Evolving model of amino acid networks

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.