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Chakraborty I, Rahamim G, Avinery R, Roichman Y, Beck R. Nanoparticle Mobility over a Surface as a Probe for Weak Transient Disordered Peptide-Peptide Interactions. NANO LETTERS 2019; 19:6524-6534. [PMID: 31456409 DOI: 10.1021/acs.nanolett.9b02764] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Weak interactions form the core basis of a vast number of biological processes, in particular, those involving intrinsically disordered proteins. Here, we establish a new technique capable of probing these weak interactions between synthetic unfolded polypeptides using a convenient yet efficient, quantitative method based on single particle tracking of peptide-coated gold nanoparticles over peptide-coated surfaces. We demonstrate that our technique is sensitive enough to observe the influence of a single amino acid mutation on the transient peptide-peptide interactions. Furthermore, the effects of buffer salinity, which are expected to alter weak electrostatic interactions, are also readily detected and examined in detail. The method presented here has the potential to evaluate, in a high-throughput manner, weak interactions for a wide range of disordered proteins, polypeptides, and other biomolecules.
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Affiliation(s)
| | - Gil Rahamim
- School of Physics and Astronomy , Tel Aviv University , Tel Aviv 6997801 , Israel
| | - Ram Avinery
- School of Physics and Astronomy , Tel Aviv University , Tel Aviv 6997801 , Israel
| | - Yael Roichman
- School of Chemistry , Tel Aviv University , Tel Aviv 6997801 , Israel
- School of Physics and Astronomy , Tel Aviv University , Tel Aviv 6997801 , Israel
| | - Roy Beck
- School of Physics and Astronomy , Tel Aviv University , Tel Aviv 6997801 , Israel
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Liu J, Wang X, Zhang W. Atomic Force Microscopy Imaging Study of Aligning DNA by Dumbbell-like Au-Fe 3O 4 Magnetic Nanoparticles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:14875-14881. [PMID: 30011364 DOI: 10.1021/acs.langmuir.8b01784] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Studies on nucleic acid structure and interactions between nucleic acid and its binding molecules are of great importance for understanding and controlling many important biological processes. Atomic force microscopy (AFM) imaging is one of the most efficient methods to disclose the DNA structure and binding modes between DNA and DNA-binding molecules. Long-chain DNA tends to form a random coiled structure, which prevents direct AFM imaging observation of the subtle structure formed by DNA itself or protein binding. Aligning DNA from the random coiled state into the extended state is not only important for applications in DNA nanotechnology but also for elucidating the interaction mechanism between DNA and other molecules. Here, we developed an efficient method based on the magnetic field to align long-chain DNA on a silicon surface. We used AFM imaging to study the alignment of DNA at the single-molecule level, showing that DNA can be stretched and highly aligned by the manipulation of magnetic nanoparticles tethered to one end of DNA and that the aligned DNA can be imaged clearly by AFM. In the absence of the magnetic field, the aligned DNA can relax back to a random coiled state upon rinsing. Such alignment and relaxation can be repeated many times, which provides an efficient method for the manipulation of individual DNA molecules and the investigation of DNA and DNA-binding molecule interactions.
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Affiliation(s)
- Jianyu Liu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry , Jilin University , Changchun 130012 , People's Republic of China
| | - Xinxin Wang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry , Jilin University , Changchun 130012 , People's Republic of China
| | - Wenke Zhang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry , Jilin University , Changchun 130012 , People's Republic of China
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Gan C, Wang K, Tang Q, Chen Y. Comparative investigation on the sizes and scavenger receptor binding of human native and modified lipoprotein particles with atomic force microscopy. J Nanobiotechnology 2018; 16:25. [PMID: 29592798 PMCID: PMC5872389 DOI: 10.1186/s12951-018-0352-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 03/13/2018] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND The size and receptor-binding abilities of plasma lipoproteins are closely related with their structure/functions. Presently, the sizes of native lipoproteins have been measured by various methods including atomic force microscopy (AFM) whereas the sizes of modified lipoproteins are poorly determined and the receptor-binding ability of lipoproteins is less detected and compared at the nanoscale. METHODS Here, AFM was utilized to detect/compare the size and scavenger receptor-binding properties of three native human lipoproteins including high-density lipoprotein, low-density lipoprotein (LDL), and very low-density lipoprotein, and two modified human lipoproteins including oxidized and acetylated LDL, as well as bovine serum albumin and their antibodies as negative and positive controls, respectively. RESULTS AFM detected that the sizes of these lipoproteins are close to the commonly known values and the previously-reported AFM-detected sizes and that native and modified LDL have different height/size. AFM also revealed that the CD36-binding abilities of the five lipoproteins are different from one another and from their SR-B1-binding abilities and that the anti-CD36/SR-B1 antibodies as positive controls have strong CD36/SR-B1-binding abilities. CONCLUSIONS The data provide important information on lipoproteins for better understanding their structures/functions. Moreover, the data certify that besides size measurement AFM also can visualize receptor-lipoprotein binding at the nanoscale, as well as antigen-antibody (scavenger receptors and their antibodies) binding.
