Molecular dynamics study on proteins searching for the recognition sequence of DNA

2017 Fiscal Year Final Research Report

• Project/Area Number: 26800228
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Multi-year Fund
• Research Field: Biological physics/Chemical physics/Soft matter physics
• Research Institution: National Institutes for Quantum and Radiological Science and Technology (2016-2017); Japan Atomic Energy Agency (2014-2015)
• Principal Investigator: YONETANI YOSHITERU 国立研究開発法人量子科学技術研究開発機構, 高崎量子応用研究所 東海量子ビーム応用研究センター, 主幹研究員(定常) (80399419)
• Project Period (FY): 2014-04-01 – 2018-03-31
• Keywords: 分子動力学シミュレーション / 自由エネルギー / レアイベント / カイネティクス / レートコンスタント / 生体分子

Outline of Final Research Achievements

Molecular dynamics simulations are performed to explore the kinetics of a protein searching for the recognition sequence of DNA. By applying bias force, various protein motions were induced. Among them, a possible motion was obtained when the bias force was applied to the direction from the binding site to the protein center of mass. Simulations with this setting successfully produced spiral motion of protein where the protein slides on the DNA while maintaining the DNA-protein contact surface. Results of free-energy calculations suggest that such protein sliding is much preferred to dissociation. Relation between free-energy profiles and transition rate constant is also discussed within the framework of transition state theory, which enables us to make more reliable discussion about the protein kinetics.

Free Research Field

化学物理・生物物理