Design of protein binders based on the activation energy of interaction
| Project/Area Number |
15K17882
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| Research Category |
Grant-in-Aid for Young Scientists (B)
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| Allocation Type | Multi-year Fund |
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| Research Field |
Bio-related chemistry
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| Research Institution | The University of Tokyo |
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Principal Investigator |
NAGATOISHI SATORU 東京大学, 大学院工学系研究科(工学部), 助教 (30550248)
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| Project Period (FY) |
2015-04-01 – 2017-03-31
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| Project Status |
Completed (Fiscal Year 2016)
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| Budget Amount *help |
¥4,160,000 (Direct Cost: ¥3,200,000、Indirect Cost: ¥960,000)
Fiscal Year 2016: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
Fiscal Year 2015: ¥2,730,000 (Direct Cost: ¥2,100,000、Indirect Cost: ¥630,000)
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| Keywords | 蛋白質 / 薬剤 / 熱力学 / 速度論 / 活性化エネルギー / 阻害剤 / 低分子創薬 / リガンド |
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| Outline of Final Research Achievements |
This study focused on the process of the interaction. Since it is assumed that a small compound forms some intermediate states with various amino acids and finally binds to the energy-stable site of protein, the process is possibly differ among proteins. Here, the binding kinetic analysis was carried out to elucidate the binding process of the compound to protein. In this study, complexed energy transition in the binding process is simplified as two state reaction and the state where a compound is in process is regarded as transition state. From the analysis of thermodynamic parameters in transition state, the transition state is examined at amino acid level and the relationship between transition state and binding process is discussed. This allows us to verify the possibility of obtaining an important indicator for drug design.
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Report
(3 results)
Research Products
(30 results)
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[Journal Article] Structural basis for amino-acid export by DMT superfamily transporter YddG2016
Author(s)
H. Tsuchiya, S. Doki, M. Takemoto, T. Ikuta, T. Higuchi, K. Fukui, Y. Usuda, E. Tabuchi, S. Nagatoishi, K. Tsumoto, T. Nishizawa, K. Ito, N. Dohmae, R. Ishitani and O. Nureki
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Journal Title
Nature
Volume: 534
Issue: 7607
Pages: 417-420
DOI
Related Report
Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
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[Journal Article] Epiregulin Recognition Mechanisms by Anti-epiregulin Antibody 9E5: STRUCTURAL, FUNCTIONAL, AND MOLECULAR DYNAMICS SIMULATION ANALYSES.2016
Author(s)
Kado Y1, Mizohata E2, Nagatoishi S3, Iijima M4, Shinoda K4, Miyafusa T3, Nakayama T2, Yoshizumi T2, Sugiyama A4, Kawamura T4, Lee YH4, Matsumura H2, Doi H4, Fujitani H4, Kodama T4, Shibasaki Y4, Tsumoto K5, Inoue T6.
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Journal Title
J Biol Chem.
Volume: 291
Issue: 5
Pages: 2319-2330
DOI
Related Report
Peer Reviewed / Open Access / Int'l Joint Research
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