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Kumar Bandela A, Sadihov‐Hanoch H, Cohen‐Luria R, Gordon C, Blake A, Poppitz G, Lynn DG, Ashkenasy G. The Systems Chemistry of Nucleic‐acid‐Peptide Networks. Isr J Chem 2022. [DOI: 10.1002/ijch.202200030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Anil Kumar Bandela
- Department of Chemistry Ben-Gurion University of the Negev Beer-Sheva 84105 Israel
| | - Hava Sadihov‐Hanoch
- Department of Chemistry Ben-Gurion University of the Negev Beer-Sheva 84105 Israel
| | - Rivka Cohen‐Luria
- Department of Chemistry Ben-Gurion University of the Negev Beer-Sheva 84105 Israel
| | - Christella Gordon
- Chemistry and Biology Emory University 1521 Dickey Drive NE Atlanta GA 30322 USA
| | - Alexis Blake
- Chemistry and Biology Emory University 1521 Dickey Drive NE Atlanta GA 30322 USA
| | - George Poppitz
- Chemistry and Biology Emory University 1521 Dickey Drive NE Atlanta GA 30322 USA
| | - David G. Lynn
- Chemistry and Biology Emory University 1521 Dickey Drive NE Atlanta GA 30322 USA
| | - Gonen Ashkenasy
- Department of Chemistry Ben-Gurion University of the Negev Beer-Sheva 84105 Israel
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2
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Pal S, Goswami S, Das D. Cross β amyloid assemblies as complex catalytic machinery. Chem Commun (Camb) 2021; 57:7597-7609. [PMID: 34278403 DOI: 10.1039/d1cc02880d] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
How modern enzymes evolved as complex catalytic machineries to facilitate diverse chemical transformations is an open question for the emerging field of systems chemistry. Inspired by Nature's ingenuity in creating complex catalytic structures for exotic functions, short peptide-based cross β amyloid sequences have been shown to access intricate binding surfaces demonstrating the traits of extant enzymes and proteins. Based on their catalytic proficiencies reported recently, these amyloid assemblies have been argued as the earliest protein folds. Herein, we map out the recent progress made by our laboratory and other research groups that demonstrate the catalytic diversity of cross β amyloid assemblies. The important role of morphology and specific mutations in peptide sequences has been underpinned in this review. We have divided the feature article into different sections where examples from biology have been covered demonstrating the mechanism of extant biocatalysts and compared with recent works on cross β amyloid folds showing covalent catalysis, aldolase, hydrolase, peroxidase-like activities and complex cascade catalysis. Beyond equilibrium, we have extended our discussion towards transient catalytic amyloid phases mimicking the energy driven cytoskeleton polymerization. Finally, a future outlook has been provided on the way ahead for short peptide-based systems chemistry approaches that can lead to the development of robust catalytic networks with improved enzyme-like proficiencies and higher complexities. The discussed examples along with the rationale behind selecting specific amino acids sequence will benefit readers to design systems for achieving catalytic reactivity similar to natural complex enzymes.
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Affiliation(s)
- Sumit Pal
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur-741246, India.
| | - Surashree Goswami
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur-741246, India.
| | - Dibyendu Das
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur-741246, India.
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3
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Ohtani R, Anegawa Y, Watanabe H, Tajima Y, Kinoshita M, Matsumori N, Kawano K, Yanaka S, Kato K, Nakamura M, Ohba M, Hayami S. Metal Complex Lipids for Fluid–Fluid Phase Separation in Coassembled Phospholipid Membranes. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202102774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Ryo Ohtani
- Department of Chemistry Faculty of Science Kyushu University 744 Motooka, Nishi-ku Fukuoka 819-0395 Japan
| | - Yuka Anegawa
- Department of Chemistry Graduate School of Science Kumamoto University 2-39-1 Kurokami, Chuo-ku Kumamoto 860-8555 Japan
| | - Hikaru Watanabe
- Department of Chemistry Faculty of Science Kyushu University 744 Motooka, Nishi-ku Fukuoka 819-0395 Japan
| | - Yutaro Tajima
- Department of Chemistry Faculty of Science Kyushu University 744 Motooka, Nishi-ku Fukuoka 819-0395 Japan
| | - Masanao Kinoshita
- Department of Chemistry Faculty of Science Kyushu University 744 Motooka, Nishi-ku Fukuoka 819-0395 Japan
| | - Nobuaki Matsumori
- Department of Chemistry Faculty of Science Kyushu University 744 Motooka, Nishi-ku Fukuoka 819-0395 Japan
| | - Kenichi Kawano
- Institute for Chemical Research Kyoto University Uji Kyoto 611-0011 Japan
| | - Saeko Yanaka
