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Kalita M, Yadav K, Archana A, Gopakumar TG, Vasudev PG, Ramapanicker R. Incorporation of phenylcarbonyl groups in the sidechain: A tool to induce ordered assembly of peptides on surfaces. J Pept Sci 2024:e3629. [PMID: 38898708 DOI: 10.1002/psc.3629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 05/16/2024] [Accepted: 06/05/2024] [Indexed: 06/21/2024]
Abstract
The possibility of introducing various functionalities on peptides with relative ease allows them to be used for molecular applications. However, oligopeptides prepared entirely from proteinogenic amino acids seldom assemble as ordered structures on surfaces. Therefore, sidechain modifications of peptides that can increase the intermolecular interactions without altering the constitution of a given peptide become an attractive route to self-assembling them on surfaces. We find that replacing phenylalanine residues with unusual amino acids that have phenylcarbonyl sidechains in oligopeptides increases the formation of ordered self-assembly on a highly ordered pyrolytic graphite surface. Peptides containing the modified amino acids provided extended long-range ordered assemblies, while the analogous peptides containing phenylalanine residues failed to form long-range assemblies. X-ray crystallographic analysis of the bulk structures of these peptides and the analogous peptides containing phenylalanine residues reveal that such modifications do not alter the secondary structure in crystals. It also reveals that the secondary hydrogen bonding interaction through phenylcarbonyl sidechains facilitates extended growth of the peptides on graphite.
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Affiliation(s)
- Mrinal Kalita
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Khushboo Yadav
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Archana Archana
- Molecular and Structural Biology Department, CSIR - Central Institute of Medicinal and Aromatic Plants, Lucknow, India
| | | | - Prema G Vasudev
- Molecular and Structural Biology Department, CSIR - Central Institute of Medicinal and Aromatic Plants, Lucknow, India
| | - Ramesh Ramapanicker
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
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2
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Sønderby TV, Zou Y, Wang P, Wang C, Otzen DE. Molecular-level insights into the surface-induced assembly of functional bacterial amyloid. Biophys J 2022; 121:3422-3434. [PMID: 35982614 PMCID: PMC9515228 DOI: 10.1016/j.bpj.2022.08.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 08/07/2022] [Accepted: 08/15/2022] [Indexed: 11/26/2022] Open
Abstract
Protein coating material is important in many technological fields. The interaction between carbon nanomaterial and protein is especially interesting since it makes the development of novel hybrid materials possible. Functional bacterial amyloid (FuBA) is promising as a coating material because of its desirable features, such as well-defined molecular structure, robustness against harsh conditions, and easily engineerable functionality. Here, we report the systematic assembly of the functional amyloid protein, CsgA, from Escherichia coli (E. coli) on graphite. We characterize the assemblies using scanning tunneling microscopy (STM) and show that CsgA forms assemblies according to systematic patterns, dictated by the graphite lattice. In addition, we show that graphite flakes induce the fibrillization of CsgA, in vitro, suggesting a surface-induced conformational change of CsgA facilitated by the graphite lattice. Using coarse-grained molecular dynamics simulations, we model the adhesion and lamellar formation of a CsgA-derived peptide and conclude that peptides are adsorbed both as monomers and smaller aggregates leading initially to unordered graphite-bound aggregates, which are followed by rearrangement into lamellar structures. Finally, we show that CsgA-derived peptides can be immobilized in very systematic assemblies and their molecular orientation can be tuned using a small chaperone-like molecule. Our findings have implications for the development of FuBA-based biosensors, catalysts, and other technologies requiring well-defined protein assemblies on graphite.
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Affiliation(s)
- Thorbjørn Vincent Sønderby
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, Denmark; Sino-Danish Center (SDC), Eastern Yanqihu Campus, University of Chinese Academy of Sciences, Beijing, China
| | - Yimin Zou
- National Center for Nanoscience and Technology, Beijing, China
| | - Pengyu Wang
- National Center for Nanoscience and Technology, Beijing, China
| | - Chen Wang
- National Center for Nanoscience and Technology, Beijing, China.
| | - Daniel Erik Otzen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, Denmark.
