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.
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.
Congratulations to Dr. Ying Diao, Assistant Professor of Chemical and Biomolecular Engineering, and graduate student Zahra Shamsi. Both were honored by the School of Chemical Sciences for their teaching excellence in the 2016-2017 school year.
“The award recognizes the entire scope of our educational efforts, from course development to in-class instruction. Excellence in teaching is not only intellectually satisfying, but our instructional efforts immeasurably strengthen our research mission,” said Dr. Jonathan Sweedler, director of the School of Chemical Sciences.
Diao, a Dow Chemical Company Faculty Scholar, pursues fundamental understanding and control of molecular assembly processes to advance innovations in printed electronics for energy and healthcare. She joined the department in 2015 and earned her PhD from MIT and her BS from Tsinghua University.
Other faculty recipients of the award for 2016-2017 include So Hirata and Christian Ray from the Department of Chemistry.
Zahra Shamsi is a 3M Fellow and member of Dr. Diwakar Shukla‘s research group. She earned her BS and MS from the Sharif University of Technology in 2014 and joined the department in 2015.
Other graduate students who received the award include Nels Anderson, Emily Geddes, and Yusef Shari’ati from Chemistry.
When it comes to efficiency, sometimes it helps to look to Mother Nature for advice – even in technology as advanced as printable, flexible electronics.
Researchers at the University of Illinois have developed bio-inspired dynamic templates used to manufacture organic semiconductor materials that produce printable electronics. It uses a process similar to biomineralization – the way that bones and teeth form. This technique is also eco-friendly compared with how conventional electronics are made, which gives the researchers the chance to return the favor to nature.
Templating is used for making near-perfect semiconductors to enhance their electronic properties, or to modulate the spacing between atoms for better electronic properties. These templates help to properly align the atoms of semiconductor materials, typically silicon or germanium, into the form that is needed.
However, this conventional methodology only works well for rigid nanoelectronic devices. The larger, more disordered organic polymer molecules needed to make flexible electronics cannot arrange around a fixed template.
In a new report in the journal Nature Communications, chemical and biomolecular engineering professor Ying Diao, graduate student Erfan Mohammadi and co-authors describe how the biomineralization-like technique works.
In nature, some biological organisms build mineralized structures by harvesting or recruiting inorganic ions using flexible biologic polymers. Similarly, the templates Diao’s group developed are made up of ions that reconfigure themselves around the atomic structure of the semiconductor polymers. This way, the large polymer molecules can form highly ordered, templated structure, Diao said.
This highly ordered structure overcomes the quality control issues that have plagued organic semiconductors, slowing development of flexible devices.
“Our templates allow us to control the assembly of these polymers by encouraging them to arrange on a molecular level. Unlike printing of newspapers, where the ordering of the ink molecules does not matter, it is critical in electronics,” Diao said.
The manufacturing process that can use these dynamic templates is also eco-friendly. Unlike conventional semiconductor manufacturing methods, which require temperatures of about 3,000 degrees Fahrenheit and produce a significant amount of organic waste, this process produces little waste and can be done at room temperature, cutting energy costs, Diao said.
“Our research looks to nature for solutions,” Diao said. “In nature, polymers are used to template ions, and we did the opposite – we use ions to template polymers to produce flexible, lightweight, biointegrated electronics at low cost and large scale.”
Other co-authors of this work include graduate student Ge Qu and postdoctoral scholar Fengjiao Zhang of chemical and biomolecular engineering; professor Jian-Min Zuo and graduate student Yifei Meng of materials science and engineering; and professor Jianguo Mei and graduate student Xikang Zhao of Purdue University.
The U. of I., the National Science Foundation, the United States Department of Energy and the Office of Naval Research Young Investigator Program supported this research.
By Lois Yoksoulian, Physical Sciences Editor, University of Illinois News Bureau; 217-244-2788; email@example.com
To reach Ying Diao, call 217-300-3505; firstname.lastname@example.org.
The paper “Dynamic-template-directed multiscale assembly for large-area coating of highly-aligned conjugated polymer thin films” is available from the U. of I. News Bureau.