Custom-designed proteins made with the aid of computers could fight chemical weapons such as nerve gas and help decontaminate toxic-waste sites, scientists say.
In recent years, computer design of proteins has made great leaps forward, developing molecules with new kinds of structures and properties. However, few efforts have been made to incorporate metals into these computationally designed molecules. Metals are key, highly reactive parts of many proteins — for instance, the iron in the blood-protein hemoglobin helps it transport oxygen inside our bodies.
Now, researchers have used computers to design a protein containing zinc that can degrade molecules similarly to sarin gas, a weapon of mass destruction created by Germany during World War II that attacks the nervous system.
"The ability to computationally redesign metal sites in proteins opens up a number of opportunities to use metal ions for performing new and useful reactions of human interest — for example, degrading chemical toxins and synthesizing new drug molecules," researcher Sagar Khare, a computational biologist at the University of Washington, told InnovationNewsDaily.
The scientists first analyzed about 150 known zinc-containing enzymes. This research helped them identify 12 with shapes they could redesign for new reactions.
Sarin is a type of molecule known as an organophosphate, which also includes many pesticides and pollutants found in toxic-waste sites, which authorities are eager to treat. Since nature has not had time to come up with catalysts that can efficiently break down these relatively new compounds, "we decided to see if we could speed up the process," Khare said.
One of the new enzymes, a redesigned mouse protein, broke apart an organophosphate similar to sarin about 10 million times more effectively than its original counterpart.
"This was a proof-of-principle effort, and the designer enzyme was not developed against actual nerve agents," Khare said. "However, because the method is completely general, it should be possible to use it for developing antidotes and decontamination agents."
One goal of improving computational design of new enzymes "is to have the capability to come up with degradation strategies for new chemical warfare agents that we have not seen yet: readily, efficiently and cheaply," Khare said. "The next steps are to develop catalysts for actual nerve-agent degradation, and extend these methods to the degradation of other environmental toxins."
Khare, along with David Baker and their colleagues, detailed their findings online Feb. 5 in the journal Nature Chemical Biology.
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