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3
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Mukherjee D, Das P, Prasad GN, Katha AR, Gumma S, Mandal B. Hierarchical graphite oxide decorated UiO-66 for ultrahigh adsorption of dye with synergistic effect of ultrasonication: Experimental and density functional theory study. Sep Purif Technol 2022. [DOI: 10.1016/j.seppur.2022.121217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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4
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Ealias AM, Saravanakumar MP. Application of protein-functionalised aluminium nanosheets synthesised from sewage sludge for dye removal in a fixed-bed column: Investigation on design parameters and kinetic models. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:2955-2976. [PMID: 31836990 DOI: 10.1007/s11356-019-07139-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 11/20/2019] [Indexed: 06/10/2023]
Abstract
Protein-functionalised aluminium nanosheets (PRS-AlNs) were packed in a continuous fixed-bed column to remove crystal violet (CV) and Congo red (CR) dyes. A group of characterisation techniques, like SEM, TEM, AFM, XRD, BET, DSC and Raman spectroscopy, was performed for PRS-AlNs. The influence of several factors like bed depth (1, 2 and 3 cm), inlet dye concentration (50, 100 and 150 mg/L) and inlet flow rate (1.17, 2.26 and 3.34 mL/min) on the characteristics of the breakthrough profile of the adsorption process was examined at optimum pH 9.8 and 3.5 for CV and CR, respectively. The maximum adsorption capacity was achieved as 38.70 and 57.86 mg/g for CV and CR at 1 cm bed depth, 150 mg/L inlet concentration of the dye and 3.34 mL/min inlet rate of flow. The experimental data were analysed using kinetic models like the Yoon-Nelson, Adams-Bohart and Thomas models. Also, a detailed mechanism behind the CV and CR adsorption using PRS-AlNs was proposed in this research work. Graphical abstract .
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Affiliation(s)
- Anu Mary Ealias
- Department of Environmental & Water Resources Engineering, School of Civil Engineering, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| | - Manickam Puratchiveeran Saravanakumar
- Department of Environmental & Water Resources Engineering, School of Civil Engineering, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India.
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5
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Lin Y, Xu J, Yu L, Yang Y, Wang C. Probing Molecular Basis for Constructing Interface Bionanostructures. Top Catal 2018. [DOI: 10.1007/s11244-018-0953-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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6
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Claridge SA, Thomas JC, Silverman MA, Schwartz JJ, Yang Y, Wang C, Weiss PS. Differentiating amino acid residues and side chain orientations in peptides using scanning tunneling microscopy. J Am Chem Soc 2013; 135:18528-35. [PMID: 24219245 PMCID: PMC4117194 DOI: 10.1021/ja408550a] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Single-molecule measurements of complex biological structures such as proteins are an attractive route for determining structures of the large number of important biomolecules that have proved refractory to analysis through standard techniques such as X-ray crystallography and nuclear magnetic resonance. We use a custom-built low-current scanning tunneling microscope to image peptide structures at the single-molecule scale in a model peptide that forms β sheets, a structural motif common in protein misfolding diseases. We successfully differentiate between histidine and alanine amino acid residues, and further differentiate side chain orientations in individual histidine residues, by correlating features in scanning tunneling microscope images with those in energy-optimized models. Beta sheets containing histidine residues are used as a model system due to the role histidine plays in transition metal binding associated with amyloid oligomerization in Alzheimer's and other diseases. Such measurements are a first step toward analyzing peptide and protein structures at the single-molecule level.
