John Jumper: UChicago Department of Chemistry alum and the 2024 Nobel Prize winner in Chemistry
by Brian Foley
In a remarkable achievement for both the scientific community and the University of Chicago Department of Chemistry, Dr. John Jumper (PhD ’17) has been awarded the 2024 Nobel Prize in Chemistry.
The Royal Swedish Academy of Sciences honored Jumper, who received his master’s degree in 2012 and his Ph.D. from the University of Chicago in 2017, along with Demis Hassabis, for their work on "protein structure prediction." The prize is also shared with Prof. David Baker of the University of Washington "for computational protein design."
John Jumper is the 19th person affiliated with the University of Chicago to receive the Nobel Prize in Chemistry and the 100th member of the UChicago community to earn a Nobel Prize. Most recently, the 2023 Nobel Prize in Chemistry was awarded to Moungi Bawendi, PhD’88, for the discovery of quantum dots; and the 2019 prize to John Goodenough, PhD’52, for the invention of lithium batteries.
Dr. Jumper was selected for the prestigious accolade for his groundbreaking work in the field of computational chemistry, particularly his innovative approaches to protein folding and molecular modeling developed while serving as a research scientist at Google DeepMind. He has spent over a decade investigating the intricacies of protein structures and their functions. His work is rooted in the understanding that proteins, the pillars of biological systems, perform their functions based on their three-dimensional shapes. Predicting these shapes from the linear sequences of amino acids has long been a significant goal in biochemistry.
Jumper's breakthrough came with the development of an advanced algorithm that leverages artificial intelligence and machine learning techniques to predict protein structures with unprecedented accuracy. This algorithm, known as AlphaFold 2, informs an advanced artificial intelligence system that utilizes vast datasets of known protein structures to refine its predictive capabilities.
During his tenure in the Department of Chemistry at the University of Chicago, Dr. Jumper collaborated closely with esteemed faculty members, Karl Freed, the Henry G. Gale Distinguished Professor Emeritus of Chemistry, and Tobin Sosnick, the William B. Graham Professor of Biochemistry and Molecular Biology and current chair of the Department of Biochemistry and Molecular Biology.
Under Freed’s guidance, Jumper honed his skills in computational modeling and theoretical chemistry, exploring the intricate dynamics of molecular interactions. Meanwhile, his work with Sosnick focused on experimental biophysics, particularly in studying protein folding and stability. This unique blend of computational and experimental approaches allowed Jumper to develop innovative algorithms that would ultimately lead to the development of the AlphaFold 2, enabling researchers to understand how proteins fold based on their amino acid sequences.
In 2023, Sosnick remarked, "Following the July 2021 online publication of AlphaFold, I sent my colleagues an email with the subject line 'Revolution in structural biology.' The phrase 'I alphafolded it' is now something I hear almost every day, whether in the lab, during a thesis defense, or at a scientific conference. This transformation of a noun into a verb, similar to 'I googled it,' reflects the profound changes that have taken place in the biological sciences over the past two and a half years."
In late 2020, a team from Google DeepMind, led by John Jumper and including Richard Evans, Aidan Hughes, Pushmeet Kohli and co-founder Demis Hassabis, solved the protein folding problem using their machine learning algorithm, AlphaFold 2, which they later made available online for free. By providing accurate models of protein structures, their has significantly advanced the understanding of viral proteins, aiding in the development of vaccines and therapeutics during global health crises such as the COVID-19 pandemic.
AlphaFold 2 has also opened new avenues for studying complex diseases, such as Alzheimer's and cancer, by enabling scientists to model the interactions between proteins involved in these conditions. The ability to visualize these interactions at the molecular level has the potential to revolutionize drug design, allowing for the creation of more targeted and effective therapies.
The announcement of the Jumper’s 2024 Nobel Prize in Chemistry has been met with widespread acclaim.
"What a joy to see our alumni, John Jumper and Moungi Bawendi, recognized with Nobel Prizes two years in a row!" said Prof. Jiwoong Park, chair of UChicago's Department of Chemistry. "Dr. Jumper's Nobel recognition is a testament to the pioneering research conducted at UChicago chemistry, leading to real-world impacts, and the success of our mission to train future leaders in the field of chemistry."
Park added that Jumper is scheduled to deliver the 2025 Bloch Lecture at UChicago, "so we’re looking forward to welcoming him back to campus next year."
Jumper’s award, while unanimously celebrated, is not without expectation. In September, Time Magazine recently named Jumper as one of the “100 Most Influential People in AI”.
In their profile, Jumper was quoted as saying, “What I'm most proud of is the extent to which it's making all of structural biology five or ten per cent faster. AlphaFold, in many cases, lets them skip that one or two years.”
Dr. Jumper's innovative work at the University of Chicago and with Google DeepMind has set a new standard for protein structure prediction and his recognition as a Nobel Laureate underscores the critical role that computational methods play in modern chemistry and biology. As the UChicago community celebrates this achievement, we look forward to the continued impact of Jumper's research on our understanding of the molecular foundations of life.
Selected references of John Jumper at the University of Chicago:
o Wang, Zongan et al. On the Interpretation of Force-Induced Unfolding Studies of Membrane Proteins Using Fast Simulations. Biophysical Journal, Volume 117, Issue 8, 1429 – 1441 (2019) DOI: 10.1016/j.bpj.2019.09.011
o Jumper JM, Faruk NF, Freed KF, Sosnick TR (2018) Trajectory-based training enables protein simulations with accurate folding and Boltzmann ensembles in cpu-hours. PLoS Comput Biol 14(12): e1006578 (2018) DOI: 10.1371/journal.pcbi.1006578
o Jumper JM, Faruk NF, Freed KF, Sosnick TR (2018) Accurate calculation of side chain packing and free energy with applications to protein molecular dynamics. PLoS Comput Biol 14 (12): e1006342. (2018) DOI: 10.1371/journal.pcbi.1006342
o Joshua A. Riback et al., Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water. Science358, 238-241 (2017) DOI:10.1126/science.aan5774
o Jumper, J. M., Freed, K. F., & Sosnick, T. R. Rapid calculation of side chain packing and free energy with applications to protein molecular dynamics. arXiv.org (2016) DOI: https://arxiv.org/abs/1610.07277
o John F. Zimmerman, Graeme F. Murray, Yucai Wang, John M. Jumper, Jotham R. Austin II, and Bozhi Tian. Free-Standing Kinked Silicon Nanowires for Probing Inter- and Intracellular Force Dynamics. Nano Letters 2015 15 (8), 5492-5498 (2015) DOI: 10.1021/acs.nanolett.5b01963
o Baxa, M. C., Haddadian, E. J., Jumper, J. M., Freed, K. F., & Sosnick, T. R. . Loss of conformational entropy in protein folding calculated using realistic ensembles and its implications for NMR-based calculations. Proceedings of the National Academy of Sciences, 111(43), 15396–15401 (2014) DOI: 10.1073/pnas.1407768111
Selected publicity on 2024 Nobel Prize in Chemistry:
o Nobel Prize in chemistry awarded to three scientists for work on proteins | Washington Post
o American Scientists among chemistry Nobel winners for pioneering protein work | NBC News
o Work on protein structure and design wins the 2024 chemistry Nobel | Science News
This story has been adapted from an article by Louise Lerner at UChicago News