Analysis of the stoichiometric structure of metabolic networks provides insights into the relationships between structure, function, and regulation of metabolic systems. Based on knowledge of only reaction stoichiometry, certain aspects of network functionality and robustness can be predicted. Current theories focus on breaking a metabolic network down into non-decomposable pathways able to ope...

Little is known about the evolutionary origins of metabolism. However, key biochemical reactions of glycolysis and the pentose phosphate pathway (PPP), ancient metabolic pathways central to the metabolic network, have non-enzymatic pendants that occur in a prebiotically plausible reaction milieu reconstituted to contain Archean sediment metal components. These non-enzymatic reactions could have...

Domain architectures and catalytic functions of enzymes constitute the centerpieces of a metabolic network. These types of information are formulated as a two-layered network consisting of domains, proteins, and reactions-a domain-protein-reaction (DPR) network. We propose an algorithm to reconstruct the evolutionary history of DPR networks across multiple species and categorize the mechanisms ...

A novel approach to metabolic network analysis using a Nash Equilibrium formulation is proposed. Enzymes are considered to be players in a multi-player game in which each player attempts to minimize the dimensionless Gibbs free energy associated with the biochemical reaction(s) it catalyzes subject to elemental mass balances. Mathematical formulation of the metabolic network as a set of nonline...

The set of chemicals producible and usable by metabolic pathways must have evolved in parallel with the enzymes that catalyze them. One implication of this common historical path should be a correspondence between the innovation steps that gradually added new metabolic reactions to the biosphere-level biochemical toolkit, and the gradual sequence changes that must have slowly shaped the corresp...

We discuss chemical reaction networks and metabolic pathways based on stoichiometric network analysis, and introduce deformed toric ideal constraints by the algebraic geometrical approach. With the deformed toric ideal constraints, the shape of flux is constrained without introducing ad hoc constraints. To illustrate the effectiveness of such constraints, we discuss two examples of chemical rea...

The metabolic network of a living cell involves several hundreds or thousands of interconnected biochemical reactions. Previous research has shown that under realistic conditions only a fraction of these reactions is concurrently active in any given cell. This is partially determined by nutrient availability, but is also strongly dependent on the metabolic function and network structure. Here, ...

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 includ...

Various networks, such as transcriptional, gene regulatory, metabolic or protein-protein interaction networks of various organisms have been studied, which provide insights into metabolism and regulation. Here, we have attempted to construct the metabolic network of Mycobacterium tuberculosis wherein the fatty acid biosynthesis pathway was chosen for analysis of the potential drug targeting. Th...