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Peng S, Liu X, Lu C, Wang H, Liu X, Gong Q, Tao H, Xu H, Tian C, Xu G, Li JB. Efficient Chemical Synthesis of Multi-Monoubiquitylated and Diubiquitylated Histones by the α-Halogen Ketone-Mediated Strategy. Bioconjug Chem 2024. [PMID: 38954775 DOI: 10.1021/acs.bioconjchem.4c00130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2024]
Abstract
The chemical synthesis of homogeneously ubiquitylated histones is a powerful approach to decipher histone ubiquitylation-dependent epigenetic regulation. Among the various methods, α-halogen ketone-mediated conjugation chemistry has recently been an attractive strategy to generate single-monoubiquitylated histones for biochemical and structural studies. Herein, we report the use of this strategy to prepare not only dual- and even triple-monoubiquitylated histones but also diubiquitin-modified histones. We were surprised to find that the synthetic efficiencies of multi-monoubiquitylated histones were comparable to those of single-monoubiquitylated ones, suggesting that this strategy is highly tolerant to the number of ubiquitin monomers installed onto histones. The facile generation of a series of single-, dual-, and triple-monoubiquitylated H3 proteins enabled us to evaluate the influence of ubiquitylation patterns on the binding of DNA methyltransferase 1 (DNMT1) to nucleosomes. Our study highlights the potential of site-specific conjugation chemistry to generate chemically defined histones for epigenetic studies.
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Affiliation(s)
- Shuai Peng
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou 215123, China
| | - Xin Liu
- The First Affiliated Hospital of USTC, School of Life Sciences, Division of Life Sciences and Medicine, Joint Center for Biological Analytical Chemistry, Anhui Engineering Laboratory of Peptide Drug, Anhui Laboratory of Advanced Photonic Science and Technology, University of Science and Technology of China, Hefei 230026, China
| | - Chengpiao Lu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou 215123, China
| | - Haibo Wang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou 215123, China
| | - Xiaotong Liu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou 215123, China
| | - Qingyue Gong
- The First Affiliated Hospital of USTC, School of Life Sciences, Division of Life Sciences and Medicine, Joint Center for Biological Analytical Chemistry, Anhui Engineering Laboratory of Peptide Drug, Anhui Laboratory of Advanced Photonic Science and Technology, University of Science and Technology of China, Hefei 230026, China
| | - Huizhong Tao
- The First Affiliated Hospital of USTC, School of Life Sciences, Division of Life Sciences and Medicine, Joint Center for Biological Analytical Chemistry, Anhui Engineering Laboratory of Peptide Drug, Anhui Laboratory of Advanced Photonic Science and Technology, University of Science and Technology of China, Hefei 230026, China
| | - Hongrui Xu
- Suzhou Municipal Center for Disease Control and Prevention, Suzhou 215004, China
| | - Changlin Tian
- The First Affiliated Hospital of USTC, School of Life Sciences, Division of Life Sciences and Medicine, Joint Center for Biological Analytical Chemistry, Anhui Engineering Laboratory of Peptide Drug, Anhui Laboratory of Advanced Photonic Science and Technology, University of Science and Technology of China, Hefei 230026, China
| | - Guoqiang Xu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou 215123, China
| | - Jia-Bin Li
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou 215123, China
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2
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Li Z, Tong Z, Gong Q, Ai H, Peng S, Chen C, Chu GC, Li JB. The expedient, CAET-assisted synthesis of dual-monoubiquitinated histone H3 enables evaluation of its interaction with DNMT1. Chem Sci 2023; 14:5681-5688. [PMID: 37265717 PMCID: PMC10231317 DOI: 10.1039/d3sc00332a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 04/30/2023] [Indexed: 06/03/2023] Open
Abstract
Site-selective conjugation chemistry has proven effective to synthesize homogenously ubiquitinated histones. Recently, a powerful strategy using 2-((2-chloroethyl) amino) ethane-1-thiol (CAET) as a bifunctional handle was developed to generate chemically stable ubiquitin chains without racemization and homodimerization. Herein, we extend this strategy to the expedient synthesis of ubiquitinated histones, exemplifying its utility to not only synthesize single-monoubiquitinated histones, but dual-monoubiquitinated histones as well. The synthetic histones enabled us to evaluate the binding of DNMT1 to ubiquitinated nucleosomes and map the hotspots of this interaction. Our work highlights the potential of modern chemical protein synthesis to synthesize ubiquitinated histones for epigenetic studies.
