Title:

Topological determinants of protein unfolding rates

12/28/2004 生資所 謝忠儒

Abstract:

Based on previous studies and experimental results, the folding rates are influenced by their native structures for proteins that fold by two-state kinetics. The objectives of this research is to verify that the unfolding rates are also closely related to the native structures of proteins, and to discover important topological quantities from a protein structure that determine its unfolding rate. In this paper, graphs were constructed from protein native structures to investigate the relationships between unfolding rates and various topological quantities, as well as the correlation between the unfolding rate and the clustering coefficient of the graph of a protein native structure. The results show 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. The results also indicate that there is no correlation between the unfolding rate and the clustering coefficient of the graph of a protein native structure. This study also reveals 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 findings, the authors conclude that the protein unfolding process is closely related to the protein native structure.

Source:
Proteins: Structure, Function, and Bioinfomatics 2004 Nov 19; [Epub ahead of print]
http://www3.interscience.wiley.com/cgi-bin/fulltext/109799038/HTMLSTART

Reference:
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