Researchers harness the power of a supercomputer to better understand plant enzymes


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By exploiting the power of a supercomputer, University of Illinois researchers have been able to simulate the process behind plant enzymes that are critical for growth and development.

A team of investigators from the Department of Chemical and Biomolecular Engineering, Department of Plant Biology and the Center for Biophysics and Quantitative Biology are interested in understanding the process behind a key protein as it transitions between its active and inactive configurations in plants. The particular protein simulated by the research group, BAK1 kinase, plays an important role in plant growth, and this work provides an opportunity to understand processes important for regulating growth and potentially design of novel chemicals to enhance growth.

“Molecular simulation has immense and broad potential for revolutionizing research, teaching, and understanding of plants, from accelerating their engineering for improved resource use efficiency to better understanding the future of our planet and its sustainability. My research group is trying to harness this potential,” said Diwakar Shukla, Blue Waters Assistant Professor in Chemical and Biomolecular Engineering and one of the study’s authors.

Their results were recently published in Biophysical Journal.

Shukla at whiteboard
Diwakar Shukla at whiteboard

The BAK1 kinase has a specific, three-dimensional structure and, like many proteins, its entire structure reconfigures as the protein transforms between its inactive and active states. Scientists can determine the exact structure of these states using a technique called X-ray crystallography. To date, there have been relatively few structures of these critical proteins in plants, which limits our ability to regulate their function. The algorithm simulated on Blue Waters knows only a single starting configuration of the protein, the active, and discovers the ways the protein could rearrange itself to get to inactive states and others due to the modification of protein.

Typically, a regular computer can crunch out maybe ten nanoseconds of simulation data for these proteins per day. By utilizing the power of the Blue Waters supercomputer at the National Center for Supercomputing Applications at the University of Illinois, the Shukla group could run hundreds of these simulations simultaneously to reach hundreds of microseconds data.

“Blue Waters is a unique resource, critical to our research effort and provides us with pieces of this puzzle that have not been seen before,” Shukla said.

“Plants cannot move, so they have to get creative in terms of their biochemistry in order to respond to environmental changes. A single rice plant has over three times the number of these signaling proteins than a human does,” said Alexander Moffett, a graduate student in Shukla Group and the lead author of this study. His research is focused on understanding this complex sensing and signaling system in plants. “Our work takes a detailed look at the nanoscale dynamics of these proteins, providing insight into how these signaling proteins can be switched on or off in response to external signals.”

“The application of molecular simulations to the study of post-translational modifications of a plant receptor kinase have elucidated striking conformational changes in the protein that explain site-specific effects of redox regulation,” said Steven Huber, Professor of Plant Biology and Crop Sciences at Illinois and a co-author. “The unique approaches taken are groundbreaking advances and will almost certainly find rapid application by other research groups studying plant protein kinases.”

Shukla said he believes this work represents a synergistic effort, which is due to the university’s its traditional strengths in plant, computational and engineering sciences.

Dr. Kyle Bender, a former postdoctoral fellow in the Department of Plant Biology at Illinois, was also an author on the paper.


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This story was published December 5, 2017.