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Tsai CL, Wu SY, Hsu HK, Huang SB, Lin CH, Chan YT, Wang SK. Preparation and conformational analysis of polyproline tri-helix macrocycle nanoscaffolds of varied sizes. NANOSCALE 2021; 13:4592-4601. [PMID: 33605962 DOI: 10.1039/d0nr08184a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Ligand patterns at the nanoscale are essential in modulating biological recognition and signaling through binding to receptor oligomers. Biocompatible nanoscaffolds that allow precise control of multiple ligand presentation would be of great use in manipulating cellular processes and understanding membrane receptor biology. We have previously developed tri-helix and tetra-helix macrocycle scaffolds based on the Pro9 peptide helix to control ligand arrangements that can selectively target receptor oligomers. A better understanding of the structure of these macromolecules would significantly reduce the difficulty in designing matching ligand positions for target receptors. In this work, we expand the arsenal of ligand patterns by preparing polyproline tri-helix macrocycle scaffolds of different sizes. These synthetic nanoscaffolds composed of peptide helices ranging from Pro6 to Pro12 also allowed us to systematically investigate their properties. With a combination of circular dichroism spectroscopy and ion mobility spectrometry-mass spectrometry (IMS-MS), the measurement for varied sizes of these scaffolds indicated the connecting dihedral angle between both ends of the helix affects the strain in the cyclic scaffold. The experimental collision cross section obtained from IMS-MS favors a propeller model for the helix arrangements. The results not only contribute conformational insights for the polyproline tri-helix system, but also provide precious information for the future design and synthesis of cyclic nanostructures based on peptide helices.
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Affiliation(s)
- Chia-Lung Tsai
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan.
| | - Shao-Yong Wu
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan.
| | - Hung-Kai Hsu
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan.
| | - Sheng-Bo Huang
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan.
| | - Cin-Hao Lin
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan.
| | - Yi-Tsu Chan
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan. and Center for Emerging Materials and Advanced Devices, National Taiwan University, Taipei 10617, Taiwan
| | - Sheng-Kai Wang
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan. and Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, Hsinchu 30013, Taiwan
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Lin CH, Wen HC, Chiang CC, Huang JS, Chen Y, Wang SK. Polyproline Tri-Helix Macrocycles as Nanosized Scaffolds to Control Ligand Patterns for Selective Protein Oligomer Interactions. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1900561. [PMID: 30977296 DOI: 10.1002/smll.201900561] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Indexed: 06/09/2023]
Abstract
Multivalent ligand-receptor interactions play essential roles in biological recognition and signaling. As the receptor arrangement on the cell surface can alter the outcome of cell signaling and also provide spatial specificity for ligand binding, controlling the presentation of ligands has become a promising strategy to manipulate or selectively target protein receptors. The lack of adjustable universal tools to control ligand positions at the size of a few nanometers has prompted the development of polyproline tri-helix macrocycles as scaffolds to present ligands in designated patterns. Model lectin Helix pomatia agglutinin has shown selectivity toward the matching GalNAc ligand pattern matching its binding sites arrangement. The GalNAc pattern selectivity is also observed on intact asialoglycoprotein receptor oligomer on human hepatoma cells showing the pattern-selective interaction can be achieved not only on isolated protein oligomers but also the receptors arranged on the cell surface. As the scaffold design allows convenient creation of versatile ligand patterns, it can be expected as a promising tool to probe the arrangement of receptors on the cell surface and as nanomedicine to manipulate signaling or cell recognition.
