March 19, 2008
Molecular engineers design new enzymes from scratch
Many important chemical reactions are slow and unwieldy because no enzyme exists to prod them to greater efficiency. Designing new enzymes from scratch is of practical interest in biomedicine, biotechnology, environmental cleanup, and other industries. Precisely engineered enzymes, built to match the specific task at hand, could improve many processes in these fields by triggering, speeding up, and controlling the necessary chemical reactions.
For many years University of Washington (UW) and Howard Huges Medical Institute experts and their collaborators from other institutions have been using computer modeling to create previously non-existent protein molecules. This group, headed by Dr. David Baker, UW professor of biochemistry and an investigator for the Howard Hughes Medical Institute, has been successful in predicting protein structures and protein folding from chains of amino acids, and in re-programming protein interactions by designing interaction surfaces for proteins that do not normally interact. As part of this effort, they are designing and testing new enzymes to fit specific needs. They don’t start with available proteins. These enzymes originate on the “drawing board” of their minds and computers. Their progress in enzyme design was reported earlier this month in Science and this week in Nature.
In the March 7 edition of Science, Baker and his group discussed their attempts in designing enzymes that could break bonds between carbon atoms. Carbon bonds are the mainstay of all types of materials derived from living things, from fossil fuels to food. Being able to break carbon bonds more quickly and efficiently could lead to improvements in cleaning up organic waste and in developing renewable energy sources.
In thinking up new enzymes, the researchers imagine what an ideal active site would look like on the enzyme. This active site is a place within the enzyme where a reaction could take place. The active site would have to be configured exactly, and have the precise chemical makeup, to be a catalyst for the desired chemical reaction. Some parts of the enzyme would form a sort of container for the reaction; other parts would join in the reaction.
The researchers would then create many computer models of proteins with this kind of site, then rank these models based on their ability to bind with and hold onto the reacting chemicals. In the research published in Science and in Nature, the scientists manufactured the top-ranking computer-designed proteins by figuring out their gene sequences, and giving bacteria these genetic directions to make the desired protein. In the work reported in Science, the scientists then tested these proteins to see how well they could catalyze a carbon-carbon bond breaking reaction. The winning enzyme sped up the reaction 10,000 times, compared to the rate without a catalyst.
In the research findings reported in the March 19 edition of Nature, the scientists created eight computer designs for enzymes for a reaction for which no enzymes exist. The particular reaction they studied is the Kemp elimination reaction — proton transfer from carbon. Normally the activation of this proton transfer is restricted by the high energy barriers to be overcome. The scientists also tried a widely used technique called directed evolution — several rounds of random mutations and shuffling to create variants of the enzyme molecule — to fine-tune the computational enzyme design by revealing subtleties missing from the original design.
According to Baker, the enzymes designed by computer are nowhere near approaching the ability of naturally occurring enzymes to speed up chemical reactions. The manufactured enzymes run like a tortoise by comparison.
Nevertheless, combining computational enzyme design with molecular evolution, the authors suggested, could become a powerful route to create new enzyme catalysts for the wide range of chemical reactions for which naturally occurring enzymes don’t exist. Computational design, they added, also provides a critical testing ground for refining knowledge about how enzymes work.
