This Article Full Text Full Text (PDF) Supplement All Versions of this Article: biophysj.105.076661v1 91/4/1213    most recent Alert me when this article is cited Alert me if a correction is posted Services Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via Google Scholar Google Scholar Articles by Sawada, Y. Articles by Honda, S. Search for Related Content PubMed PubMed Citation Articles by Sawada, Y. Articles by Honda, S.

Structural Diversity of Protein Segments Follows a Power-Law Distribution

National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan

Correspondence: Address reprint requests to Shinya Honda, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Tsukuba, 305-8566 Japan. E-mail: s.honda{at}aist.go.jp.

The local structures of protein segments were classified and their distribution was analyzed to explore the structural diversity of proteins. Representative proteins were divided into short segments using a sliding L-residue window. Each set of local structures consisting of consecutive 1–31 amino acids was classified using a single-pass clustering method. The results demonstrate that the local structures of proteins are very unevenly distributed in the protein universe. The distribution of local structures of relatively long segments shows a power-law behavior that is formulated well by Zipf's law, implying that a protein structure possesses recursive and fractal characteristics. The degree of effective conformational freedom per residue as well as the structure entropy per residue decreases gradually with an increasing value of L and then converges to constant values. This suggests that the number of protein conformations resides within the range between 1.2^L and 1.5^L and that 10- to 20-residue segments are already proteinlike in terms of their structural diversity.