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Yu L, Yang Y, Wang C. Peptide Self-Assembly and Its Modulation: Imaging on the Nanoscale. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1174:35-60. [PMID: 31713196 DOI: 10.1007/978-981-13-9791-2_2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This chapter intends to review the progress in obtaining site-specific structural information for peptide assemblies using scanning tunneling microscopy. The effects on assembly propensity due to mutations and modifications in peptide sequences, small organic molecules and conformational transitions of peptides are identified. The obtained structural insights into the sequence-dependent assembly propensity could inspire rational design of peptide architectures at the molecular level.
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Affiliation(s)
- Lanlan Yu
- National Center for Nanoscience and Technology, Chinese Academy of Sciences, Beijing, China
| | - Yanlian Yang
- National Center for Nanoscience and Technology, Chinese Academy of Sciences, Beijing, China
| | - Chen Wang
- National Center for Nanoscience and Technology, Chinese Academy of Sciences, Beijing, China.
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Goronzy DP, Ebrahimi M, Rosei F, Fang Y, De Feyter S, Tait SL, Wang C, Beton PH, Wee ATS, Weiss PS, Perepichka DF. Supramolecular Assemblies on Surfaces: Nanopatterning, Functionality, and Reactivity. ACS NANO 2018; 12:7445-7481. [PMID: 30010321 DOI: 10.1021/acsnano.8b03513] [Citation(s) in RCA: 147] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Understanding how molecules interact to form large-scale hierarchical structures on surfaces holds promise for building designer nanoscale constructs with defined chemical and physical properties. Here, we describe early advances in this field and highlight upcoming opportunities and challenges. Both direct intermolecular interactions and those that are mediated by coordinated metal centers or substrates are discussed. These interactions can be additive, but they can also interfere with each other, leading to new assemblies in which electrical potentials vary at distances much larger than those of typical chemical interactions. Earlier spectroscopic and surface measurements have provided partial information on such interfacial effects. In the interim, scanning probe microscopies have assumed defining roles in the field of molecular organization on surfaces, delivering deeper understanding of interactions, structures, and local potentials. Self-assembly is a key strategy to form extended structures on surfaces, advancing nanolithography into the chemical dimension and providing simultaneous control at multiple scales. In parallel, the emergence of graphene and the resulting impetus to explore 2D materials have broadened the field, as surface-confined reactions of molecular building blocks provide access to such materials as 2D polymers and graphene nanoribbons. In this Review, we describe recent advances and point out promising directions that will lead to even greater and more robust capabilities to exploit designer surfaces.
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Affiliation(s)
- Dominic P Goronzy
- California NanoSystems Institute , University of California, Los Angeles , Los Angeles , California 90095 , United States
- Department of Chemistry and Biochemistry , University of California, Los Angeles , Los Angeles , California 90095 , United States
| | - Maryam Ebrahimi
- INRS Centre for Energy, Materials and Telecommunications , 1650 Boul. Lionel Boulet , Varennes , Quebec J3X 1S2 , Canada
| | - Federico Rosei
- INRS Centre for Energy, Materials and Telecommunications , 1650 Boul. Lionel Boulet , Varennes , Quebec J3X 1S2 , Canada
- Institute for Fundamental and Frontier Science , University of Electronic Science and Technology of China , Chengdu 610054 , P.R. China
| | - Yuan Fang
- Department of Chemistry , McGill University , Montreal H3A 0B8 , Canada
| | - Steven De Feyter
- Department of Chemistry , KU Leuven , Celestijnenlaan 200F , Leuven 3001 , Belgium
| | - Steven L Tait
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
| | - Chen Wang
- National Center for Nanoscience and Technology , Beijing 100190 , China
| | - Peter H Beton
- School of Physics & Astronomy , University of Nottingham , Nottingham NG7 2RD , United Kingdom
| | - Andrew T S Wee
- Department of Physics , National University of Singapore , 117542 Singapore
| | - Paul S Weiss
- California NanoSystems Institute , University of California, Los Angeles , Los Angeles , California 90095 , United States
- Department of Chemistry and Biochemistry , University of California, Los Angeles , Los Angeles , California 90095 , United States
- Department of Materials Science and Engineering , University of California, Los Angeles , Los Angeles , California 90095 , United States
| | - Dmitrii F Perepichka
- California NanoSystems Institute , University of California, Los Angeles , Los Angeles , California 90095 , United States
- Department of Chemistry , McGill University , Montreal H3A 0B8 , Canada
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Dai HL, Geng YF, Zeng QD, Wang C. Photo-regulation of 2D supramolecular self-assembly: On-surface photochemistry studied by STM. CHINESE CHEM LETT 2017. [DOI: 10.1016/j.cclet.2016.09.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Geng YF, Li P, Li JZ, Zhang XM, Zeng QD, Wang C. STM probing the supramolecular coordination chemistry on solid surface: Structure, dynamic, and reactivity. Coord Chem Rev 2017. [DOI: 10.1016/j.ccr.2017.01.014] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Dai H, Yi W, Deng K, Wang H, Zeng Q. Formation of Coronene Clusters in Concentration and Temperature Controlled Two-Dimensional Porous Network. ACS APPLIED MATERIALS & INTERFACES 2016; 8:21095-21100. [PMID: 27463768 DOI: 10.1021/acsami.6b06638] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
