On optimum properties in the design of metabolic and epigenetic systems

The actual potential of a metabolic system is determined by its enzyme "spectrum", i.e. the amount of the various enzymes present. The paper addresses the problem whether this spectrum can be designed in accordance with a general principle. The long prehistory of selection of any real metabolic system suggests the optimal adaptation to a given set of selection criteria as a possible design principle. It is shown that not every (bio)chemical reactor automatically displays an optimal construction in this sense, but metabolic systems are structured such that they can do so. Structural features that lead to optimizable dynamics include: kinetic autocatalysis, stoichiometric autocatalysis, competition for the allocation of biosynthetic capacity, required economy in external resources of the system, and competition of systems for common nutrients or other resources. In these circumstances the enzyme spectrum has a distinct optimum that can be approached by stepwise adaptation and selection.