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS) National Institutes of Natural Sciences 5-1 Higashiyama Myodaiji Okazaki 444-8787 Japan
- Graduate School of Pharmaceutical Sciences Nagoya City University 3-1 Tanabe-dori, Mizuho-ku Nagoya Aichi 467-8603 Japan
| | - Koichi Kato
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS) National Institutes of Natural Sciences 5-1 Higashiyama Myodaiji Okazaki 444-8787 Japan
- Graduate School of Pharmaceutical Sciences Nagoya City University 3-1 Tanabe-dori, Mizuho-ku Nagoya Aichi 467-8603 Japan
| | - Masaaki Nakamura
- Department of Chemistry Graduate School of Science Kumamoto University 2-39-1 Kurokami, Chuo-ku Kumamoto 860-8555 Japan
| | - Masaaki Ohba
- Department of Chemistry Faculty of Science Kyushu University 744 Motooka, Nishi-ku Fukuoka 819-0395 Japan
| | - Shinya Hayami
- Department of Chemistry Graduate School of Science Kumamoto University 2-39-1 Kurokami, Chuo-ku Kumamoto 860-8555 Japan
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4
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Ohtani R, Anegawa Y, Watanabe H, Tajima Y, Kinoshita M, Matsumori N, Kawano K, Yanaka S, Kato K, Nakamura M, Ohba M, Hayami S. Metal Complex Lipids for Fluid-Fluid Phase Separation in Coassembled Phospholipid Membranes. Angew Chem Int Ed Engl 2021; 60:13603-13608. [PMID: 33723910 DOI: 10.1002/anie.202102774] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Indexed: 11/08/2022]
Abstract
We demonstrate a fluid-fluid phase separation in 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) membranes using a metal complex lipid of type [Mn(L1)] (1; HL1=1-(2-hydroxybenzamide)-2-(2-hydroxy-3-formyl-5-hexadecyloxybenzylideneamino)ethane). Small amount of 1 produces two separated domains in DMPC, whose phase transition temperatures of lipids (Tc ) are both lower than that of the pristine DMPC. Variable temperature fluorescent microscopy for giant-unilamellar vesicles of DMPC/1 hybrids demonstrates that visible phase separations remain in fluid phases up to 37 °C, which is clearly over the Tc of DMPC. This provides a new dimension for the application of metal complex lipids toward controlling lipid distributions in fluid membranes.
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Affiliation(s)
- Ryo Ohtani
- Department of Chemistry, Faculty of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Yuka Anegawa
- Department of Chemistry, Graduate School of Science, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto, 860-8555, Japan
| | - Hikaru Watanabe
- Department of Chemistry, Faculty of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Yutaro Tajima
- Department of Chemistry, Faculty of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Masanao Kinoshita
- Department of Chemistry, Faculty of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Nobuaki Matsumori
- Department of Chemistry, Faculty of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Kenichi Kawano
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Saeko Yanaka
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, 444-8787, Japan.,Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi, 467-8603, Japan
| | - Koichi Kato
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, 444-8787, Japan.,Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi, 467-8603, Japan
| | - Masaaki Nakamura
- Department of Chemistry, Graduate School of Science, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto, 860-8555, Japan
| | - Masaaki Ohba
- Department of Chemistry, Faculty of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Shinya Hayami
- Department of Chemistry, Graduate School of Science, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto, 860-8555, Japan
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Yuan C, Yang M, Ren X, Zou Q, Yan X. Porphyrin/Ionic‐Liquid Co‐assembly Polymorphism Controlled by Liquid–Liquid Phase Separation. Angew Chem Int Ed Engl 2020; 59:17456-17460. [DOI: 10.1002/anie.202007459] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Indexed: 12/19/2022]
Affiliation(s)
- Chengqian Yuan
- State Key Laboratory of Biochemical Engineering Institute of Process Engineering Chinese Academy of Sciences Beijing 100190 P. R. China
| | - Mengyao Yang
- State Key Laboratory of Biochemical Engineering Institute of Process Engineering Chinese Academy of Sciences Beijing 100190 P. R. China
- School of Chemical Engineering University of Chinese Academy of Sciences Beijing 100049 P. R. China
| | - Xiaokang Ren
- State Key Laboratory of Biochemical Engineering Institute of Process Engineering Chinese Academy of Sciences Beijing 100190 P. R. China
- School of Chemical Engineering University of Chinese Academy of Sciences Beijing 100049 P. R. China
| | - Qianli Zou
- State Key Laboratory of Biochemical Engineering Institute of Process Engineering Chinese Academy of Sciences Beijing 100190 P. R. China
| | - Xuehai Yan
- State Key Laboratory of Biochemical Engineering Institute of Process Engineering Chinese Academy of Sciences Beijing 100190 P. R. China
