Newswise — WASHINGTON, D.C., February 14, 2017 -- Climate change will bring worsening droughts that threaten crops. One potential way to protect crops is by spraying them with a compound that induces the plants to become more drought resistant. Now, by identifying the key molecular mechanism that enables a plant to minimize water loss, researchers may be one step closer to that goal.
Faced with dry conditions, plants can mount a natural defense. They produce a hormone, called abscisic acid, or ABA, that binds to a protein, called a PYL receptor, triggering a chain of reactions that eventually closes the plant's pores on its leaves. "There is no or little water loss from the plants," explained Saurabh Shukla, a graduate student at the University of Illinois. "They conserve water resources and they survive for longer periods of time."
The key is the ABA hormone. Because of its moderate stability and molecular complexity, ABA can't be directly sprayed in fields. But, Shukla said, "If we can understand how the hormone works, we can design some molecule that can be sprayed and does the same job for us." If researchers can find a molecule that not only works the same way as the ABA hormone, but also is cheap, stable and environmentally friendly, then farmers can use it to make their crops become drought-resistant.
But the details for how ABA works have been elusive. Experimental techniques such as X-ray diffraction can take snapshots of the hormone before and after binding to the PYL receptor, but they can't catch the two in the act. So Shukla and his colleagues turned to supercomputers.
Using molecular dynamic simulations, the researchers have, for the first time, revealed the molecular details for how ABA binds with the PYL receptor. The simulations show, frame by frame, how and where the hormone binds with the protein and causes it to change shape, which allows it to activate the next protein in the sequence that eventually enables the plant to close its pores.
"You know exactly what is happening at the microscopic scale," Shukla said. "It’s like a movie."
And the movie ends the way it should. The final frames of the hormone bound with the receptor precisely match the X-ray diffraction predicted crystal structures, confirming the accuracy of the simulations. The team will present its work during the 61st Meeting of the Biophysical Society held Feb. 11-15, 2017 in New Orleans.
The researchers simulated only two specific types of PYL receptors, found in a small, flowering plant called A. thaliana. Still, Shukla said, their results are widely applicable because the structure of PYL receptors is very similar across all species. For PYL receptors whose crystal structures are known, their binding pocket -- the part of the protein that binds to ABA -- is the same. The structure surrounding the pocket is also similar. Such similarities mean the same binding mechanism probably takes place in all plants.
While researchers may still want to confirm this mechanism in other plants, such as rice -- whose PYL receptor structure is known -- the hunt for an ABA mimic can now begin, Shukla said. Researchers will have to conduct rigorous computational and genetic studies to identify such a compound. The goal is to find a compound that can work on all species without resorting to genetic engineering. But it will likely be at least a decade before any product will be on the market, Shukla said.
Session 184.02 - Posters: Protein Small Molecule Interactions, 1721-Pos/B32, "Machine learning guided ligand-protein simulation approach elucidates the binding mechanism of abscisic acid," is authored by Saurabh Shukla, Moeen Meigooni, Chuankai Zhao and Diwakar Shukla. It will be at 1:45-3:45 p.m. Central Time on Tuesday, Feb 14, 2017 in Hall B-2 & C of the Ernest N. Morial Convention Center.
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