In this research, with the assistance of scanning tunneling microscopy (STM), we observed the two-dimensional (2D) self-assembly transition of a star-shaped oligofluorene derivative (StOF) from disordered structure to honeycomb network by adjusting StOF concentration in solution. By introducing guest molecules coronene (COR), we for the first time achieved novel triangle-shaped COR trimers on liquid/highly oriented pyrolytic graphite (HOPG) interface in both honeycomb network and the disordered structure. In thermal tests, the COR/StOF-disorder system underwent a structural conformation to form well-ordered ladder structures, while the COR/StOF-honeycomb system remained the perfect hexagonal network with COR trimers included in the cavities. Density functional theory (DFT) calculations have been employed to investigate the forming mechanism of the molecular nanoarrays. These studies are expected to enhance controlling on 2D self-assembly and provide a facial approach toward constructing on-surface molecular clusters.
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Affiliation(s)
- Hongliang Dai
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST) , Beijing 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Wenjing Yi
- Engineering Research Center for Nanomaterials, Henan University , Kaifeng 475004, P. R. China
| | - Ke Deng
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST) , Beijing 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Hua Wang
- Engineering Research Center for Nanomaterials, Henan University , Kaifeng 475004, P. R. China
| | - Qingdao Zeng
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST) , Beijing 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
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Yu Y, Yang Y, Wang C. Site-specific Analysis of Amyloid Assemblies by Using Scanning Tunneling Microscopy. CHINESE J CHEM 2014. [DOI: 10.1002/cjoc.201400631] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Xu J, Zeng Q. Two-dimensional (2D) Supramolecular Coordination at Liquid/Solid Interfaces Studied by Scanning Tunneling Microscopy. CHINESE J CHEM 2014. [DOI: 10.1002/cjoc.201400499] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Li Y, Liu C, Xie Y, Li X, Fan X, Yuan L, Zeng Q. Single-molecule observation of the K(+)-induced switching of valinomycin within a template network. Chem Commun (Camb) 2014; 49:9021-3. [PMID: 23977669 DOI: 10.1039/c3cc44978e] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The K(+)-induced switching of valinomycin has been studied using a molecular template formed by an aromatic oligoamide macrocycle at the liquid/solid interface by scanning tunneling microscopy (STM). Individual valinomycin and its K(+) complex can be identified and resolved in the molecular template, and the high-resolution STM images of valinomycin and its K(+) complex show triangle-like and cyclic structural characteristics, respectively.
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Affiliation(s)
- Yibao Li
- Key Laboratory of Organo-pharmaceutical Chemistry, Gannan Normal University, Ganzhou 341000, P. R. China.
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Luo D, Zhang X, Shen Y, Xu J, Shu L, Zeng Q, Wang C. Two-dimensional supramolecular spring: coordination driven reversible extension and contraction of bridged half rings. Chem Commun (Camb) 2014; 50:9369-71. [DOI: 10.1039/c4cc02120g] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A tetraethylene glycol ether bridged derivative 9 has been designed and synthesized, and its two-dimensional (2D) self-assembled behavior has been investigated at the single-molecule level.
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Affiliation(s)
- Dapeng Luo
- Key laboratory of Organosilicon Chemistry and Material Technology of Ministry of Education
- Hangzhou Normal University
- Hangzhou 310012, China
| | - Xuemei Zhang
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology
- National Centre for Nanoscience and Technology
- Beijing 100190, China
| | - Yongtao Shen
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology
- National Centre for Nanoscience and Technology
- Beijing 100190, China
| | - Jing Xu
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology
- National Centre for Nanoscience and Technology
- Beijing 100190, China
| | - Lijin Shu
- Key laboratory of Organosilicon Chemistry and Material Technology of Ministry of Education
- Hangzhou Normal University
- Hangzhou 310012, China
| | - Qingdao Zeng
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology
- National Centre for Nanoscience and Technology
- Beijing 100190, China
| | - Chen Wang
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology
- National Centre for Nanoscience and Technology
- Beijing 100190, China
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Yang Y, Wang C. Single-molecule studies on individual peptides and peptide assemblies on surfaces. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2013; 371:20120311. [PMID: 24000363 DOI: 10.1098/rsta.2012.0311] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
This review is intended to reflect the recent progress in single-molecule studies of individual peptides and peptide assemblies on surfaces. The structures and the mechanism of peptide assembly are discussed in detail. The contents include the following topics: structural analysis of single peptide molecules, adsorption and assembly of peptides on surfaces, folding structures of the amyloid peptides, interaction between amyloid peptides and dye or drug molecules, and modulation of peptide assemblies by small molecules. The explorations of peptide adsorption and assembly will benefit the understanding of the mechanisms for protein-protein interactions, protein-drug interactions and the pathogenesis of amyloidoses. The investigations on peptide assembly and its modulations could also provide a potential approach towards the treatment of the amyloidoses.
