Effects on p53 diffusion along dsDNA and nonspecific binding constant between p53 and dsDNA of hyper-mobile water control

2021 Fiscal Year Final Research Report

• Project/Area Number: 19K06576
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Review Section: Basic Section 43040:Biophysics-related
• Research Institution: Tohoku University
• Principal Investigator: Suzuki Makoto 東北大学, 多元物質科学研究所, 名誉教授 (60282109)
• Co-Investigator(Kenkyū-buntansha): 鎌形 清人 東北大学, 多元物質科学研究所, 准教授 (90432492) ; 最上 譲二 東北大学, 工学研究科, 助教 (70713022)
• Project Period (FY): 2019-04-01 – 2022-03-31
• Keywords: DNAタンパク質相互作用 / DNA水和 / 誘電分光水和解析 / ラマン分光水和解析 / OH stretch band / cooperative vibration / 水分子間協同振動モード

Outline of Final Research Achievements

The binding between a protein molecule and DNA is an intermolecular interaction in water. Electrostatic force and van der Waals force are the protagonists and depend on the nature of water. Here, we investigated how the water around DNA differs from the properties of pure water. High-resolution microwave dielectric spectroscopy, high-resolution Raman OH stretch band spectroscopy, and molecular dynamics (MD) computation were used in the study. Dielectric spectroscopy detected water around dsDNA that had a faster and slower orientation response than pure water. And from Raman spectroscopy, a new band of cooperative vibration mode of many water molecules at the low wavenumber side of the OH stretch band of pure water was detected. By these results and MD calculation, it was found that more than ten times the volume of water as DNA is different from pure water. It will deepen our understanding of DNA protein binding and sequence recognition.

Free Research Field

生体分子の溶液科学

Academic Significance and Societal Importance of the Research Achievements

この研究は、dsDNA鎖上をガン抑制蛋白質p53の１次元拡散係数が溶液内のMgやCaイオンの添加により高まるとの論文に興味を持ち、DNA鎖が周りの水に与える影響とDNA周りの水への各イオンの影響を調べるこの研究を進めた。その結果これまで観測されたことのないDNA鎖周りの水の密度等性質が通常水と大きく異なることを高分解誘電とラマン分光法とMD計算で明らかにした。水の性質のDNA-蛋白質等分子間相互作用への影響は物理化学分野の課題であり、DNA関連生化学や医学薬学分野につながると思われる。