Nishikawa T, Go N
Department of Physics, Faculty of Science, Kyushu University, Fukuoka, Japan.
Proteins. 1987;2(4):308-29. doi: 10.1002/prot.340020407.
The normal mode analysis of conformational fluctuation is carried out for a small globular protein, bovine pancreatic trypsin inhibitor. Results are analyzed mainly to reveal the mechanical construction of the protein molecule. We take dihedral angles, including peptide omega angles, as independent variables for the normal mode analysis. There are 306 such angles in this molecule. Motions in modes with frequencies lower than 120 cm-1 are shown to involve atoms in the whole protein molecule, and spatial change of displacement vectors is continuous, i.e., those of atoms near in space are similar. To quantitate the observation of the continuity, a correlation function of direction vectors of atomic displacements is calculated. From this function we define a quantity that is interpreted as the wave length of an equivalent elastic plane wave. From this quantity we deduce effective Young's modulus for each mode. For the mode with the lowest frequency 4.4 cm-1, it turned out to be 0.8 x 10(9) dyn cm-2, the value two orders of magnitude softer than, for instance, alpha-helices. Prompted by this observation, the four lowest frequency modes and also the harmonic motions in the thermal equilibrium are analyzed further mainly to detect relatively rigid structural elements in the molecule. From this analysis emerges a mechanical picture of the protein molecule that is made up of relatively rigid elements held together by very soft parts.
对一种小的球状蛋白质——牛胰蛋白酶抑制剂进行了构象波动的正常模式分析。主要对结果进行分析以揭示蛋白质分子的机械结构。我们将二面角，包括肽ω角，作为正常模式分析的自变量。该分子中有306个这样的角。频率低于120 cm-1的模式中的运动显示涉及整个蛋白质分子中的原子，并且位移矢量的空间变化是连续的，即空间上靠近的原子的位移矢量相似。为了定量观察这种连续性，计算了原子位移方向矢量的相关函数。从这个函数中我们定义了一个量，它被解释为等效弹性平面波的波长。从这个量中我们推导出每个模式的有效杨氏模量。对于最低频率4.4 cm-1的模式，结果表明其为0.8×10(9) dyn cm-2，该值比例如α螺旋软两个数量级。受此观察结果的启发，进一步分析了四个最低频率模式以及热平衡中的简谐运动，主要是为了检测分子中相对刚性的结构元件。从该分析中出现了蛋白质分子的机械图像，它由通过非常柔软的部分连接在一起的相对刚性的元件组成。
