the Foresight Institute
Overlay of the Des1 crystal structure (blue) and the FLS model (green, with mutated residues brown) with the docked DHA product (purple). The four active site mutations (BAL vs. Des1) are shown in sticks, conserved amino acids in lines. Credit: Siegel et al. PNAS March 24, 2015
More evidence that computational protein design can create not only novel proteins but also novel functions that do not exist in nature comes from the creation of an entire novel metabolic pathway. A large collaboration involving scientists from the University of California, Davis, two research groups at the University of Washington (including the lab of David Baker, who shared the 2004 Foresight Institute Feynman Prize for theoretical work), the Fred Hutchinson Cancer Research Center, and several other institutions in California and Israel published a paper last year in PNAS “Computational protein design enables a novel one-carbon assimilation pathway” that describes a novel computationally designed enzyme they designate “formolase” that catalyzes the carboligation of three one-carbon formaldehyde molecules into one three-carbon dihydroxy acetone molecule. This complex project comprised many steps to create three novel enzyme functions, not previously known, in the process creating a microbial metabolic pathway that could be further optimized for enhanced production of desired products. This research demonstrates the feasibility of organizing multiple engineered enzymes into a sequence that does not exist in nature. In this particular case the goal is to address current challenges in energy storage and carbon sequestration by converting one carbon compounds, such as CO2, into multicarbon fuels and other high-value chemicals. One could also envision such systems as components along the path to productive nanosystems, leading eventually to general purpose, high throughput atomically precise manufacturing.
The authors note that the lack of one-carbon anabolic pathways in microbes suitable to address current needs in energy storage and carbon sequestration could arise from unfavorable chemical driving force at one or more pathway steps, the inherent complexity and inefficiency of the steps, or the environmental sensitivity of the steps (the ability to function efficiently under both aerobic and anaerobic conditions). Despite the lack of such a pathway in nature, they further note, the established electrochemical reduction of CO2 to formate provides an attractive starting point for a one-carbon fixation pathway. They describe in this paper the computational design of an enzyme that catalyzes the carboligation of three one-carbon formaldehyde molecules into one three-carbon molecule. The new enzyme enables the construction of the ‘formolase’ pathway, which converts formate into the centrally important metabolite dihydroxyacetone phosphate.