David Baker, a Ph.D. from UC Berkeley, received the Nobel Prize in Chemistry in 2024

This year's Nobel Prize in Chemistry went to David Baker, a biochemist who received his Ph.D. He graduated from UC Berkeley in 1989 working with Randy Schekman, a professor of molecular and cellular biology who won the Nobel Prize in Physiology or Medicine in 2013.

At Berkeley, Baker's research focused on protein transport and trafficking in yeast, the field in which Schekman won the prize. But after a postdoctoral fellowship at UCSF, he joined the biochemistry faculty at the University of Washington School of Medicine in Seattle and began working on computational methods to predict and design the structures and functions of proteins.

In 2003, he used a computer program he had developed called Rosetta to design an entirely new protein that was unlike any other known. Baker and colleagues further demonstrated that a variety of protein structures can be designed using Rosetta software.

“Since then, his research group has produced one imaginative protein creation after another, including proteins that can be used as drugs, vaccines, nanomaterials and tiny sensors,” said a press release from the Nobel Foundation. Baker, according to the foundation, “has learned to master the building blocks of life and create entirely new proteins.”

Baker, 62, received half of the prize, while the other half was shared by two scientists – Demis Hassabis and John Jumper – from Google DeepMind in London, who developed AlphaFold, a machine learning tool that can predict the 3Dl structure of any protein its amino acid sequence.

A protein's 3D structure is critical to its function, but since the 1970s, scientists have struggled to understand how a protein's amino acid sequence encodes that structure. Then, in 2020, Hassabis and Jumper developed a new version of the AI ​​tool, AlphaFold2.

“With its help, they were able to predict the structure of virtually all 200 million proteins that researchers have identified,” according to the Nobel Foundation.

“It's a really exciting day for those of us interested in protein folding,” said Susan Marqusee, a distinguished professor of molecular and cellular biology and chemistry at UC Berkeley. “David has done as much as any living scientist to show the path between the amino acid sequences of proteins and their three-dimensional structures. Given the ability to design structures at will, the challenge for the future is to integrate the dynamic movements and structural changes required for all types of biological functions.”

Earlier this week, another Berkeley graduate, Gary Ruvkun, received the Nobel Prize in Physiology or Medicine for discovering the critical role that microRNAs play in regulating genes. Ruvkun, who grew up in Berkeley, graduated in 1973 with a BA in biophysics. He is currently a professor of genetics at Harvard Medical School and a researcher at Massachusetts General Hospital.

“This recognition follows years of anticipation for this prize and coincides with the recognition of another Berkeley graduate, Andrew Fire, who shared the Nobel Prize with Craig Mello for the discovery of small interfering RNAs that, when introduced into cells, become double-stranded “Structures form RNA molecules that can control gene expression in a similar way,” said Schekman. “Both discoveries have had significant implications for our understanding and ability to manipulate the expression of genes in higher organisms.”

This year's Nobel Prize in Physics also went to a scientist with ties to Berkeley. John Hopfield was an assistant professor in the physics department between 1961 and 1964 before moving to Princeton University and the department changed from theoretical condensed matter physics to biophysics. Marvin Cohen, now a professor emeritus of physics at Berkeley, was hired as his successor.

“I took over his graduate students after he left,” Cohen said. “Eventually he (Hopfield) switched to biological physics. I remember trying to talk him out of it. He has made outstanding contributions to this field and I believe his diverse background has prepared him for the work he has done, which has been recognized by the Nobel Committee.”

The Nobel Foundation cited his “fundamental discoveries and inventions that enable machine learning with artificial neural networks.”

Hopfield had another connection to Berkeley: His father, John Joseph Hopfield, a Polish immigrant, received his Ph.D. He completed his physics degree at Berkeley in 1923 with the late Raymond Birge as his advisor. As a spectroscopist, Hopfield became a lecturer and assistant professor of physics before moving to Berlin in 1928 to conduct research there. His son was born in 1933.

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