Molecular Recognition Mechanism of RNA aptamer
| Project/Area Number |
18K11536
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| Research Category |
Grant-in-Aid for Scientific Research (C)
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| Allocation Type | Multi-year Fund |
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| Section | 一般 |
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| Review Section |
Basic Section 62010:Life, health and medical informatics-related
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| Research Institution | Nihon University |
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Principal Investigator |
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| Co-Investigator(Kenkyū-buntansha) |
坂本 泰一 千葉工業大学, 先進工学部, 教授 (40383369)
石川 岳志 鹿児島大学, 理工学域工学系, 教授 (80505909)
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| Project Period (FY) |
2018-04-01 – 2021-03-31
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| Project Status |
Completed (Fiscal Year 2020)
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| Budget Amount *help |
¥4,290,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥990,000)
Fiscal Year 2020: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2019: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
Fiscal Year 2018: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000)
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| Keywords | RNAアプタマー / 計算化学 / 分子シミュレーション / 分子動力学計算 / フラグメント分子軌道計算 / 核酸 / シミュレーション / 分子認識 |
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| Outline of Final Research Achievements |
We performed ab initio FMO calculation for the RNA aptamer-hFc1 complex to understand the high affinity and specificity of the RNA aptamer. We analyzed the intermolecular interactions between each nucleotide of the aptamer and each amino acid of hFc1 using FMO-IFIE analysis. The G7 nucleotide shows the strongest interaction energy with hFc1 among all groups. In particular, ionic interaction of the phosphate group of the G7 nucleotide with Lys340 results in a robust electrostatic interaction between the RNA aptamer and hFc1. We furthermore performed molecular dynamics simulation for the RNA aptamer-hFc1 complex with and without Ca2+ ions in a solvent. Only in the absence of Ca2+ ions, the RMSD increased and the structure of the aptamer changed from the initial structure. This result indicates that Ca2+ ions play a role in maintaining the conformation of the RNA aptamer to the binding form.
This study provides physicochemical insights into the binding of the RNA aptamer to hFc1.
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| Academic Significance and Societal Importance of the Research Achievements |
本研究により、論理的根拠に基づいたRNAアプタマーの設計が可能になり、アプタマー開発の大きな部分を占めていた配列の最適化や修飾基の導入工程を飛躍的に効率化させることができる。今までの方法では予測できなかった修飾を加えることで、活性を向上・変化させることも可能となり、画期的なRNAアプタマーの開発につながる。これにより、これまで有効な治療法のなかった疾患に対する治療薬の開発も期待でき、社会的にも大きな意義を持つ。
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Report
(4 results)
Research Products
(91 results)
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[Journal Article] Specific Inhibition of FGF5-induced Cell Proliferation by RNA Aptamers2021
Author(s)
Amano, R., Namekata, M., Horiuchi, M., Saso, M., Yanagisawa, T., Tanaka, Y., Ghani, F.I., Yamamoto, M., Sakamoto T.
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Journal Title
Scientific Reports
Volume: 11
Issue: 1
Pages: 2976-2976
DOI
Related Report
Peer Reviewed / Open Access / Int'l Joint Research
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[Journal Article] A G-quadruplex-forming RNA aptamer binds to the MTG8 TAFH domain and dissociates the leukemic AML1-MTG8 fusion protein from DNA2020
Author(s)
Fukunaga, J., Nomura, Y., Tanaka, Y., Torigoe, H., Nakamura, Y., Sakamoto, T., Kozu, T.
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Journal Title
FEBS Letters
Volume: 594
Issue: 21
Pages: 3477-3489
DOI
Related Report
Peer Reviewed
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[Journal Article] Development of analysis toolkit to visualize interaction energies generated by fragment molecular orbital calculations2018
Author(s)
Takaki Tokiwa, Shogo Nakano, Yuta Yamamoto, Takeshi Ishikawa, Sohei Ito, Vladimir Sladek, Kaori Fukuzawa, Yuji Mochizuki, Hiroaki Tokiwa, Fuminori Misaizu, and Yasuteru Shigeta
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Journal Title
J. Chem. Info. Model
Volume: 59(1)
Issue: 1
Pages: 25-30
DOI
Related Report
Peer Reviewed / Open Access / Int'l Joint Research
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