蛋白质动力学中快速运动的层次性
The Hierarchy of Fast Motions in Protein Dynamics
摘要：
对于分子动力学（MD）的许多生物学应用，构象空间中良好采样的重要性使得有必要从系统中消除最快运动以增加时间步长。对这些运动的准确认识是这种努力的必要先决条件。众所周知，键长和键角的谐波振动在蛋白质中产生最高频率。也有快速的非谐运动，如原子间碰撞，当键长和键角固定时，这可能是最重要的。然而，与所有这些限制相对应的具体时间尺度并不确切。为了澄清上述问题，本文分析了时间步长的限制因素，在一系列的数值试验中，使用内坐标分子动力学的方法，它允许选定的内坐标被冻结。据发现，在蛋白质中，有一个相当复杂的层次结构的快速运动，谐波和非谐波效应混合在一起，在几个密切的时间尺度。非键的相互作用，特别是强氢键，产生局部分布的正常模式的频率类似于非氢原子之间的键拉伸。它们还从相当小的步长开始施加普遍存在的非谐波限制。在固定的标准氨基酸几何形状下，氢键合的羟基的旋转将时间步长限制在5fsec水平。下一个重要的限制出现在10飞秒左右，是由非氢原子之间的碰撞产生的。
英文摘要：
For many biological applications of molecular dynamics (MD) the importance of good sampling in conformational space makes it necessary to eliminate the fastest motions from the system in order to increase the time step. An accurate knowledge of these motions is a necessary prerequisite for such efforts. It is known that harmonic vibrations of bond lengths and bond angles produce the highest frequencies in proteins. There are also fast anharmonic motions, such as inter-atomic collisions, which are probably most important when bond lengths and bond angles are fixed. However, the specific time scales corresponding to all these limitations are not known precisely. In order to clarify the above issue this paper analyses time step limiting factors in a series of numerical tests by using an internal coordinate molecular dynamics approach, which allows chosen internal coordinates to be frozen. It is found that, in proteins, there is a rather complicated hierarchy of fast motions, with both harmonic and anharmonic effects mixed together at several close time scales. Non-bonded interactions, notably strong hydrogen bonding, create locally distributed normal modes with frequencies similar to those of bond stretching between non-hydrogen atoms. They also impose ubiquitous anharmonic limitations starting from rather small step sizes. With fixed standard amino acid geometry, rotations of hydrogen bonded hydroxyl groups limit time steps at the 5 fsec level. The next important limitation occurs around 10 fsec and is created by collisions between non-hydrogen atoms.
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