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Affiliation(s)
- Shelley A. Claridge
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095-7227, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095-7227, United States
| | - John C. Thomas
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095-7227, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095-7227, United States
| | - Miles A. Silverman
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095-7227, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095-7227, United States
| | - Jeffrey J. Schwartz
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095-7227, United States
- Department of Physics and Astronomy, University of California, Los Angeles, Los Angeles, CA 90095-7227, United States
| | - Yanlian Yang
- National Center for Nanoscience and Technology, Beijing 100190, PR China
| | - Chen Wang
- National Center for Nanoscience and Technology, Beijing 100190, PR China
| | - Paul S. Weiss
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095-7227, United States
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095-7227, United States
- Department of Physics and Astronomy, University of California, Los Angeles, Los Angeles, CA 90095-7227, United States
- Department of Materials Science and Engineering, University of California, Los Angeles, Los Angeles, CA 90095-7227, United States
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7
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Claridge SA, Liao WS, Thomas JC, Zhao Y, Cao H, Cheunkar S, Serino AC, Andrews AM, Weiss PS. From the bottom up: dimensional control and characterization in molecular monolayers. Chem Soc Rev 2013; 42:2725-45. [PMID: 23258565 PMCID: PMC3596502 DOI: 10.1039/c2cs35365b] [Citation(s) in RCA: 106] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Self-assembled monolayers are a unique class of nanostructured materials, with properties determined by their molecular lattice structures, as well as the interfaces with their substrates and environments. As with other nanostructured materials, defects and dimensionality play important roles in the physical, chemical, and biological properties of the monolayers. In this review, we discuss monolayer structures ranging from surfaces (two-dimensional) down to single molecules (zero-dimensional), with a focus on applications of each type of structure, and on techniques that enable characterization of monolayer physical properties down to the single-molecule scale.
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Affiliation(s)
- Shelley A. Claridge
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry & Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Wei-Ssu Liao
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry & Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - John C. Thomas
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry & Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Yuxi Zhao
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry & Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Huan Cao
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry & Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Sarawut Cheunkar
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry & Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Andrew C. Serino
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry & Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Anne M. Andrews
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry & Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Psychiatry, University of California, Los Angeles, Los Angeles, California 90095, United States
- Semel Institute for Neuroscience & Human Behavior, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Paul S. Weiss
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry & Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Materials Science & Engineering, University of California, Los Angeles, Los Angeles, California 90095, United States
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8
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Mao X, Guo Y, Luo Y, Niu L, Liu L, Ma X, Wang H, Yang Y, Wei G, Wang C. Sequence Effects on Peptide Assembly Characteristics Observed by Using Scanning Tunneling Microscopy. J Am Chem Soc 2013; 135:2181-7. [DOI: 10.1021/ja307198u] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xiaobo Mao
- National Center for Nanoscience and Technology, 11 Beiyitiao Zhongguancun,
Beijing 100190, China
| | - Yuanyuan Guo
- National Center for Nanoscience and Technology, 11 Beiyitiao Zhongguancun,
Beijing 100190, China
| | - Yin Luo
- State
Key Laboratory of Surface
Physics, Key Laboratory for Computational Physical Sciences (Ministry
of Education), and Department of Physics, Fudan University, 220 Handan Road, Shanghai 200433, China
| | - Lin Niu
- National Center for Nanoscience and Technology, 11 Beiyitiao Zhongguancun,
Beijing 100190, China
| | - Lei Liu
- National Center for Nanoscience and Technology, 11 Beiyitiao Zhongguancun,
Beijing 100190, China
| | - Xiaojing Ma
- National Center for Nanoscience and Technology, 11 Beiyitiao Zhongguancun,
Beijing 100190, China
| | - Huibin Wang
- National Center for Nanoscience and Technology, 11 Beiyitiao Zhongguancun,
Beijing 100190, China
| | - Yanlian Yang
