The Scaffold Idea

The steric proximity of enzymes can cause higher yield and production rates of final goods in metabolic processes. Different catalysation cascades can be found in nature that show intermediates that are transported to their next destination through channels or enzymes that are located closely to each other (Huang et al. 2001). This leads to an increased local concentration of metabolites near the enzymes und is especially useful in case of unstable or toxic intermediates of a reaction. To make use of such possibilities in synthetic biology, the Keasling Lab developed a construction of an easily and universally applicable protein scaffold. Its potency was proven in two examples with an up to 77-fold increase in yield (Dueber et al. 2009). The scaffold consists of three protein binding domains that may be linked by any number and in any order (Fig. 1). The scaffold can interlink with enzymes through domain-specific tags that are added to the catalytic proteins. The scaffold offers regulatory options for the stoichiometry of enzymes in steric proximity and may thereby counteract bottlenecks and excessive production of intermediates.

Fig 1: The scaffold molecule consists of three different interaction-domains, that can be freely combined (x, y, z). Chosen enzymes get attached to the scaffold through a tag complementary to the specific desired binding domains. This arrangement creates a production chain which generates higher yields.