Characterization and comparison of protein structures. Part I - Characterization

The quantitative criteria characterizing the regularity of C-alpha-backbones in the protein structures are presented. A technique is based on the Fourier remapping of the Cartesian coordinates for the C-alpha-chain. The Fourier spectra identify the hidden periodicities and symmetries in protein structures, while the integral regularity is assessed via the spectral structural entropies. The formal unification of digitizing and the similarities in statistics for the random counterparts allow study of the direct correlations between the distribution of physico-chemical characteristics along the amino acid sequence and the spatial conformation of the polypeptide chain. The significant correlations are found for both hydrophobicity and side-chain volumes, though, as expected, the effects for hydrophobicity turn out essentially stronger. A scheme is illustrated by the set of 120 protein structures comprising the representatives from the main superfamilies and superfolds. (C) 1999 Academic Press.