Yakushevich Ludmila
Institute of Cell Biophysics of the Russian Academy of Sciences, Institutskaya str. 3, Pushchino, Moscow Region, 142290, Russian Federation.
J Biol Phys. 2017 Mar;43(1):113-125. doi: 10.1007/s10867-016-9437-0. Epub 2016 Dec 30.
The creation of mechanical analogues of biological systems is known as a useful instrument that helps to understand better the dynamical mechanisms of the functioning of living organisms. Mechanical analogues of biomolecules are usually constructed for imitation of their internal mobility, which is one of the most important properties of the molecules. Among the different types of internal motions, angular oscillations of nitrous bases are of special interest because they make a substantial contribution to the base pairs opening that in turn is an important element of the process of the DNA-protein recognition. In this paper, we investigate the possibility to construct a mechanical analogue for imitation of angular oscillations of nitrous bases in inhomogeneous DNA. It is shown that the analogue has the form of a mechanical chain of non-identical pendulums that oscillate in the gravitational field of the Earth and coupled by identical springs. The masses and lengths of pendulums, as well as the distances between neighboring pendulums and the rigidity of springs are calculated. To illustrate the approach, we present the result of construction of the mechanical analogue of the fragment of the sequence of bacteriophage T7D.
创建生物系统的机械模拟物是一种有用的工具，有助于更好地理解生物体功能的动力学机制。生物分子的机械模拟物通常用于模仿其内部流动性，这是分子最重要的特性之一。在不同类型的内部运动中，含氮碱基的角振荡特别受关注，因为它们对碱基对的打开有很大贡献，而碱基对的打开又是DNA-蛋白质识别过程的一个重要元素。在本文中，我们研究了构建一个机械模拟物来模仿非均匀DNA中含氮碱基角振荡的可能性。结果表明，该模拟物具有由在地球引力场中振荡且通过相同弹簧耦合的不同摆组成的机械链的形式。计算了摆的质量和长度，以及相邻摆之间的距离和弹簧的刚度。为了说明该方法，我们展示了噬菌体T7D序列片段的机械模拟物的构建结果。