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Affiliation(s)
- Chaoye Gan
- Nanoscale Science and Technology Laboratory, Institute for Advanced Study, Nanchang University, 999 Xuefu Ave., Honggutan District, Nanchang, 330031, Jiangxi, China.,College of Life Sciences, Nanchang University, Nanchang, 330031, Jiangxi, China
| | - Kun Wang
- Nanoscale Science and Technology Laboratory, Institute for Advanced Study, Nanchang University, 999 Xuefu Ave., Honggutan District, Nanchang, 330031, Jiangxi, China.,College of Life Sciences, Nanchang University, Nanchang, 330031, Jiangxi, China
| | - Qisheng Tang
- Nanoscale Science and Technology Laboratory, Institute for Advanced Study, Nanchang University, 999 Xuefu Ave., Honggutan District, Nanchang, 330031, Jiangxi, China.,College of Life Sciences, Nanchang University, Nanchang, 330031, Jiangxi, China
| | - Yong Chen
- Nanoscale Science and Technology Laboratory, Institute for Advanced Study, Nanchang University, 999 Xuefu Ave., Honggutan District, Nanchang, 330031, Jiangxi, China. .,College of Life Sciences, Nanchang University, Nanchang, 330031, Jiangxi, China.
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Braet F, Taatjes DJ. Foreword to the special issue on applications of atomic force microscopy in cell biology. Semin Cell Dev Biol 2017; 73:1-3. [PMID: 28673678 DOI: 10.1016/j.semcdb.2017.06.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 06/28/2017] [Accepted: 06/29/2017] [Indexed: 10/19/2022]
Affiliation(s)
- Filip Braet
- School of Medical Sciences (Discipline of Anatomy and Histology) - The Bosch Institute, The University of Sydney, NSW 2006, Australia; Australian Centre for Microscopy & Microanalysis, The University of Sydney, NSW 2006, Australia; Charles Perkins Centre (Cellular Imaging Facility), The University of Sydney, NSW 2006, Australia.
| | - Douglas J Taatjes
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, VT, 05405, USA; Microscopy Imaging Center, Larner College of Medicine, University of Vermont, Burlington, VT, 05405, USA.
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Narita A, Usukura E, Yagi A, Tateyama K, Akizuki S, Kikumoto M, Matsumoto T, Maéda Y, Ito S, Usukura J. Direct observation of the actin filament by tip-scan atomic force microscopy. Microscopy (Oxf) 2016; 65:370-7. [PMID: 27242058 PMCID: PMC5895109 DOI: 10.1093/jmicro/dfw017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 04/28/2016] [Indexed: 11/13/2022] Open
Abstract
Actin filaments, the actin–myosin complex and the actin–tropomyosin complex were observed by a tip-scan atomic force microscope (AFM), which was recently developed by Olympus as the AFM part of a correlative microscope. This newly developed AFM uses cantilevers of similar size as stage-scan AFMs to improve substantially the spatial and temporal resolution. Such an approach has previously never been possible by a tip-scan system, in which a cantilever moves in the x, y and z directions. We evaluated the performance of this developed tip-scan AFM by observing the molecular structure of actin filaments and the actin–tropomyosin complex. In the image of the actin filament, the molecular interval of the actin subunits (∼5.5 nm) was clearly observed as stripes. From the shape of the stripes, the polarity of the actin filament was directly determined and the results were consistent with the polarity determined by myosin binding. In the image of the actin–tropomyosin complex, each tropomyosin molecule (∼2 nm in diameter) on the actin filament was directly observed without averaging images of different molecules. Each tropomyosin molecule on the actin filament has never been directly observed by AFM or electron microscopy. Thus, our developed tip-scan AFM offers significant potential in observing purified proteins and cellular structures at nanometer resolution. Current results represent an important step in the development of a new correlative microscope to observe nm-order structures at an acceptable frame rate (∼10 s/frame) by AFM at the position indicated by the fluorescent dye observed under a light microscope.
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Affiliation(s)
- Akihiro Narita
- Structural Biology Research Center, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan JST PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
| | - Eiji Usukura
- Structural Biology Research Center, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
| | - Akira Yagi
- R&D Group, Olympus Corporation, 2-3 Kuboyama-cho, Hachioji, Tokyo 192-8512, Japan
| | - Kiyohiko Tateyama
- R&D Group, Olympus Corporation, 2-3 Kuboyama-cho, Hachioji, Tokyo 192-8512, Japan
| | - Shogo Akizuki
- Structural Biology Research Center, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
| | - Mahito Kikumoto
- Structural Biology Research Center, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
| | - Tomoharu Matsumoto
- Structural Biology Research Center, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
| | - Yuichiro Maéda
- Structural Biology Research Center, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
| | - Shuichi Ito
- R&D Group, Olympus Corporation, 2-3 Kuboyama-cho, Hachioji, Tokyo 192-8512, Japan
| | - Jiro Usukura
- Structural Biology Research Center, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
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