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Affiliation(s)
- Cin-Hao Lin
- Department of Chemistry, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Hsin-Chuan Wen
- Department of Chemistry, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Cheng-Chin Chiang
- Institute of Biomedical Engineering, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Jen-Sheng Huang
- Department of Chemistry, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Yunching Chen
- Institute of Biomedical Engineering, National Tsing Hua University, Hsinchu, 30013, Taiwan
- Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Sheng-Kai Wang
- Department of Chemistry, National Tsing Hua University, Hsinchu, 30013, Taiwan
- Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, Hsinchu, 30013, Taiwan
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Tashiro S, Chiba M, Shionoya M. Arrangement of Proteinogenic α-Amino Acids on a Cyclic Peptide Comprising Alternate Biphenyl-Cored ζ-Amino Acids. Chem Asian J 2017; 12:1087-1094. [DOI: 10.1002/asia.201700203] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 03/25/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Shohei Tashiro
- Department of Chemistry; Graduate School of Science; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Masayuki Chiba
- Department of Chemistry; Graduate School of Science; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Mitsuhiko Shionoya
- Department of Chemistry; Graduate School of Science; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
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Uji H, Ito T, Matsumoto M, Kimura S. Prevailing Photocurrent Generation of D−π–A Type Oligo(phenyleneethynylene) in Contact with Gold over Dexter-Type Energy-Transfer Quenching. J Phys Chem A 2016; 120:1190-6. [DOI: 10.1021/acs.jpca.5b12532] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hirotaka Uji
- Department of Material Chemistry,
Graduate School of Engineering, Kyoto University, Kyoto-Daigaku-Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Taichi Ito
- Department of Material Chemistry,
Graduate School of Engineering, Kyoto University, Kyoto-Daigaku-Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Mitsuaki Matsumoto
- Department of Material Chemistry,
Graduate School of Engineering, Kyoto University, Kyoto-Daigaku-Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Shunsaku Kimura
- Department of Material Chemistry,
Graduate School of Engineering, Kyoto University, Kyoto-Daigaku-Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
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pH-controlled aggregation polymorphism of amyloidogenic Aβ(16-22): insights for obtaining peptide tapes and peptide nanotubes, as function of the N-terminal capping moiety. Eur J Med Chem 2014; 88:55-65. [PMID: 25087966 DOI: 10.1016/j.ejmech.2014.07.089] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 07/24/2014] [Accepted: 07/24/2014] [Indexed: 11/23/2022]
Abstract
Peptide and protein self-assembly resulting in the formation of amyloidogenic aggregates is generally thought of as a pathological event associated with severe diseases. However, amyloid formation may also provide a basis for advanced bionanomaterials, since amyloid fibrils combine unique material-like properties that make them very useful for design of new types of conducting nanowires, bioactive ligands, and biodegradable coatings as drug-encapsulating materials. The morphology of the supramolecular aggregates determines the properties and application range of these bionanomaterials. An important parameter to control the supramolecular morphology, is the overall charge of the peptide, which is related to the pH of the environment. Herein, we describe the design, synthesis and morphological analysis of a series of N-terminally functionalized Aβ(16-22) peptides (∼Lys-Leu-Val-Phe-Phe-Ala-Glu-OH), that underwent a pH-induced polymorphism, ranging from lamellar sheets, helical tapes, peptide nanotubes, and amyloid fibrils as was observed by transmission electron microscopy. Infrared spectroscopy and wide angle X-ray scattering studies showed that peptide self-assembly was driven by β-sheet formation, and that the supramolecular morphology was directed by subtle variations in electrostatic interactions. Finally, a structural model and hierarchy of self-assembly of a peptide nanotube, assembled at pH 1, is proposed.
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Nakayama H, Kimura S. Suppression of HOMO–LUMO Transition in a Twist Form of Oligo(phenyleneethynylene) Clamped by a Right-Handed Helical Peptide. J Phys Chem A 2011; 115:8960-8. [DOI: 10.1021/jp200997c] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hidenori Nakayama
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku-Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Shunsaku Kimura
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku-Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
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Koga K, Sudo A, Nishida H, Endo T. Convenient and useful synthesis ofN-carboxyanhydride monomers through selective cyclization of urethane derivatives of α-amino acids. ACTA ACUST UNITED AC 2009. [DOI: 10.1002/pola.23450] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Okamoto S, Morita T, Kimura S. Electron transfer through a self-assembled monolayer of a double-helix peptide with linking the terminals by ferrocene. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2009; 25:3297-3304. [PMID: 19437730 DOI: 10.1021/la8034962] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
A unique molecular structure, a double-helix peptide, was self-assembled on gold, and the electron transfer through the monolayer was studied. The double-helix peptide consists of two 9mer 3(10)-helical peptide chains having a disulfide group at each N terminal and being linked by a ferrocene dicarboxylic acid between the C terminals. Each helical peptide chain has three naphthyl groups in a linear arrangement along the helix. The monolayer properties and the electron transfer from the ferrocene unit to gold were studied with reference peptides with a similar double helix but without naphthyl groups, a single helix with a dicarboxylic ferrocene unit, and a single helix with a monocarboxylic ferrocene unit. It was demonstrated that the naphthyl groups on the side chains had no effect on electron transfer, and the electron-transfer rate in the double-helix monolayer was not promoted, despite the two electron pathways in the molecule. We propose that in the double-helix monolayer, molecular motions are suppressed, possibly by its rigid structure tethered by the two linkers on gold to cancel out acceleration effects of the 2-fold electron pathways and the ferrocene substitution number. The factors that affect the electron-transfer reaction across the helical peptide SAMs are discussed in depth.
