2018 Fiscal Year Final Research Report
Elucidation of dependence of secondary structure on the formation of protein structure and development of new forcefield incorporating effects of secondary structure
| Project/Area Number |
16K07325
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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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| Research Field |
Biophysics
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| Research Institution | Hiroshima City University |
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Principal Investigator |
Takano Yu 広島市立大学, 情報科学研究科, 教授 (30403017)
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| Research Collaborator |
NAKAMURA Haruki
SAITO Toru
KONDO Hiroko
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| Project Period (FY) |
2016-04-01 – 2019-03-31
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| Keywords | 水素結合 / タンパク質 / 高次構造 / 構造形成 / 二次構造 |
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| Outline of Final Research Achievements |
The classical molecular dynamics simulation is important for the understanding of the protein functions. However, the accuracy of the molecular force field used in the simulation is insufficient. Since hydrogen bonds (H-bonds) in protein backbones are essential to form their characteristic three-dimensional structures based on their ordered secondary structures, alpha-helices and beta-sheets, H-bond interaction energies in α-helices of short alanine peptides were systematically examined by precise DFT calculations in this project. Our computations showed that H-bond interaction energies in alpha-helices were always significantly weaker than those in the minimal H-bond models, in which only H-bond donors and acceptors exist. we found that the reduced H-bond energy originated from the depolarizations of both the H-bond donor and acceptor groups, due to the repulsive interactions with the neighboring polar peptide groups in the alpha-helix backbone.
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| Free Research Field |
生物物理学
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| Academic Significance and Societal Importance of the Research Achievements |
タンパク質構造形成に重要であるアミノ酸主鎖の水素結合エネルギーには高次構造依存性が代表的な二次構造であるαヘリックスに関して示され、その起源も明らかにした。この成果は、構造形成に関わる水素結合が二次構造の影響を受けているという力場の本質的な問題を顕わにし、二次構造にもとづく分子力場の開発の必要性を示した。今後、高次構造依存性をとりこんだ新たな力場により、これまで力場の問題のために到達できないと思われていたミリ秒から秒にわたる長時間MDによるタンパク質の動的構造の追跡にも挑戦することが可能となり、タンパク質構造予測等の計算の信頼性が向上し、タンパク質設計による新規機能性分子の創成も期待される。
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