A Simple Way to Identify Functional Sites in Protein

II. Interaction of Trypsin and its Substrate

Abstract

Functional sites of F-protein of Newcastle disease virus (NDV-F) are determined by the DEV analysis. It includes 91-R that is already known by experiment to be the cleavage site. Interaction of trypsin and its substrate, NDV-F, is then investigated by two mechanisms: two- or mono-molecular interactions. By the two-molecular mechanism, a functional site other than the region containing active sites of trypsin, or a cleavage site of NDV-F interacts as the initial step. By mono-molecular mechanism, a possible interacted complex is visualized between functional sites of trypsin and a cleavage site of NDV-F. In addition, some region that connects functional sites (connector) is found to be important to make complex. Several model complexes are made and analyzed. Results suggest the fluctuated nature of interaction. The interaction between the 84-D region of trypsin and the hydrophobic amino acid sequence in NDV-F, which is always observed from the beginning, is considered to be the key process in the trypsin catalysis.