David Baker (biochemist)

Last updated

David Baker
David Baker at 2024 Nobel Prize Conference 3.jpg
Baker in 2024
Born (1962-10-06) October 6, 1962 (age 62)
Seattle, Washington, U.S.
Alma mater
Known for
Spouse Hannele Ruohola-Baker
Awards
Scientific career
Fields Computational biology
Institutions
Thesis Reconstitution of intercompartmental protein transport in yeast extracts  (1989)
Doctoral advisor Randy Schekman
Other academic advisors David Agard
Doctoral students Richard Bonneau
Other notable students Brian Kuhlman, Tanja Kortemme
Website www.bakerlab.org

David Baker (born October 6, 1962) is an American biochemist and computational biologist who has pioneered methods to design proteins and predict their three-dimensional structures. He is the Henrietta and Aubrey Davis Endowed Professor in Biochemistry, an investigator with the Howard Hughes Medical Institute, and an adjunct professor of genome sciences, bioengineering, chemical engineering, computer science, and physics at the University of Washington. He was awarded the shared 2024 Nobel Prize in Chemistry for his work on computational protein design. [3] [4]

Contents

Baker is a member of the United States National Academy of Sciences and the director of the University of Washington's Institute for Protein Design. [5] He has co-founded more than a dozen biotechnology companies and was included in Time magazine's inaugural list of the 100 Most Influential People in health in 2024. [6]

Biography

Early life and education

Baker was born into a Jewish family in Seattle, Washington on October 6, 1962, the son of physicist Marshall Baker and geophysicist Marcia (née Bourgin) Baker. [7] He graduated from Seattle's Garfield High School. [8]

Baker received a Bachelor of Arts degree with a major in biology from Harvard University in 1984. He then joined the laboratory of Randy Schekman, where he worked primarily on protein transport and trafficking in yeast, and obtained a Doctor of Philosophy in biochemistry from the University of California, Berkeley in 1989. [9] In 1993, he completed his postdoctoral training in biophysics with David Agard at the University of California, San Francisco.

Career

Baker joined the Department of Biochemistry at the University of Washington School of Medicine as a faculty member in 1993. He became a Howard Hughes Medical Institute investigator in 2000. [10] Baker was elected a Fellow of the American Academy of Arts and Sciences in 2009. [11]

Personal life

Baker is married to Hannele Ruohola-Baker, another biochemist at the University of Washington. They have two children.

Research

Although primarily known for the development of computational methods for predicting and designing the structures and functions of proteins, Baker maintains an active experimental biochemistry group. [12] He has authored over 600 scientific papers. [13]

Baker's group developed the Rosetta algorithm for ab initio protein structure prediction, which has been extended into a tool for protein design, a distributed computing project called Rosetta@home, [12] [14] [15] and the computer game Foldit. [16] [17] [18] Baker served as the director of the Rosetta Commons, a consortium of labs and researchers that develop biomolecular structure prediction and design software. Baker's group has regularly competed in the CASP structure prediction competition, specializing in ab initio methods, including both manually assisted and automated variants of the Rosetta protocol. [19] [20] Using artificial intelligence, his group has developed later a newer version of the program known as RoseTTAFold. [21] [22]

Baker's group is also active in the field of protein design; [12] [23] they are noted for designing Top7, the first artificial protein with a novel fold. [24]

In 2017, Baker's Institute for Protein Design received over $11 million from Open Philanthropy, [25] [26] followed by an additional $3 million donation in 2021. [27]

In April 2019, Baker gave a TED talk titled "5 challenges we could solve by designing new proteins" at TED2019 in Vancouver, Canada. [28]

Baker has co-founded several biotechnology companies, including Prospect Genomics which was acquired by an Eli Lilly subsidiary in 2001, [29] Icosavax which was acquired by AstraZeneca in 2023, [30] Sana Biotechnology, Lyell Immunotherapeutics, and Xaira Therapeutics.

Awards

Baker delivering a lecture during 2024 Nobel Week David Baker, 2024 Nobel Prize Laureate in Chemistry.jpg
Baker delivering a lecture during 2024 Nobel Week

For his work on protein folding, Baker has received numerous awards, including the Overton Prize (2002), [31] the Sackler International Prize in Biophysics (2008), [32] the Wiley Prize (2022) [33] and the BBVA Foundation Frontiers of Knowledge Award in the category "Biology and Biomedicine" (2022). [34]

For his work on protein design, Baker has received the Newcomb Cleveland Prize (2004), [35] the Feynman Prize in Nanotechnology (2004), [36] and the Breakthrough Prize in Life Sciences (2021). [37]

In 2024, Baker was awarded half of the Nobel Prize in Chemistry for his work on protein design; the other half went to John M. Jumper and Demis Hassabis for development of AlphaFold, a program for protein structure prediction. [3] [4]

See also

Related Research Articles

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Structural biology, as defined by the Journal of Structural Biology, deals with structural analysis of living material at every level of organization.

