Detection method of function site of proteins by the finding of amino acid residues at the similar three dimensional positions (4): Study using serine protease groups.

Abstract

It is important problem in a protein science to detect active sites on protein structures. Recently some automatic detection methods were presented; finding a similar structure to known protein active sites, finding pockets and/or cavities on protein surfaces, and so on. We already presented a method to detect amino acid residues, which construct a function site, using the similarity in 3-D structure of same function proteins. In this study, we applied our method to protein pairs of serine proteases for clear the scope and limits of the method. Serine proteases are classified into subgroup by amino acid sequence similarity and into group by folding types. The extraction of active sites from same subgroup, different subgroup but same group and different group serine protease pairs were investigated with various threshold values of allowance distance between amino acid residues. By considering the extracted amino acid residues, it is found that the method could be obtained the true active site residues using pair of proteins with different amino acid sequences but same folding type.