Chemical Continuity of Reaction Centers Along Successive Metabolic Reactions

Cellular functions often come from intricate networks of molecular interactions, which involve not only proteins and nucleic acids but also small chemical compounds. To understand the complexity of life system it is required to know the characteristics of network diagram of those molecules. In this decade, lots of efforts have been made to investigate various types of biological networks including metabolic pathways, which is one of the most significant network in biological system. For metabolic pathways, in particular, the statistical parameters of network or sub-networks have been identified as the parameters of scale-free network, and the characteristic patterns of sub-pathway have been described and compared to the other types of clusters like gene clusters in genome or compound clusters having conserved chemical structures along pathways. The prediction of enzymatic reaction has also been focused in these years, because there are many reactions whose EC numbers are left unknown [2,4]. If we could find the correct catalytic function of enzymes as EC sub-subclasses only from chemical structures, such problematic reactions may turn to be available for improvements of the other analyses. Consequently, they will help us to better understand the complicated metabolic strategy of biology, more specifically, both the variation of available enzymatic reactions in each organism and the development process of various chemical compounds. In this context, we have developed the RPAIR database containing the atom alignments of reactant pairs because summarizing the chemical information of enzymatic reactions has become significant for us to consider the function of the complex system [2,3]. Along with this, we have successfully applied the RPAIR database to infer the appropriate reaction mechanism only from chemical compound structures [4]. Thus, we can now analyze the metabolic pathway from a viewpoint of enzymology and elucidate the chemical aspects of metabolic pathways. In this study, we have aimed to detect the continuity of reaction centers observed along enzymatic reaction processes.