Identifying the Nucleus Residues in Proteins by Network Approach

Identifying nucleus residues is crucial for studying the folding mechanisms of proteins. In this work, the protein structure is modeled as a network with the amino acid residues the vertices and contacts between them the edges. The amino acid networks for native states of 81 proteins are constructed. The amino acid networks have the typical property of small-world network. We performed two independent MD simulations of 12 ns for GB1 and CI2 at 498 K, respectively. The amino acid networks of protein GB1 and CI2 are constructed at three different states, the native, the transition, and denatured states on the unfolding pathway. The nucleus residues of GB1 and CI2 are identified by the analysis of the network parameter: betweenness of transition states. The results are consistent with the previous experimental and theoretical studies. This work is helpful to study the relationship between structure and function of protein.