JUL 26, 2020 1:10 PM PDT

AI Creates Proteins that Rival Those in Nature

WRITTEN BY: Annie Lennon

Proteins are crucial for the function of cells in living organisms. Now, researchers have developed a machine leaning-led process capable of designing proteins better that rival the functionality of those in nature. 

Proteins consist of hundreds or thousands of amino acids that specify both its structure and function. Although past methods have been able to design proper structure, function has been more difficult.

To address these issues, Rama Ranganathan, a professor of biochemistry and molecular biology at the University of Chicago, and his colleagues realized that in the last 15 years, genome bases have been growing exponentially and contain massive amounts of data about both protein structure and function. Creating mathematical models from the data, they were then able to use machine-learning methods to unlock new information about their design rules.

"We generally assume that to build something, you have to first deeply understand how it works," says Ranganathan. "But if you have enough data examples, you can use deep learning methods to learn the rules of design, even as you are understanding how it works or why it's built that way."

In the research, the team studied the chorismate mutase family of metabolic enzymes, a kind of protein essential for bacteria, fungi, and plants. With their machine-learning models, they were then able to decode the design rules behind the proteins. 

To see how they worked, the researchers then created synthetic genes to encode for proteins, cloned them into bacteria, and watched them proliferate. All in all, they saw that their artificial proteins had the same catalytic function as natural chorismate mutase proteins. 

The researchers will now work to understand how the models came to their conclusions. They also hope to use their new platform to develop proteins that may be able to address societal problems like climate change. Ranganathan and Associate Professor Andrew Ferguson have already created a company called Evozyne to commercialize their technology in domains spanning energy, environment, catalysis, and agriculture. 

"This system gives us a platform for rationally engineering protein molecules in a way that we always dreamed we could," says Ranganathan. "Not only can it teach us the physics of how proteins work and how they evolve, it can help us find solutions for issues like carbon capture and energy harvesting. Even more generally, the studies in proteins might even help teach us how the deep neural networks behind modern machine learning actually work."

 

Sources: PhysUniversity of Chicago 

About the Author
  • Science writer with keen interests in technology and behavioral biology. Her current focus is on the interplay between these fields to create meaningful interactions, applications and environments.
You May Also Like
AUG 24, 2020
Drug Discovery & Development
New Drug Reduces Swelling in Asthma and COPD
AUG 24, 2020
New Drug Reduces Swelling in Asthma and COPD
Researchers from the University of Glasgow, Scotland, and the University of Technology Sydney in Australia have identifi ...
SEP 03, 2020
Immunology
A Low-Cost COVID-19 Treatment, Made in Horses
SEP 03, 2020
A Low-Cost COVID-19 Treatment, Made in Horses
Researchers in Costa Rica are turning to horses as an unlikely source of potential therapeutic antibodies against COVID- ...
SEP 04, 2020
Drug Discovery & Development
Fecal Transplant Successfully Treats Alcoholism
SEP 04, 2020
Fecal Transplant Successfully Treats Alcoholism
Researchers from Virginia Commonwealth University have found that fecal transplants can reduce drinking behaviors in peo ...
SEP 08, 2020
Space & Astronomy
New Drug May Allow Astronauts to Spend Years in Space
SEP 08, 2020
New Drug May Allow Astronauts to Spend Years in Space
Without gravity from Earth, muscles and bones tend to weaken quickly. To combat this, astronauts usually need to spend t ...
SEP 15, 2020
Drug Discovery & Development
How Can Genetic Data Make Informed Decisions About Drug Development?
SEP 15, 2020
How Can Genetic Data Make Informed Decisions About Drug Development?
How Can Genetic Data Make Informed Decisions About Drug Development? Scientists at the Integrative Epidemiology Unit (MR ...
SEP 29, 2020
Cardiology
Improving Acute Myocardial Ischemia Treatment with Nitro Fatty Acids
SEP 29, 2020
Improving Acute Myocardial Ischemia Treatment with Nitro Fatty Acids
Acute myocardial ischemia occurs when blood flow is restricted in the heart. This usually leads to cardiovascular issues ...
Loading Comments...