Evolving model of amino acid networks
Evolving model of amino acid networks
复制标题
氨基酸网络的进化模型
DOI：
10.1103/physreve.77.061920
复制
发表时间：
2008-06-01
影响因子：
2.4
通讯作者：
Wang, Cun-xin
中科院分区：
文献类型：
--
作者：
Chang, Shan;Jiao, Xiong;Wang, Cun-xin
蛋白质的三维结构可以看作是由氨基酸组成的复杂网络，网络的性质可以帮助我们理解结构与功能之间的关系。由于蛋白质的氨基酸网络是在蛋白质折叠过程中形成的，一般的网络模型很难解释其演化机制。基于蛋白质折叠的观点，我们提出了一个氨基酸网络的演化模型。在我们的模型中，进化从天然蛋白质的氨基酸序列开始，并由两个通用假设指导：即，邻居优先规则和能量优先规则。我们发现，邻居优先规则主导的一般网络特性和能量优先规则主导的特定的生物结构特征。应用于天然蛋白质，我们的模型很好地模仿了氨基酸网络的功能。
The three-dimensional structure of a protein can be treated as a complex network composed of amino acids, and the network properties can help us to understand the relationship between structure and function. Since the amino acid network of a protein is formed in the process of protein folding, it is difficult for general network models to explain its evolving mechanism. Based on the perspective of protein folding, we propose an evolving model for amino acid networks. In our model, the evolution starts from the amino acid sequence of a native protein and it is guided by two generic assumptions: i.e., the neighbor preferential rule and the energy preferential rule. We find that the neighbor preferential rule predominates the general network properties and the energy preferential rule predominates the specific biological structure characteristics. Applied to native proteins, our model mimics the features of amino acid networks well.