Structural diversity of protein segments follows a power-law distribution.
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 1.2L and 1.5L and that 10- to 20-residue segments are already proteinlike in terms of their structural diversity.
Sawada
Yoshito
Y
National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan.
Honda
Shinya
S
D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D003198:Computer Simulation; D003627:Data Interpretation, Statistical; D030562:Databases, Protein; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D020539:Sequence Analysis, Protein / Q000379:methods*; D017386:Sequence Homology, Amino Acid; D016008:Statistical Distributions
D011506:Proteins