By Jonny Lupsha, Wondrium Staff Writer
A London lab has programmed an artificial intelligence to predict protein shapes, The New York Times reported. The program, called AlphaFold, can look at a string of amino acids and accurately predict which 3D shape they will form when they become a protein. Why does protein folding matter?
According to The New York Times, a lab in London may have developed an artificial intelligence that can do a years-long task in less than a day, solving a longstanding problem of biology. “For biologists, identifying the precise shape of a protein often requires months, years, or even decades of experimentation,” the article said. “It requires skill, intelligence, and more than a little elbow grease.
“Now, an artificial intelligence lab in London has built a computer system that can do the job in a few hours—perhaps even a few minutes.”
The article said that the laboratory in question, DeepMind, analyzes a string of amino acids that make up a protein and then “rapidly and reliably” predicts its shape. But why is that so important?
The Anfinsen Experiments
The study of folding proteins began in the 1950s with American biochemist Christian Anfinsen playing a key role.
“The first experiments began by taking a protein out of the cell, unfolding it, and then seeing if it could refold in a test tube, independent of any cellular factors,” said Dr. Kevin Ahern, Professor of Biochemistry and Biophysics at Oregon State University. “The protein Christian Anfinsen picked was the enzyme ribonuclease A, also known as RNase, which turned out to be a serendipitous choice. RNase is relatively small as proteins go—about 100 amino acids—and it is also extraordinarily stable.”
Dr. Ahern said that most enzymes are very sensitive to changes in temperature or pH balance, but RNase is not. Anfinsen showed that once an enzyme is unfolded, it’s capable of refolding outside the cell. His work earned him the 1972 Nobel Prize for Chemistry. Dr. Ahern also said that this process is called “renaturation” because the protein gets returned to its native or natural state.
Humanity has been studying protein folding for over 60 years. What happens when proteins fold incorrectly? As it turns out, nothing good.
“These are the so-called prion diseases, also known as transmissible spongiform encephalopathies or TSEs,” Dr. Ahern said. “Prion diseases affect humans and other animals. They are a group of degenerative disorders that affect the brain, creating microscopic holes that make the tissue look like a sponge.”
He also said that one of the best-known prion diseases is bovine spongiform encephalopathy, also known as Mad Cow Disease. Animals that had it would exhibit behaviors that were consistent with neurological damage, and finding a common cause among them was difficult.
“Stanley Prusiner at the University of California at San Francisco ultimately identified the infectious agent as a protein—a proteinaceous infectious article he called a prion,” Dr. Ahern said. “That a protein could be infectious by itself was unheard of at the time. And [it] turned out to be a cellular protein found on the membrane of healthy cells; though its function to this day remains uncertain.”
Protein misfolding causes several serious diseases and helps explain why the study of protein folding matters so much.
Dr. Kevin Ahern contributed to this article. Dr. Ahern is a Professor of Biochemistry and Biophysics at Oregon State University (OSU), where he also received his PhD in Biochemistry and Biophysics.