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Affiliation(s)
- Shinpei Okamoto
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku-Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
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Kamei Y, Sudo A, Endo T. Synthesis of Polypeptide Having Defined Terminal Structures Through Polymerization of Activated Urethane-Derivative of γ-Benzyl-l-glutamate. Macromolecules 2008. [DOI: 10.1021/ma801315r] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yasutaka Kamei
- Molecular Engineering Institute, Kinki University, 11-6 Kayanomori, Iizuka, Fukuoka 820-8555, Japan, Department of Polymer Science and Engineering, Faculty of Engineering, Yamagata University, 4-3-16 Jonan, Yonezawa, Yamagata 992-8510, Japan
| | - Atsushi Sudo
- Molecular Engineering Institute, Kinki University, 11-6 Kayanomori, Iizuka, Fukuoka 820-8555, Japan, Department of Polymer Science and Engineering, Faculty of Engineering, Yamagata University, 4-3-16 Jonan, Yonezawa, Yamagata 992-8510, Japan
| | - Takeshi Endo
- Molecular Engineering Institute, Kinki University, 11-6 Kayanomori, Iizuka, Fukuoka 820-8555, Japan, Department of Polymer Science and Engineering, Faculty of Engineering, Yamagata University, 4-3-16 Jonan, Yonezawa, Yamagata 992-8510, Japan
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Bogdan N, Condamine E, Toupet L, Ramondenc Y, Bogdan E, Grosu I. New [4.4]Cyclophanes: Molecular Parallelograms, Triangles, Rhombuses, Pentagons, and Supramolecular Constructions. J Org Chem 2008; 73:5831-8. [DOI: 10.1021/jo8006489] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Niculina Bogdan
- Marie Curie Excellence Team, Dept. Chemie, LS AC, Technische Universität München, 4, Lichtenbergstrasse, 85747 Garching, Germany, Faculty of Chemistry and Chemical Engineering, “Babes-Bolyai” University, 11 Arany Janos str., 400028 Cluj-Napoca, Romania, IRCOF, UMR 6014, Université de Rouen, 76821 Mont Saint-Aignan, Cedex, France, and Université de Rennes, I, UMR 6251, 35042 Rennes Cedex, France
| | - Eric Condamine
- Marie Curie Excellence Team, Dept. Chemie, LS AC, Technische Universität München, 4, Lichtenbergstrasse, 85747 Garching, Germany, Faculty of Chemistry and Chemical Engineering, “Babes-Bolyai” University, 11 Arany Janos str., 400028 Cluj-Napoca, Romania, IRCOF, UMR 6014, Université de Rouen, 76821 Mont Saint-Aignan, Cedex, France, and Université de Rennes, I, UMR 6251, 35042 Rennes Cedex, France
| | - Loïc Toupet
- Marie Curie Excellence Team, Dept. Chemie, LS AC, Technische Universität München, 4, Lichtenbergstrasse, 85747 Garching, Germany, Faculty of Chemistry and Chemical Engineering, “Babes-Bolyai” University, 11 Arany Janos str., 400028 Cluj-Napoca, Romania, IRCOF, UMR 6014, Université de Rouen, 76821 Mont Saint-Aignan, Cedex, France, and Université de Rennes, I, UMR 6251, 35042 Rennes Cedex, France
| | - Yvan Ramondenc
- Marie Curie Excellence Team, Dept. Chemie, LS AC, Technische Universität München, 4, Lichtenbergstrasse, 85747 Garching, Germany, Faculty of Chemistry and Chemical Engineering, “Babes-Bolyai” University, 11 Arany Janos str., 400028 Cluj-Napoca, Romania, IRCOF, UMR 6014, Université de Rouen, 76821 Mont Saint-Aignan, Cedex, France, and Université de Rennes, I, UMR 6251, 35042 Rennes Cedex, France
| | - Elena Bogdan
- Marie Curie Excellence Team, Dept. Chemie, LS AC, Technische Universität München, 4, Lichtenbergstrasse, 85747 Garching, Germany, Faculty of Chemistry and Chemical Engineering, “Babes-Bolyai” University, 11 Arany Janos str., 400028 Cluj-Napoca, Romania, IRCOF, UMR 6014, Université de Rouen, 76821 Mont Saint-Aignan, Cedex, France, and Université de Rennes, I, UMR 6251, 35042 Rennes Cedex, France