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Affiliation(s)
- Yanlian Yang
- National Center for Nanoscience and Technology, Beijing 100190, People's Republic of China
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Zhang X, Zeng Q, Wang C. Molecular templates and nano-reactors: two-dimensional hydrogen bonded supramolecular networks on solid/liquid interfaces. RSC Adv 2013. [DOI: 10.1039/c3ra40473k] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Wang Y, Li Y, Luo Y, Xu M, Zhang X, Guo Y, Wei G, Yuan L, Gong B, Yang Y, Wang C. Study on Molecular Cavity of Oligoamide Macrocycles by Using Scanning Tunneling Microscopy. Chemphyschem 2012; 13:3598-604. [DOI: 10.1002/cphc.201200288] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2012] [Revised: 07/23/2012] [Indexed: 11/10/2022]
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Bai Y, Abbott NL. Enantiomeric interactions between liquid crystals and organized monolayers of tyrosine-containing dipeptides. J Am Chem Soc 2012; 134:548-58. [PMID: 22091988 PMCID: PMC3257416 DOI: 10.1021/ja2089475] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have examined the orientational ordering of nematic liquid crystals (LCs) supported on organized monolayers of dipeptides with the goal of understanding how peptide-based interfaces encode intermolecular interactions that are amplified into supramolecular ordering. By characterizing the orientations of nematic LCs (4-cyano-4'-pentylbiphenyl and TL205 (a mixture of mesogens containing cyclohexane-fluorinated biphenyls and fluorinated terphenyls)) on monolayers of l-cysteine-l-tyrosine, l-cysteine-l-phenylalanine, or l-cysteine-l-phosphotyrosine formed on crystallographically textured films of gold, we conclude that patterns of hydrogen bonds generated by the organized monolayers of dipeptides are transduced via macroscopic orientational ordering of the LCs. This conclusion is supported by the observation that the ordering exhibited by the achiral LCs is specific to the enantiomers used to form the dipeptide-based monolayers. The dominant role of the -OH group of tyrosine in dictating the patterns of hydrogen bonds that orient the LCs was also evidenced by the effects of phosphorylation of the tyrosine on the ordering of the LCs. Overall, these results reveal that crystallographic texturing of gold films can direct the formation of monolayers of dipeptides with long-range order, thus unmasking the influence of hydrogen bonding, chirality, and phosphorylation on the macroscopic orientational ordering of LCs supported on these surfaces. These results suggest new approaches based on supramolecular assembly for reporting the chemical functionality and stereochemistry of synthetic and biological peptide-based molecules displayed at surfaces.
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Affiliation(s)
- Yiqun Bai
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison WI 53705, United States
| | - Nicholas L. Abbott
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison WI 53705, United States
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Xu LP, Liu Y, Zhang X. Interfacial self-assembly of amino acids and peptides: scanning tunneling microscopy investigation. NANOSCALE 2011; 3:4901-4915. [PMID: 22057641 DOI: 10.1039/c1nr11070e] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Proteins play important roles in human daily life. To take advantage of the lessons learned from nature, it is essential to investigate the self-assembly of subunits of proteins, i.e., amino acids and polypeptides. Due to its high resolution and versatility of working environment, scanning tunneling microscopy (STM) has become a powerful tool for studying interfacial molecular assembly structures. This review is intended to reflect the progress in studying interfacial self-assembly of amino acids and peptides by STM. In particular, we focus on environment-induced polymorphism, chiral recognition, and coadsorption behavior with molecular templates. These studies would be highly beneficial to research endeavors exploring the mechanism and nanoscale-controlling molecular assemblies of amino acids and polypeptides on surfaces, understanding the origin of life, unravelling the essence of disease at the molecular level and deeming what is necessary for the "bottom-up" nanofabrication of molecular devices and biosensors being constructed with useful properties and desired performance.
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Affiliation(s)
- Li-Ping Xu
- Research Center for Bioengineering and Sensing Technology, University of Science & Technology Beijing, Beijing, 100083, PR China.
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