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Affiliation(s)
- Zichen Li
- Department of Chemistry, Tsinghua-Peking Center for Life Sciences, Tsinghua University Beijing 100084 China
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University Suzhou, 215123 China
| | - Zebin Tong
- Department of Chemistry, Tsinghua-Peking Center for Life Sciences, Tsinghua University Beijing 100084 China
| | - Qingyue Gong
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University Suzhou, 215123 China
- School of Life Sciences, University of Science and Technology of China Hefei 230026 China
| | - Huasong Ai
- Department of Chemistry, Tsinghua-Peking Center for Life Sciences, Tsinghua University Beijing 100084 China
| | - Shuai Peng
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University Suzhou, 215123 China
| | - Cong Chen
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University Suzhou, 215123 China
| | - Guo-Chao Chu
- Department of Chemistry, Tsinghua-Peking Center for Life Sciences, Tsinghua University Beijing 100084 China
| | - Jia-Bin Li
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University Suzhou, 215123 China
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3
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Maas MN, Hintzen JCJ, Mecinović J. Probing lysine posttranslational modifications by unnatural amino acids. Chem Commun (Camb) 2022; 58:7216-7231. [PMID: 35678513 DOI: 10.1039/d2cc00708h] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Posttranslational modifications, typically small chemical tags attached on amino acids following protein biosynthesis, have a profound effect on protein structure and function. Numerous chemically and structurally diverse posttranslational modifications, including methylation, acetylation, hydroxylation, and ubiquitination, have been identified and characterised on lysine residues in proteins. In this feature article, we focus on chemical tools that rely on the site-specific incorporation of unnatural amino acids into peptides and proteins to probe posttranslational modifications of lysine. We highlight that simple amino acid mimics enable detailed mechanistic and functional assignment of enzymes that install and remove such modifications, and proteins that specifically recognise lysine posttranslational modifications.
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Affiliation(s)
- Marijn N Maas
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark.
| | - Jordi C J Hintzen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark.
| | - Jasmin Mecinović
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark.
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Mishima Y, Brueckner L, Takahashi S, Kawakami T, Otani J, Shinohara A, Takeshita K, Garvilles RG, Watanabe M, Sakai N, Takeshima H, Nachtegael C, Nishiyama A, Nakanishi M, Arita K, Nakashima K, Hojo H, Suetake I. Enhanced processivity of Dnmt1 by monoubiquitinated histone H3. Genes Cells 2019; 25:22-32. [DOI: 10.1111/gtc.12732] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 10/30/2019] [Accepted: 10/30/2019] [Indexed: 12/30/2022]
Affiliation(s)
- Yuichi Mishima
- Laboratory of Epigenetics Institute for Protein Research Osaka University Suita Japan
| | - Laura Brueckner
- Laboratory of Epigenetics Institute for Protein Research Osaka University Suita Japan
| | - Saori Takahashi
- Laboratory of Epigenetics Institute for Protein Research Osaka University Suita Japan
| | - Toru Kawakami
- Laboratory of Organic Chemistry Institute for Protein Research Osaka University Suita Japan
| | - Junji Otani
- Laboratory of Epigenetics Institute for Protein Research Osaka University Suita Japan
| | - Akira Shinohara
- Laboratory of Genome‐Chromosome Function Institute for Protein Research Osaka University Suita Japan
| | | | | | - Mikio Watanabe
- Center for Twin Research Graduate School of Medicine Osaka University Suita Japan
| | - Norio Sakai
- Center for Twin Research Graduate School of Medicine Osaka University Suita Japan
| | - Hideyuki Takeshima
- Division of Epigenomics National Cancer Center Research Institute Tokyo Japan
| | - Charlotte Nachtegael