- National Center for Nanoscience and Technology, 11 Beiyitiao Zhongguancun,
Beijing 100190, China
| | - Guanghong Wei
- State
Key Laboratory of Surface
Physics, Key Laboratory for Computational Physical Sciences (Ministry
of Education), and Department of Physics, Fudan University, 220 Handan Road, Shanghai 200433, China
| | - Chen Wang
- National Center for Nanoscience and Technology, 11 Beiyitiao Zhongguancun,
Beijing 100190, China
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9
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Silly F. Moiré pattern induced by the electronic coupling between 1-octanol self-assembled monolayers and graphite surface. NANOTECHNOLOGY 2012; 23:225603. [PMID: 22572595 DOI: 10.1088/0957-4484/23/22/225603] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Two-dimensional self-assembly of 1-octanol molecules on a graphite surface is investigated using scanning tunneling microscopy (STM) at the solid/liquid interface. STM images reveal that this molecule self-assembles into a compact hydrogen-bonded herringbone nanoarchitecture. Molecules are preferentially arranged in a head-to-head and tail-to-tail fashion. A Moiré pattern appears in the STM images when the 1-octanol layer is covering the graphite surface. The large Moiré stripes are perpendicular to the 1-octanol lamellae. Interpretation of the STM images suggests that the Moiré periodicity is governed by the electronic properties of the graphite surface and the 1-octanol layer periodicity.
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Affiliation(s)
- Fabien Silly
- CEA, IRAMIS, SPCSI, Hybrid Magnetic Nanoarchitectures, F-91191 Gif sur Yvette, France
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10
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Wang C, Yang A, Li X, Li D, Zhang M, Du H, Li C, Guo Y, Mao X, Dong M, Besenbacher F, Yang Y, Wang C. Observation of molecular inhibition and binding structures of amyloid peptides. NANOSCALE 2012; 4:1895-909. [PMID: 22334382 DOI: 10.1039/c2nr11508e] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Unveiling interactions between labeling molecules and amyloid fibrils is essential to develop new detection methods for studying amyloid structures under various conditions. This review endeavours to reflect the progress in studying interactions between molecular inhibitors and amyloid peptides using a series of experimental approaches, such as X-ray diffraction, nuclear magnetic resonance, scanning probe microscopy, and electron microscopy. The revealed binding mechanisms of anti-amyloid drugs and target proteins could benefit the rational design of drugs for prevention or treatment of amyloidal diseases.
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Affiliation(s)
- Chenxuan Wang
- National Center for Nanoscience and Technology, Beijing, 100190, PR China
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11
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Wang C, Mao X, Yang A, Niu L, Wang S, Li D, Guo Y, Wang Y, Yang Y, Wang C. Determination of relative binding affinities of labeling molecules with amino acids by using scanning tunneling microscopy. Chem Commun (Camb) 2011; 47:10638-40. [PMID: 21869951 DOI: 10.1039/c1cc12380g] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The binding behaviour of labeling molecule copper phthalocyanine tetrasulfonate sodium (PcCu(SO(3)Na)(4)) on the assemblies of representative polyamino acids has been studied by using scanning tunneling microscopy (STM). By directly visualizing the adsorption and distribution of the labeling species on the peptide assemblies in STM images, one could obtain relative binding affinities of the labeling molecule with different amino acid residues.
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Affiliation(s)
- Chenxuan Wang
- National Center for Nanoscience and Technology, Beijing 100190, China
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12
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Mao X, Guo Y, Wang C, Zhang M, Ma X, Liu L, Niu L, Zeng Q, Yang Y, Wang C. Binding modes of thioflavin T molecules to prion peptide assemblies identified by using scanning tunneling microscopy. ACS Chem Neurosci 2011; 2:281-7. [PMID: 22778872 DOI: 10.1021/cn200006h] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Accepted: 03/30/2011] [Indexed: 11/30/2022] Open
Abstract
The widely used method to monitor the aggregation process of amyloid peptide is thioflavin T (ThT) assay, while the detailed molecular mechanism is still not clear. In this work, we report here the direct identification of the binding modes of ThT molecules with the prion peptide GNNQQNY by using scanning tunneling microscopy (STM). The assembly structures of GNNQQNY were first observed by STM on a graphite surface, and the introduction of ThT molecules to the surface facilitated the STM observations of the adsorption conformations of ThT with peptide strands. ThT molecules are apt to adsorb on the peptide assembly with β-sheet structure and oriented parallel with the peptide strands adopting four different binding modes. This effort could benefit the understanding of the mechanisms of the interactions between labeling species or inhibitory ligands and amyloid peptides, which is keenly needed for developing diagnostic and therapeutic approaches.