Levinthal's paradox is a thought experiment in the field of computational protein structure prediction; protein folding seeks a stable energy configuration. An algorithmic search through all possible conformations to identify the minimum energy configuration would take an immense duration; however in reality protein folding happens very quickly, even in the case of the most complex structures, suggesting that the transitions are somehow guided into a stable state through an uneven energy landscape.

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<span class="mw-page-title-main">Rosetta@home</span> BOINC based volunteer computing project researching protein folding

Rosetta@home is a volunteer computing project researching protein structure prediction on the Berkeley Open Infrastructure for Network Computing (BOINC) platform, run by the Baker lab. Rosetta@home aims to predict protein–protein docking and design new proteins with the help of about fifty-five thousand active volunteered computers processing at over 487,946 GigaFLOPS on average as of September 19, 2020. Foldit, a Rosetta@home videogame, aims to reach these goals with a crowdsourcing approach. Though much of the project is oriented toward basic research to improve the accuracy and robustness of proteomics methods, Rosetta@home also does applied research on malaria, Alzheimer's disease, and other pathologies.

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AlphaFold is an artificial intelligence (AI) program developed by DeepMind, a subsidiary of Alphabet, which performs predictions of protein structure. The program is designed as a deep learning system.

Jens Meiler is a German-American biologist and structural chemist. He currently serves as a Professor of Chemistry and Associate Professor of Pharmacology and Biomedical Informatics at Vanderbilt University. His research focuses on protein structures and computational biology, drawing on interdisciplinary techniques from other sciences.

<span class="mw-page-title-main">John M. Jumper</span> American computational biologist (born 1985)

John Michael Jumper is an American chemist and computer scientist. He currently serves as director at Google DeepMind. Jumper and his colleagues created AlphaFold, an artificial intelligence (AI) model to predict protein structures from their amino acid sequence with high accuracy. Jumper stated that the AlphaFold team plans to release 100 million protein structures.