- Laboratory of Epigenetics Institute for Protein Research Osaka University Suita Japan
- Interuniversity Institute of Bioinformatics in Brussels Universite Libre de Bruxelles‐Vrije Universiteit Brussel Brussels Belgium
| | - Atsuya Nishiyama
- Division of Cancer Cell Biology The Institute of Medical Science The University of Tokyo Tokyo Japan
| | - Makoto Nakanishi
- Division of Cancer Cell Biology The Institute of Medical Science The University of Tokyo Tokyo Japan
| | - Kyohei Arita
- Graduate School of Medical Life Science Yokohama City University Yokohama Japan
| | - Kinichi Nakashima
- Department of Stem Cell Biology and Medicine Graduate School of Medical Sciences Kyushu University Fukuoka Japan
| | - Hironobu Hojo
- Laboratory of Organic Chemistry Institute for Protein Research Osaka University Suita Japan
| | - Isao Suetake
- Laboratory of Epigenetics Institute for Protein Research Osaka University Suita Japan
- Center for Twin Research Graduate School of Medicine Osaka University Suita Japan
- College of Nutrition Koshien University Takarazuka Japan
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5
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Liang J, Gong Q, Li Y, Zheng Y, Zheng JS, Tian C, Li JB. Thiirane linkers directed histone H2A diubiquitination suggests plasticity in 53BP1 recognition. Chem Commun (Camb) 2019; 55:12639-12642. [PMID: 31580339 DOI: 10.1039/c9cc05526f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Polyubiquitination with diverse linkages on histones provides another layer of accuracy and complexity for epigenetic regulation, which is rarely studied. Herein, K27 or K48-diubiquitin modified H2A analogues were chemically synthesized using thiirane linkers. These permitted in vitro binding studies suggested the plasticity of ubiquitin chains in 53BP1 recognition.
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Affiliation(s)
- Jun Liang
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Science, University of Science and Technology of China, Hefei 230026, China.
| | - Qingyue Gong
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Science, University of Science and Technology of China, Hefei 230026, China. and Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China.
| | - Ying Li
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Science, University of Science and Technology of China, Hefei 230026, China.
| | - Yong Zheng
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Science, University of Science and Technology of China, Hefei 230026, China.
| | - Ji-Shen Zheng
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Science, University of Science and Technology of China, Hefei 230026, China.
| | - Changlin Tian
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Science, University of Science and Technology of China, Hefei 230026, China.
| | - Jia-Bin Li
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China.
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6
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Kawakami T, Mishima Y, Takazawa M, Hojo H, Suetake I. Chemical synthesis of the ubiquitinated form of histone H3 and its effect on DNA methyltransferase 1. J Pept Sci 2019; 25:e3200. [PMID: 31309659 DOI: 10.1002/psc.3200] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 05/27/2019] [Accepted: 06/14/2019] [Indexed: 12/26/2022]
Abstract
Posttranslational modifications of histone proteins, which form nucleosome cores, play an important role in gene regulation. Ubiquitination is one such modification. We previously reported on the synthesis of ubiquitinated histone H3 with an isopeptide mimetic structure. In this report, we describe the preparation of ubiquitinated histone H3 peptides with a native isopeptide structure, which showed a slightly weaker effect on the enzymatic activity of DNA methyltransferase 1 than the previous ubiquitinated H3 peptide analogs. These findings show that a native structure is important for determining the mechanism of the function, although ubiquitinated H3 peptide analogs can mimic the role of the original ubiquitinated H3. We also report on the successful preparation of the ubiquitinated full length histone H3.