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Affiliation(s)
- Xiaobo Mao
- Key Laboratory for Biological Effects of Nanomaterials & Nanosafety and Key Laboratory of Standardization and Measurement for Nanotechnology (Chinese Academy of Sciences) National Center for Nanoscience and Technology, 11 Beiyitiao, Zhongguancun, Beijing 100190, P. R. China
| | - Yuanyuan Guo
- Key Laboratory for Biological Effects of Nanomaterials & Nanosafety and Key Laboratory of Standardization and Measurement for Nanotechnology (Chinese Academy of Sciences) National Center for Nanoscience and Technology, 11 Beiyitiao, Zhongguancun, Beijing 100190, P. R. China
| | - Chenxuan Wang
- Key Laboratory for Biological Effects of Nanomaterials & Nanosafety and Key Laboratory of Standardization and Measurement for Nanotechnology (Chinese Academy of Sciences) National Center for Nanoscience and Technology, 11 Beiyitiao, Zhongguancun, Beijing 100190, P. R. China
| | - Min Zhang
- Key Laboratory for Biological Effects of Nanomaterials & Nanosafety and Key Laboratory of Standardization and Measurement for Nanotechnology (Chinese Academy of Sciences) National Center for Nanoscience and Technology, 11 Beiyitiao, Zhongguancun, Beijing 100190, P. R. China
| | - Xiaojing Ma
- Key Laboratory for Biological Effects of Nanomaterials & Nanosafety and Key Laboratory of Standardization and Measurement for Nanotechnology (Chinese Academy of Sciences) National Center for Nanoscience and Technology, 11 Beiyitiao, Zhongguancun, Beijing 100190, P. R. China
| | - Lei Liu
- Key Laboratory for Biological Effects of Nanomaterials & Nanosafety and Key Laboratory of Standardization and Measurement for Nanotechnology (Chinese Academy of Sciences) National Center for Nanoscience and Technology, 11 Beiyitiao, Zhongguancun, Beijing 100190, P. R. China
| | - Lin Niu
- Key Laboratory for Biological Effects of Nanomaterials & Nanosafety and Key Laboratory of Standardization and Measurement for Nanotechnology (Chinese Academy of Sciences) National Center for Nanoscience and Technology, 11 Beiyitiao, Zhongguancun, Beijing 100190, P. R. China
| | - Qingdao Zeng
- Key Laboratory for Biological Effects of Nanomaterials & Nanosafety and Key Laboratory of Standardization and Measurement for Nanotechnology (Chinese Academy of Sciences) National Center for Nanoscience and Technology, 11 Beiyitiao, Zhongguancun, Beijing 100190, P. R. China
| | - Yanlian Yang
- Key Laboratory for Biological Effects of Nanomaterials & Nanosafety and Key Laboratory of Standardization and Measurement for Nanotechnology (Chinese Academy of Sciences) National Center for Nanoscience and Technology, 11 Beiyitiao, Zhongguancun, Beijing 100190, P. R. China
| | - Chen Wang
- Key Laboratory for Biological Effects of Nanomaterials & Nanosafety and Key Laboratory of Standardization and Measurement for Nanotechnology (Chinese Academy of Sciences) National Center for Nanoscience and Technology, 11 Beiyitiao, Zhongguancun, Beijing 100190, P. R. China
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