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.

通过分子动力学模拟研究了蛋白质分子的非谐动力学，（1）就分子内振动能传递而言，以及（2）通过移动正常模式坐标的第二个。观察到模式以及能量转移到其他模式的过程。发现振动能通过温度取决于两种不同的机制。在接近零温度下，振动能被转移到费米共振的过程中。随着温度的升高，共振类型的转移由各种模式耦合项的非谐振能量传输主导。（2）在每次通过主成分分析（PCA）的轨迹时，定义了一组正常模式坐标。一个小的时间窗口。正常模式的时间演变坐标定义了移动的正常模式坐标。 HE坐标起源的翻译分解为扩散和振动运动。两种运动的重要部分都在大振幅正常模式空间中发生。大振幅正常模式空间的旋转是在PCA的时间窗口内完成的快速放松的特征，但被限制在有限数量的大振幅正常模式的小空间中。

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。

J.G.Kim, Y.Fukunishi, A.Kidera, H.Nakamura: "Stochastic formulation of sampling dynamics in generalized ensemble methods"Physical Review B. 69. 021101 1-021101 10 (2004)

J.G.Kim、Y.Fukunishi、A.Kidera、H.Nakamura：“广义集成方法中采样动力学的随机公式”物理评论 B. 69. 021101 1-021101 10 (2004)

R.Koike, K.Kinoshita, A.Kidera: "Ring and zipper formation is the key to understanding the structural variety in all beta proteins"FEBS Letters. 533. 9-13 (2003)

R.Koike、K.Kinoshita、A.Kidera：“环和拉链的形成是理解所有 β 蛋白结构多样性的关键”FEBS Letters。

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)

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）