Study of Vibrational Energy Transfer in Proteins

蛋白质振动能量转移的研究

• 批准号: 14540474
• 负责人: KIDERA Akinori
• 金额: $ 2.18万
• 依托单位: Yokohama City University
• 依托单位国家: 日本
• 项目类别: Grant-in-Aid for Scientific Research (C)
• 财政年份: 2002
• 资助国家: 日本
• 起止时间: 2002 至 2003
• 项目状态: 已结题
• 来源: https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-14540474/
• 关键词: protein dynamics; molecular dynamics; anharmonic motions; vibration; diffusion; normal modes; mode coupling; principal component; タンパク質ダイナミクス; 基準振動モード; 非線型振動; 主成分解析; 多様体

Anharmonic dynamics of a protein molecule was studied by molecular dynamics simulations, (1)in terms of the intramolecular vibrational energy transfer, and (2)second through moving normal mode coordinates.(1)A small excess kinetic energy was added to a specified normal mode, and the process of the energy transfer to other modes was observed. It was found that the vibrational energy was transferred by two distinct mechanisms depending on temperature. At near zero temperature, the vibrational energy is transferred ass a process of the Fermi resonance. As the temperature increases, the resonance type transfer is dominated by the off-resonance energy transfer through various mode coupling terms.(2)A set of normal mode coordinates is defined at each time instant of the trajectory by principal component analysis (PCA) with a small time window. The time evolution of the normal mode coordinates defines the moving normal mode coordinates. Translation of he origin of he coordinates was decomposed into diffusion and vibrational motions. Significant parts of both types of motions occur in the large-amplitude normal mode space. Rotation of the large-amplitude normal mode space was characterized by fast relaxation completed within the time window of PCA, but was confined in a small space spanned by a limited number of large-amplitude normal modes.

用分子动力学模拟方法研究了蛋白质分子的非谐动力学，（1）分子内振动能量转移，（2）二次通过移动简正模坐标。(1)A在一个特定的简正模上加入少量的过剩动能，观察到能量向其它模转移的过程。结果发现，振动能量转移的两个不同的机制取决于温度。在接近零度时，振动能量通过费米共振过程转移。随着温度的升高，共振型能量转移主要是通过各种模式耦合项的非共振能量转移。(2)A通过具有小时间窗的主成分分析（PCA）在轨迹的每个时刻定义一组简正模式坐标。简正模坐标的时间演化定义了移动简正模坐标。将坐标原点的平移分解为扩散运动和振动运动。这两种类型的运动的显着部分发生在大振幅正常模式空间。旋转的大振幅正常模式空间的特点是快速弛豫完成的PCA的时间窗口内，但被限制在一个小的空间跨越有限数量的大振幅正常模式。

项目成果

K.Moritsugu, A.Kidera: "Protein motions represented in moving normal mode coordinates"J.Phys.Chem.B.. 108. 3890-3898 (2004)

K.Moritsugu、A.Kidera：“以移动法线模式坐标表示的蛋白质运动”J.Phys.Chem.B.. 108. 3890-3898 (2004)

S.Nakamura, M.Ikeguchi, K.Shimizu: "Dynamical Analysis of tRNAGln-GlnRS Complex using Normal Mode Calculation"Chem.Phys.Lett.. 372. 423-431 (2003)

S.Nakamura、M.Ikeguchi、K.Shimizu：“使用正态模式计算对 tRNAGln-GlnRS 复合物进行动态分析”Chem.Phys.Lett.. 372. 423-431 (2003)

S.Nakamura, D.Kyono, M.Ikeguchi, K.Shimizu: "A New Method for Parallel Computation of Hessian Matrix of Conformational Energy Function in Internal Coordinates"J.Comput.Chem.. 23. 463-469 (2002)

S.Nakamura、D.Kyono、M.Ikeguchi、K.Shimizu：“内坐标构象能量函数 Hessian 矩阵并行计算的新方法”J.Comput.Chem.. 23. 463-469 (2002)

K.Moritsugu, O.Miyashita, A.Kidera: "Temperature Dependence of Vibrational Energy Transfer in a Protein Molecule"Journal of Physical Chemistry B. 107. (2003)

K.Moritsugu、O.Miyashita、A.Kidera：“蛋白质分子中振动能量转移的温度依赖性”物理化学杂志 B.107。（2003 年）

K.Moritsugu, A.Kidera: "Protein motions represented in moving normal mode coordinates"J.Phys.Chem.B. 108. 3890-3898 (2004)

K.Moritsugu、A.Kidera：“以移动法线模式坐标表示的蛋白质运动”J.Phys.Chem.B。