A Simple Way to Identify Functional Sites in Protein

IV. Active Sites of Trypsin

Abstract

A small protein model that consists of no more than the functional sites of trypsin1) is designed to detect the active sites and also to evaluate our hypothesis; a folding process derived from the DEV analysis is followed by the biochemical process. In the course of study, every non-polar amino acid in the model is replaced by glycine, whereupon the biochemical characteristics of polar amino acids should become more distinguished. The DEV analyses of the models select four amino acids (H, D, S and C) as the essential members of the functional system. The first three amino acids are coincide with the active sites of trypsin (40-H, 84-D and 177-S). When the area of triangle made up of a combination of three amino acids out of the above four is measured, the triangle of HDS is found to be the minimum among those made of other combinations investigated, suggesting that they are closely located each other. By taking advantage of the results, we propose a way how to identify the active sites in a protein.