Hybrid approach to analysis of ß-sheet structures based on signal processing and statistical consideration

A number of biotechnology applications are based on protein design. For this design, the relationship between a protein's primary structure and its conformation is of vital importance. A b-sheet is a common feature of a protein's two-dimensional structure; therefore, elucidating the principles governing b-sheet structure and its stability is critical for understanding the protein-folding process. In the three-dimensional representation of protein molecules, Ca carbon coordinates (carbon atom immediately adjacent to the carboxylate group) have often been employed instead of the complete set of coordinates for the corresponding residues. Using the Ca carbon coordinates, we showed that particular amino acids are not randomly distributed within a b-sheet structure. On the basis of a new statistical approach for the analysis of a spatial distribution of amino acids in a protein, presented by their physico-chemical parameters, the electron-ion interaction potential (EIIP) and hydrophobicity, are described here. The relationship between amino acid positions inside the b-sheet and the EIIP and hydrophobicity parameters was established. The correlation between amino acid propensities related to the b-sheet was examined using multiple cross-spectra analysis. We also applied the continuous wavelet transform for the analysis of selected b-sheet structures using the EIIP and hydrophobicity parameters. The findings provide new insight into conformational propensities of amino acids for the adaption of b-sheet structures.