Determination of unfolding rate and Identification of native protein structure

Abstract

We see the results about the determination of protein unfolding rate and the recognition of protein native structure. For proteins which fold by two-state kinetics, the folding and unfolding processes are believed to be closely related to their native structures. In particular, folding and unfolding rates are influenced by the native structures of proteins. Thus we focus on finding important topological quantities from a protein structure which determine its unfolding rate. After constructing graphs from protein native structures, we investigate the relationships between unfolding rates and various topological quantities of the graphs. First, we find that the correlation between the unfolding rate and the contact order is not as prominent as in the case of the folding rate and the contact order. Next, we investigate the correlation between the unfolding rate and the clustering coefficient of the graph of a protein native structure, and observe no correlation between them. Finally, we find that a newly introduced quantity, the impact of edge removal per residue, has a good overall correlation with protein unfolding rates. The impact of edge removal is defined as the ratio of the change of the average path length to the edge removal probability. From these facts, we conclude that the protein unfolding process is closely related to the protein native structure. In addition to find the topological quantity that determine protein unfolding rate, we present a new approach for fold recognition to identify the native and near native protein structures among decoy structures using pair-wise contact potentials between amino acid residues. For a given protein structure, a new scoring function is defined as the difference between the contact energy using its native sequence and the average contact energy using random sequences for the same contact map. We have tested the new scoring function for various decoy sets available in the literature and find that the new scoring f...