Artificial intelligence designs dense protein shells

On April 20, a study published in Science showed that artificial intelligence could design extremely dense protein shells that could one day make more effective vaccines.

Photo credit: Shutterstock/Sergei Drozd

The genetic material of the virus is located in the protein shell. A similar shell made in the lab is also used in vaccines, except that it encapsulates molecules that trigger an immune response in the body.

The chemical and biological properties of these artificial shells depend on their construction. But no matter how small a defect in the structure, it reduces its efficiency, leads to instability, and unpredictable reactions occur within the cell. Isaac Lutz and colleagues at the University of Washington in Seattle wanted to see if using artificial intelligence could make the design and manufacture of these enclosures more precise.

The researchers first proposed to the AI the structure they wanted the shell to have, such as size and porosity. The AI then uses reinforcement learning. This is the same iterative process that AI systems learn to play games such as chess by trying different moves, then receiving, feedback, and trying again.

Here, the AI action is to combine, fold and wrap small protein structures called α helixes into a 20-sided shell, and then check whether the resulting design has the structure that people want.

After AI designed hundreds of thousands of shells, the researchers created about 350 shells in the lab. They examined them with electron microscopes and found that AI-made shells were denser than ever.

Lutz explains that this is because it started from very small building blocks. Researchers have previously used larger protein structures that can fit together more neatly than they are.

“It’s like we used to have to buy protein Lego bricks, and what you can build is limited by how they fit together. Now we can say what we want to build, and the AI designs and connects the exact LEGO bricks needed to accomplish that goal. He said.

To test how high density affects the use of the shell in living cells, the team embedded different molecules on the shell and inserted them into mice.

Notably, in a molecular experiment against the production of antibodies to trigger influenza, the AI-designed shell resulted in a small but statistically significant increase in immune response compared to some traditional vaccine candidates currently in clinical trials.

Lutz said this is because of the precision of the AI approach. Each molecule is precisely where it is needed in its shell, which is structured strong enough to support many of these molecules.

“It’s amazing that this team can do that.” Martin Noble of Newcastle University in the UK said: “It takes billions of years to design a single protein that folds correctly, but folding a protein so perfectly that it binds tightly and forms a closed structure is another level of complexity.” ”

Yang Zhang of the University of Michigan said that in addition to vaccines, AI-designed protein shells can also be used in gene therapy, placing genetic material inside special shells so that the patient’s cells do not react adversely. (Source: Wang Fang, China Science News)

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