Network Parameters of Protein Structure and the Folding Rate

A challenging task is to understand the relationship between sequences and folding rates of proteins. Previous studies found that one of contact order (CO), long-range order (LRO), and total contact distance (TCD) has a significant correlation with folding rate of protein. The network concept is increasingly used to describe the topology and dynamics of complex systems. In this paper, the protein structure is modeled as a network from three methods to calculate the contacts among residues and the three type networks (PCNs, LINs, SINs) are constructed to uncover the different influence of long-range and short-range interactions on two-state folding kinetics. The results show that the network parameters which contacts are calculated from the geometrical center of side chain have lower correlation with Ink_f than the other two methods. Short-range interactions play a key role in determining the connecting trend among amino acids and influence directly the folding rate of two-state proteins.