2024 Nobel chemistry prize – Part 2 of 2

2- Machine learning cracked the protein-folding problem and won the 2024 Nobel Prize in chemistry

Marc Zimmer, Professor of Chemistry, Connecticut College. The Conversation. October 9, 2024. (continued)

The challenge of protein folding

Proteins are the molecular machines of life. They make up a significant portion of our bodies, including muscles, enzymes, hormones, blood, hair and cartilage.

Understanding proteins’ structures is essential because their shapes determine their functions. Back in 1972, Christian Anfinsen won the Nobel Prize in chemistry for showing that the sequence of a protein’s amino acid building blocks dictates the protein’s shape, which, in turn, influences its function. If a protein folds incorrectly, it may not work properly and could lead to diseases such as Alzheimer’s, cystic fibrosis or diabetes.

A protein’s overall shape depends on the tiny interactions, the attractions and repulsions, between all the atoms in the amino acids its made of. Some want to be together, some don’t. The protein twists and folds itself into a final shape based on many thousands of these chemical interactions.

For decades, one of biology’s greatest challenges was predicting a protein’s shape based solely on its amino acid sequence. Although researchers can now predict the shape, we still don’t understand how the proteins maneuver into their specific shapes and minimize the repulsions of all the interatomic interactions in a few microseconds.

To understand how proteins work and to prevent misfolding, scientists needed a way to predict the way proteins fold, but solving this puzzle was no easy task.

In 2003, University of Washington biochemist David Baker wrote Rosetta, a computer program for designing proteins. With it he showed it was possible to reverse the protein-folding problem by designing a protein shape and then predicting the amino acid sequence needed to create it.

It was a phenomenal jump forward, but the shape chosen for the calculation was simple, and the calculations were complex. A major paradigm shift was required to routinely design novel proteins with desired structures.

A new era of machine learning

Machine learning is a type of AI where computers learn to solve problems by analyzing vast amounts of data. It’s been used in various fields, from game-playing and speech recognition to autonomous vehicles and scientific research. The idea behind machine learning is to use hidden patterns in data to answer complex questions.

This approach made a huge leap in 2010 when Demis Hassabis co-founded DeepMind, a company aiming to combine neuroscience with AI to solve real-world problems.

Hassabis, a chess prodigy at age 4, quickly made headlines with AlphaZero, an AI that taught itself to play chess at a superhuman level. In 2017, AlphaZero thoroughly beat the world’s top computer chess program, Stockfish-8. The AI’s ability to learn from its own gameplay, rather than relying on preprogrammed strategies, marked a turning point in the AI world.

Soon after, DeepMind applied similar techniques to Go, an ancient board game known for its immense complexity. In 2016, its AI program AlphaGo defeated one of the world’s top players, Lee Sedol, in a widely watched match that stunned millions.

In 2016, Hassabis shifted DeepMind’s focus to a new challenge: the protein-folding problem. Under the leadership of John Jumper, a chemist with a background in protein science, the AlphaFold project began. The team used a large database of experimentally determined protein structures to train the AI, which allowed it to learn the principles of protein folding. The result was AlphaFold2, an AI that could predict the 3D structure of proteins from their amino acid sequences with remarkable accuracy.

This was a significant scientific breakthrough. AlphaFold has since predicted the structures of over 200 million proteins – essentially all the proteins that scientists have sequenced to date. This massive

Episode 3025 - October 12 - Tiếng Anh - Phần 2 của 2 - Giải Nobel Hóa học 2024 - Vina Technology at AI time -

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Episode 3025 - October 12 - Tiếng Anh - Phần 2 của 2 - Giải Nobel Hóa học 2024 - Vina Technology at AI time -