How to Design a Functional Enzyme from Scratch

Feb 01, 2018

At Princeton University, in the laboratory of chemistry professor Michael Hecht, researchers are designing and building artificial proteins that can mimic natural metabolic processes. This new field of research is referred to as artificial biology, and is dedicated to creating novel proteins, cells, tissues, and ultimately, artificial life.

Hecht and his team started designing artificial proteins in 2011, and have spent the last 6 years trying to figure out how they function. Now, for the first time, Hecht has confirmed that their artificially designed proteins are capable of producing enzymatic reactions and catalyzing biological processes.

“Enzymes are key to all of biology,” says Hecht. "Biology is the system of biochemical reactions and catalysts. Each step has an enzyme that catalyzes it, because otherwise those reactions wouldn't go fast enough for life to exist.”

How Do Artificial Proteins Function

Hecht and his team, identified and mutated 4 genes essential for life in Escherichia coli. Conducting a gain-of-function screen, the researchers attempted to rescue mutant lethality by expressing their artificial proteins. Determining the molecular mechanism of each artificial protein took countless experiments. "We had four different gene deletions -- four different enzymatic functions," said Ann Donnelly, primary author on Nature Chemical Biology paper.

Of the artificial proteins tested, Syn-F4, was able to enzymatically rescue Fes, a gene required for iron extraction and metabolism. And amazingly, Syn-F4, contains a completely different amino acid sequence, indicating that many potential enzymatic solutions may exist to each biological process.

There are significant implications for industrial biotechnology. "Biotechnology commonly uses enzymes to carry out industrial processes for the production of materials, food, fuel and medicine," says Justin Siegel, a professor at the UC Davis Genome Center.

"The use of these enzymes in an industrial setting often starts with an enzyme that nature evolved for billions of years for an unrelated purpose, and then the protein is tweaked to refine its function for the modern application. The report here demonstrates that we are no longer limited to the proteins produced by nature, and that we can develop proteins, that would normally have taken billions of years to evolve, in a matter of months."

"We're starting to code for an artificial genome. We've rescued 0.1 percent of the E. coli genome,” says Hecht. “For now, it's a weird E. coli with some artificial genes that allow it to grow. Suppose you replace 10 percent or 20 percent. Then it's not just a weird E. coli with some artificial genes, then you have to say it's a novel organism.”

• Donnelly, A., Murphy, G., Digianantonio, K. & Hecht, M. A de novo enzyme catalyzes a life-sustaining reaction in Escherichia coli. Nature Chemical Biology (2018).
  DOI: http://dx.doi.org/10.1038/nchembio.2550

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