects of medicine on the biomolecular interaction have been given increasing attention in biochemistry and affinity-based analytics since the environment in vivo is complex especially for the patients. Herein, myoglobin, a biomarker of acute myocardial infarction, was used as a model, and the medicine effects on the interactions of myoglobin/aptamer and myoglobin/antibody were systematically investigated using atomic force microscopy (AFM) for the first time. The results showed that the average binding force and the binding probability of myoglobin/aptamer almost remained unchanged after myoglobin-modified gold substrate was incubated with promazine, amoxicillin, aspirin, and sodium penicillin, respectively. These parameters were changed for myoglobin/antibody after the myoglobin-modified gold substrate was treated with these medicines. For promazine and amoxicillin, they resulted in the change of binding force distribution of myoglobin/antibody (i.e., from unimodal distribution to bimodal distribution) and the increase of binding probability; for aspirin, it only resulted in the change of the binding force distribution, and for sodium penicillin, it resulted in the increase of the average binding force and the binding probability. These results may be attributed to the different interaction modes and binding sites between myoglobin/aptamer and myoglobin/antibody, the different structures between aptamer and antibody, and the effects of medicines on the conformations of myoglobin. These findings could enrich our understanding of medicine effects on the interactions of aptamer and antibody to their target proteins. Moreover, this work will lay a good foundation for better research and extensive applications of biomolecular interaction, especially in the design of biosensors in complex systems.
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Affiliation(s)
- Qing Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University , Changsha, Hunan 410082, P. R. China
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Zhang P, Huang W, Jia Z, Zhou C, Guo M, Wang Y. Conformation and adsorption behavior of associative polymer for enhanced oil recovery using single molecule force spectroscopy. JOURNAL OF POLYMER RESEARCH 2014. [DOI: 10.1007/s10965-014-0523-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Bai R, Yi S, Zhang X, Liu H, Fang X. Role of ICAM-1 polymorphisms (G241R, K469E) in mediating its single-molecule binding ability: Atomic force microscopy measurements on living cells. Biochem Biophys Res Commun 2014; 448:372-8. [DOI: 10.1016/j.bbrc.2014.04.113] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 04/22/2014] [Indexed: 11/24/2022]
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Wang C, Yadavalli VK. Investigating biomolecular recognition at the cell surface using atomic force microscopy. Micron 2014; 60:5-17. [PMID: 24602267 DOI: 10.1016/j.micron.2014.01.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 01/07/2014] [Accepted: 01/07/2014] [Indexed: 10/25/2022]
Abstract
Probing the interaction forces that drive biomolecular recognition on cell surfaces is essential for understanding diverse biological processes. Force spectroscopy has been a widely used dynamic analytical technique, allowing measurement of such interactions at the molecular and cellular level. The capabilities of working under near physiological environments, combined with excellent force and lateral resolution make atomic force microscopy (AFM)-based force spectroscopy a powerful approach to measure biomolecular interaction forces not only on non-biological substrates, but also on soft, dynamic cell surfaces. Over the last few years, AFM-based force spectroscopy has provided biophysical insight into how biomolecules on cell surfaces interact with each other and induce relevant biological processes. In this review, we focus on describing the technique of force spectroscopy using the AFM, specifically in the context of probing cell surfaces. We summarize recent progress in understanding the recognition and interactions between macromolecules that may be found at cell surfaces from a force spectroscopy perspective. We further discuss the challenges and future prospects of the application of this versatile technique.
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Affiliation(s)
- Congzhou Wang
- Department of Chemical and Life Science Engineering, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Vamsi K Yadavalli
- Department of Chemical and Life Science Engineering, Virginia Commonwealth University, Richmond, VA 23284, USA.
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Shi X, Zhang X, Xia T, Fang X. Living cell study at the single-molecule and single-cell levels by atomic force microscopy. Nanomedicine (Lond) 2012; 7:1625-37. [DOI: 10.2217/nnm.12.130] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Atomic force microscopy (AFM) has been emerging as a multifunctional molecular tool in nanobiology and nanomedicine. This review summarizes the recent advances in AFM study of living mammalian cells at the single-molecule and single-cell levels. Besides nanoscale imaging of cell membrane structure, AFM-based force measurements on living cells are mainly discussed. These include the development and application of single-molecule force spectroscopy to investigate ligand–receptor binding strength and dissociation dynamics, and the characterization of cell mechanical properties in a physiological environment. Molecular manipulation of cells by AFM to change the cellular process is also described. Living-cell AFM study offers a new approach to understand the molecular mechanisms of cell function, disease development and drug effect, as well as to develop new strategies to achieve single-cell-based diagnosis.
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Affiliation(s)
- Xiaoli Shi
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, 2 Zhongguancun North First Street, 100190 Beijing, PR China
| | - Xuejie Zhang
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, 2 Zhongguancun North First Street, 100190 Beijing, PR China
| | - Tie Xia
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, 2 Zhongguancun North First Street, 100190 Beijing, PR China
| | - Xiaohong Fang
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, 2 Zhongguancun North First Street, 100190 Beijing, PR China
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Wei Y, Zhang X, Xu L, Yi S, Li Y, Fang X, Liu H. The effect of cigarette smoke extract on thrombomodulin-thrombin binding: an atomic force microscopy study. SCIENCE CHINA. LIFE SCIENCES 2012; 55:891-7. [PMID: 23108866 DOI: 10.1007/s11427-012-4383-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2012] [Accepted: 08/07/2012] [Indexed: 10/27/2022]
Abstract
Cigarette smoking is a well-known risk factor for cardiovascular disease. Smoking can cause vascular endothelial dysfunction and consequently trigger haemostatic activation and thrombosis. However, the mechanism of how smoking promotes thrombosis is not fully understood. Thrombosis is associated with the imbalance of the coagulant system due to endothelial dysfunction. As a vital anticoagulation cofactor, thrombomodulin (TM) located on the endothelial cell surface is able to regulate intravascular coagulation by binding to thrombin, and the binding results in thrombosis inhibition. This work focused on the effects of cigarette smoke extract (CSE) on TM-thrombin binding by atomic force microscopy (AFM) based single-molecule force spectroscopy. The results from both in vitro and live-cell experiments indicated that CSE could notably reduce the binding probability of TM and thrombin. This study provided a new approach and new evidence for studying the mechanism of thrombosis triggered by cigarette smoking.
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Affiliation(s)
- Yujie Wei
- Department of Cardiology, the General Hospital of Chinese People's Armed Police Forces, Beijing 100039, China
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