Wako Hiroshi, Kato Masaki, Endo Shigeru
School of Social Sciences, Waseda University, Tokyo 169-8050, Japan.
Bioinformatics. 2004 Sep 1;20(13):2035-43. doi: 10.1093/bioinformatics/bth197. Epub 2004 Apr 1.
Although information from protein dynamics simulation is important to understand principles of architecture of a protein structure and its function, simulations such as molecular dynamics and Monte Carlo are very CPU-intensive. Although the ability of normal mode analysis (NMA) is limited because of the need for a harmonic approximation on which NMA is based, NMA is adequate to carry out routine analyses on many proteins to compute aspects of the collective motions essential to protein dynamics and function. Furthermore, it is hoped that realistic animations of the protein dynamics can be observed easily without expensive software and hardware, and that the dynamic properties for various proteins can be compared with each other.
ProMode, a database collecting NMA results on protein molecules, was constructed. The NMA calculations are performed with a full-atom model, by using dihedral angles as independent variables, faster and more efficiently than the calculations using Cartesian coordinates. In ProMode, an animation of the normal mode vibration is played with a free plug-in, Chime (MDL Information Systems, Inc.). With the full-atom model, the realistic three-dimensional motions at an atomic level are displayed with Chime. The dynamic domains and their mutual screw motions defined from the NMA results are also displayed. Properties for each normal mode vibration and their time averages, e.g. fluctuations of atom positions, fluctuations of dihedral angles and correlations between the atomic motions, are also presented graphically for characterizing the collective motions in more detail.
尽管蛋白质动力学模拟得到的信息对于理解蛋白质结构及其功能的构建原理很重要，但诸如分子动力学和蒙特卡罗等模拟计算量极大。虽然由于正常模式分析（NMA）基于谐波近似，其能力有限，但NMA足以对许多蛋白质进行常规分析，以计算蛋白质动力学和功能所必需的集体运动的各个方面。此外，人们希望无需昂贵的软件和硬件就能轻松观察到逼真的蛋白质动力学动画，并且能够相互比较各种蛋白质的动力学特性。
构建了一个收集蛋白质分子NMA结果的数据库ProMode。NMA计算采用全原子模型，以二面角作为自变量，比使用笛卡尔坐标的计算更快、更高效。在ProMode中，使用免费插件Chime（MDL信息系统公司）播放正常模式振动的动画。通过全原子模型，Chime展示了原子水平上逼真的三维运动。还展示了根据NMA结果定义的动态结构域及其相互的螺旋运动。每个正常模式振动的特性及其时间平均值，例如原子位置的波动、二面角的波动以及原子运动之间的相关性，也以图形方式呈现，以便更详细地描述集体运动。