- School of Chemical Engineering University of Chinese Academy of Sciences Beijing 100049 P. R. China
- Center for Mesoscience Institute of Process Engineering Chinese Academy of Sciences Beijing 100190 P. R. China
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6
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Yuan C, Yang M, Ren X, Zou Q, Yan X. Porphyrin/Ionic‐Liquid Co‐assembly Polymorphism Controlled by Liquid–Liquid Phase Separation. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202007459] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Chengqian Yuan
- State Key Laboratory of Biochemical Engineering Institute of Process Engineering Chinese Academy of Sciences Beijing 100190 P. R. China
| | - Mengyao Yang
- State Key Laboratory of Biochemical Engineering Institute of Process Engineering Chinese Academy of Sciences Beijing 100190 P. R. China
- School of Chemical Engineering University of Chinese Academy of Sciences Beijing 100049 P. R. China
| | - Xiaokang Ren
- State Key Laboratory of Biochemical Engineering Institute of Process Engineering Chinese Academy of Sciences Beijing 100190 P. R. China
- School of Chemical Engineering University of Chinese Academy of Sciences Beijing 100049 P. R. China
| | - Qianli Zou
- State Key Laboratory of Biochemical Engineering Institute of Process Engineering Chinese Academy of Sciences Beijing 100190 P. R. China
| | - Xuehai Yan
- State Key Laboratory of Biochemical Engineering Institute of Process Engineering Chinese Academy of Sciences Beijing 100190 P. R. China
- School of Chemical Engineering University of Chinese Academy of Sciences Beijing 100049 P. R. China
- Center for Mesoscience Institute of Process Engineering Chinese Academy of Sciences Beijing 100190 P. R. China
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7
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Jakob DS, Wang H, Zeng G, Otzen DE, Yan Y, Xu XG. Peak Force Infrared-Kelvin Probe Force Microscopy. Angew Chem Int Ed Engl 2020; 59:16083-16090. [PMID: 32463936 DOI: 10.1002/anie.202004211] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 05/10/2020] [Indexed: 12/20/2022]
Abstract
Correlative scanning probe microscopy of chemical identity, surface potential, and mechanical properties provide insight into the structure-function relationships of nanomaterials. However, simultaneous measurement with comparable and high resolution is a challenge. We seamlessly integrated nanoscale photothermal infrared imaging with Coulomb force detection to form peak force infrared-Kelvin probe force microscopy (PFIR-KPFM), which enables simultaneous nanomapping of infrared absorption, surface potential, and mechanical properties with approximately 10 nm spatial resolution in a single-pass scan. MAPbBr3 perovskite crystals of different degradation pathways were studied in situ. Nanoscale charge accumulations were observed in MAPbBr3 near the boundary to PbBr2 . PFIR-KPFM also revealed correlations between residual charges and secondary conformation in amyloid fibrils. PFIR-KPFM is applicable to other heterogeneous materials at the nanoscale for correlative multimodal characterizations.
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Affiliation(s)
- Devon S Jakob
- Department of Chemistry, Lehigh University, 6 E Packer Ave., Bethlehem, PA, 18015, USA
| | - Haomin Wang
- Department of Chemistry, Lehigh University, 6 E Packer Ave., Bethlehem, PA, 18015, USA
| | - Guanghong Zeng
- DFM A/S, Danish National Metrology Institute, Kogle Alle 5, 2970, Hørsholm, Denmark
| | - Daniel E Otzen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wields Vej 14, 8000, Aarhus C, Denmark
| | - Yong Yan
- Department of Chemistry, San Diego State University, 5500 Campanile Dr., San Diego, CA, 92182, USA
| | - Xiaoji G Xu
- Department of Chemistry, Lehigh University, 6 E Packer Ave., Bethlehem, PA, 18015, USA
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8
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Jakob DS, Wang H, Zeng G, Otzen DE, Yan Y, Xu XG. Peak Force Infrared–Kelvin Probe Force Microscopy. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202004211] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Devon S. Jakob
- Department of Chemistry Lehigh University 6 E Packer Ave. Bethlehem PA 18015 USA
| | - Haomin Wang
- Department of Chemistry Lehigh University 6 E Packer Ave. Bethlehem PA 18015 USA
| | - Guanghong Zeng
- DFM A/S, Danish National Metrology Institute Kogle Alle 5 2970 Hørsholm Denmark
| | - Daniel E. Otzen
- Interdisciplinary Nanoscience Center (iNANO) Aarhus University Gustav Wields Vej 14 8000 Aarhus C Denmark
| | - Yong Yan
- Department of Chemistry San Diego State University 5500 Campanile Dr. San Diego CA 92182 USA
| | - Xiaoji G. Xu
- Department of Chemistry Lehigh University 6 E Packer Ave. Bethlehem PA 18015 USA
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