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Affiliation(s)
- Toru Kawakami
- Institute for Protein Research, Osaka University, Suita, Japan
| | - Yuichi Mishima
- Institute for Protein Research, Osaka University, Suita, Japan
| | - Masaya Takazawa
- Institute for Protein Research, Osaka University, Suita, Japan
| | - Hironobu Hojo
- Institute for Protein Research, Osaka University, Suita, Japan
| | - Isao Suetake
- Institute for Protein Research, Osaka University, Suita, Japan.,College of Nutrition, Koshien University, Takarazuka, Japan
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7
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Asahina Y, Kawakami T, Hojo H. Glycopeptide Synthesis Based on a TFA-Labile Protection Strategy and One-Pot Four-Segment Ligation for the Synthesis of O-Glycosylated Histone H2A. European J Org Chem 2019. [DOI: 10.1002/ejoc.201801885] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Yuya Asahina
- Institute for Protein Research; Osaka University; Yamadaoka 3-2, Suita Osaka 565-0871 Japan
| | - Toru Kawakami
- Institute for Protein Research; Osaka University; Yamadaoka 3-2, Suita Osaka 565-0871 Japan
| | - Hironobu Hojo
- Institute for Protein Research; Osaka University; Yamadaoka 3-2, Suita Osaka 565-0871 Japan
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8
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Jbara M, Sun H, Kamnesky G, Brik A. Chemical chromatin ubiquitylation. Curr Opin Chem Biol 2018; 45:18-26. [PMID: 29459258 DOI: 10.1016/j.cbpa.2018.02.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 01/28/2018] [Accepted: 02/04/2018] [Indexed: 12/01/2022]
Abstract
Histone modifications dynamically regulate chromatin structure and function, thereby mediating many processes that require access to DNA. Chemical protein synthesis has emerged as a powerful approach for generating homogeneously modified histone analogues in workable amounts for subsequent incorporation into nucleosome arrays for biochemical, functional and structural studies. This short review focuses on the strength of total chemical protein synthesis and semisynthetic approaches to generate ubiquitylated histones in their native or non-native forms and the utility of these analogues to decode the role of ubiquitylation in epigenetics.
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Affiliation(s)
- Muhammad Jbara
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 3200008, Israel
| | - Hao Sun
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 3200008, Israel
| | - Guy Kamnesky
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 3200008, Israel
| | - Ashraf Brik
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 3200008, Israel.
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9
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Bi X, Pasunooti KK, Liu CF. Total chemical and semisynthetic approaches for the preparation of ubiquitinated proteins and their applications. Sci China Chem 2017. [DOI: 10.1007/s11426-017-9122-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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10
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Morimoto D, Walinda E, Sugase K, Shirakawa M. Biological and Physicochemical Functions of Ubiquitylation Revealed by Synthetic Chemistry Approaches. Int J Mol Sci 2017; 18:ijms18061145. [PMID: 28555012 PMCID: PMC5485969 DOI: 10.3390/ijms18061145] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Revised: 05/23/2017] [Accepted: 05/24/2017] [Indexed: 01/08/2023] Open
Abstract
Most intracellular proteins are subjected to post-translational modification by ubiquitin. Accordingly, it is of fundamental importance to investigate the biological and physicochemical effects of ubiquitylation on substrate proteins. However, preparation of ubiquitylated proteins by an enzymatic synthesis bears limitations in terms of yield and site-specificity. Recently established chemical ubiquitylation methodologies can overcome these problems and provide a new understanding of ubiquitylation. Herein we describe the recent chemical ubiquitylation procedures with a focus on the effects of ubiquitylation on target proteins revealed by the synthetic approach.
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Affiliation(s)
- Daichi Morimoto
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-ku, Kyoto 615-8510, Japan.
| | - Erik Walinda
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.
| | - Kenji Sugase
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-ku, Kyoto 615-8510, Japan.
| | - Masahiro Shirakawa
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-ku, Kyoto 615-8510, Japan.
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