| | - Ion Grosu
- Marie Curie Excellence Team, Dept. Chemie, LS AC, Technische Universität München, 4, Lichtenbergstrasse, 85747 Garching, Germany, Faculty of Chemistry and Chemical Engineering, “Babes-Bolyai” University, 11 Arany Janos str., 400028 Cluj-Napoca, Romania, IRCOF, UMR 6014, Université de Rouen, 76821 Mont Saint-Aignan, Cedex, France, and Université de Rennes, I, UMR 6251, 35042 Rennes Cedex, France
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Fujii S, Morita T, Kimura S. Photoinduced electron transfer in thin layers composed of fullerene-cyclic peptide conjugate and pyrene derivative. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2008; 24:5608-5614. [PMID: 18419146 DOI: 10.1021/la800269w] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
A bilayer structure was constructed on gold by Langmuir-Blodgett deposition of a fullerene (C 60)-cyclic peptide-poly(ethylene glycol) (PEG) conjugate and thereafter a pyrene derivative from the air/water interface. The cyclic peptide moiety acts as a scaffold to prevent the fullerenes from self-aggregation and accordingly makes the monolayer homogeneous and stable. In addition to this gold/C 60-cyclic peptide-PEG/pyrene bilayer, a pyrene monolayer, a gold/C 60-PEG conjugate/pyrene bilayer (lacking the peptide scaffold), and a gold/pyrene/C 60-cyclic peptide-PEG bilayer (with the opposite order of layers) were also prepared, and their anodic photocurrent generation were studied in an aqueous solution containing a sacrifice electron donor. The most efficient photocurrent generation was observed in the gold/C 60-cyclic peptide-PEG/pyrene bilayer. It is considered that the C 60 unit acts not only as sensitizer but also as an electron acceptor facilitating the electron transfer from the excited pyrene unit to gold, and that the fullerene layer suppresses quenching of the excited pyrene unit by energy transfer to gold. Furthermore, the cyclic peptide scaffold helps the fullerenes disperse without aggregation in the membrane and seems to protect their redox properties or inhibit self-quenching of their excited state. It is thus concluded that a bilayer structure with desired orientation of functional units is important for efficient photoinduced electron transfer and that a cyclic peptide scaffold is useful to locate hydrophobic functional groups properly in a thin layer.
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Affiliation(s)
- Shigekatsu Fujii
- Department of Material Chemsitry, Kyoto University, Kyoto, Japan
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Kamei Y, Sudo A, Nishida H, Kikukawa K, Endo T. Synthesis of polypeptides from activated urethane derivatives of α-amino acids. ACTA ACUST UNITED AC 2008. [DOI: 10.1002/pola.22584] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Kamei Y, Nagai A, Sudo A, Nishida H, Kikukawa K, Endo T. Convenient synthesis of poly(γ-benzyl-L-glutamate) from activated urethane derivatives of γ-benzyl-L-glutamate. ACTA ACUST UNITED AC 2008. [DOI: 10.1002/pola.22595] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Kimura S. Molecular dipole engineering: new aspects of molecular dipoles in molecular architecture and their functions. Org Biomol Chem 2008; 6:1143-8. [DOI: 10.1039/b717898k] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Ishikawa T, Morita T, Kimura S. Unique Helical Triangle Molecular Geometry Induced by Dipole–Dipole Interactions. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2007. [DOI: 10.1246/bcsj.80.1483] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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