Improvement of sequence specificity of DNA-binding protein using computational and experimental approaches

2016 Fiscal Year Final Research Report

• Project/Area Number: 26330339
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Research Field: Life / Health / Medical informatics
• Research Institution: National Institutes for Quantum and Radiological Science and Technology (2016); Japan Atomic Energy Agency (2014-2015)
• Principal Investigator: KONO HIDETOSHI 国立研究開発法人量子科学技術研究開発機構, 関西光科学研究所 量子生命科学研究部, グループリーダー(定常) (40291918)
• Co-Investigator(Renkei-kenkyūsha): SUNAMI Tomoko 国立研究開発法人量子科学技術研究開発機構, 関西光科学研究所 量子生命科学研究部, 主幹研究員 (50554648)
• Project Period (FY): 2014-04-01 – 2017-03-31
• Keywords: DNA結合蛋白質 / 分子シミュレーション / 生体生命情報学 / バイオインフォマティクス / 蛋白質設計 / B1H

Outline of Final Research Achievements

We successfully created a designed-protein which can bind to a target DNA sequence with high specificity. In the design, we connected two DNA-binding proteins after engineered one mutation which reduces the affinity of the monomer. Then, we combined these domains to create a dimer protein and confirmed that it binds to the target sequence by B1H assay. In addition, to understand the DNA sequence dependent, physico-chemical property, we carried out molecular dynamics simuations on many DNA sequences. We extracted some feature parameters from the sampled conformations using a machine learning technique. We found that the values of the feature parameters at transcription binding sites as well as within 200bp up and down streams from the binding sites are different from those of non-binding sites.

Free Research Field

生命情報科学、生物物理学、蛋白質科学