References

  1. ↑ "David Baker". Arnold and Mabel Beckman Foundation. Archived from the original on August 2, 2018. Retrieved August 1, 2018.
  2. ↑ "Institute for Protein Design wins $45M in funding from TED's Audacious Project". April 17, 2019. Archived from the original on April 18, 2019. Retrieved April 18, 2019.
  3. 1 2 "The Nobel Prize in Chemistry 2024". Nobel Media AB. Archived from the original on October 9, 2024. Retrieved October 9, 2024.
  4. 1 2 "Press release: The Nobel Prize in Chemistry 2024". NobelPrize.org. Archived from the original on October 9, 2024. Retrieved October 9, 2024.
  5. ↑ "UW to Establish Institute for Protein Design". University of Washington. April 13, 2012. Archived from the original on January 15, 2019. Retrieved January 14, 2019.
  6. ↑ Henshall, Will (May 2, 2024). "David Baker". Time. Archived from the original on October 9, 2024. Retrieved September 30, 2024.
  7. ↑ JINFO. "Jewish Nobel Prize Winners in Chemistry". www.jinfo.org. Retrieved October 9, 2024.
  8. ↑ Smith, Jenn (October 9, 2024). "David Baker, a UW professor who grew up in Seattle, wins Nobel Prize". The Seattle Times.
  9. ↑ Baker, David (1989). Reconstitution of Intercompartmental Protein Transport in Yeast Extracts (PhD thesis). University of California, Berkeley. OCLC   905883076. ProQuest   303670112.
  10. ↑ "David Baker, PhD". hhmi.org. Howard Hughes Medical Institute. Retrieved September 30, 2024.
  11. ↑ "Book of Members, 1780–2010: Chapter B" (PDF). American Academy of Arts and Sciences. Archived (PDF) from the original on July 8, 2018. Retrieved May 5, 2011.
  12. 1 2 3 Howes, Laura (July 23, 2019). "Protein wrangler, serial entrepreneur, and community builder: Inside David Baker's brain". Chemical & Engineering News.
  13. ↑ David Baker publications indexed by Google Scholar
  14. ↑ Castillo, Oscar; Melin, Patricia; Kacprzyk, Janusz, eds. (2018). Fuzzy Logic Augmentation of Neural and Optimization Algorithms: Theoretical Aspects and Real Applications. Springer. p. 455. ISBN   9783319710075. Archived from the original on October 9, 2024. Retrieved August 2, 2018.
  15. ↑ Bonneau, Richard; Ruczinski, Ingo; Tsai, Jerry; Baker, David (August 2002). "Contact order and ab initio protein structure prediction". Protein Science. 11 (8): 1937–1944. doi:10.1110/ps.3790102. PMC   2373674 . PMID   12142448.
  16. ↑ Hand, E. (2010). "Citizen science: People power". Nature. 466 (7307): 685–687. doi: 10.1038/466685a . PMID   20686547.
  17. ↑ Cooper, S.; Khatib, F.; Treuille, A.; Barbero, J.; Lee, J.; Beenen, M.; Leaver-Fay, A.; Baker, D.; Popović, Z.; Players, F. (2010). "Predicting protein structures with a multiplayer online game". Nature. 466 (7307): 756–760. Bibcode:2010Natur.466..756C. doi:10.1038/nature09304. PMC   2956414 . PMID   20686574.
  18. ↑ Marshall, Jessica (January 22, 2012). "Victory for crowdsourced biomolecule design". Nature. Nature Publishing Group. doi:10.1038/nature.2012.9872. Archived from the original on February 4, 2024. Retrieved September 30, 2024.
  19. ↑ Dimaio, F.; Terwilliger, T. C.; Read, R. J.; Wlodawer, A.; Oberdorfer, G.; Wagner, U.; Valkov, E.; Alon, A.; Fass, D.; Axelrod, H. L.; Das, D.; Vorobiev, S. M.; Iwaï, H.; Pokkuluri, P. R.; Baker, D. (2011). "Improved molecular replacement by density- and energy-guided protein structure optimization". Nature. 473 (7348): 540–3. Bibcode:2011Natur.473..540D. doi:10.1038/nature09964. PMC   3365536 . PMID   21532589.
  20. ↑ Qian, B.; Raman, S.; Das, R.; Bradley, P.; McCoy, A. J.; Read, R. J.; Baker, D. (2007). "High-resolution structure prediction and the crystallographic phase problem". Nature. 450 (7167): 259–64. Bibcode:2007Natur.450..259Q. doi:10.1038/nature06249. PMC   2504711 . PMID   17934447.
  21. ↑ "Protein structures for all". Science. American Association for the Advancement of Science. December 16, 2021. Archived from the original on December 16, 2022. Retrieved September 30, 2024.
  22. ↑ "How AI Revolutionized Protein Science, but Didn't End It". Quanta Magazine. Simons Foundation. June 26, 2024. Archived from the original on October 9, 2024. Retrieved September 30, 2024.
  23. ↑ Zimmer, Carl (December 26, 2017). "Scientists Are Designing Artisanal Proteins for Your Body". The New York Times. Archived from the original on August 2, 2018. Retrieved August 2, 2018.
  24. ↑ Kuhlman, Brian; Dantas, Gautam; Ireton, Gregory C.; Varani, Gabriele; Stoddard, Barry L.; Baker, David (November 21, 2003). "Design of a Novel Globular Protein Fold with Atomic-Level Accuracy". Science. 302 (5649): 1364–1368. Bibcode:2003Sci...302.1364K. doi:10.1126/science.1089427. PMID   14631033. S2CID   1939390.
  25. ↑ "Open Philanthropy awards $11.3 million to the Institute for Protein Design". Institute for Protein Design. April 4, 2018. Retrieved October 9, 2024.
  26. ↑ "University of Washington — Universal Flu Vaccine and Computational Protein Design (David Baker and Neil King)". Open Philanthropy. November 2017. Retrieved October 9, 2024.
  27. ↑ "University of Washington — Protein Design Research (David Baker)". Open Philanthropy. Retrieved October 9, 2024.
  28. ↑ "5 challenges we could solve by designing new proteins". June 17, 2019. Archived from the original on February 9, 2020. Retrieved February 26, 2020.
  29. ↑ Hamilton, David (2001). "Structural GenomiX to Acquire Research Firm Prospect Genomics". Archived from the original on October 9, 2024. Retrieved September 15, 2024.
  30. ↑ Soper, Taylor (December 12, 2023). "AstraZeneca will pay up to $1.1B to acquire Icosavax, a Univ. of Washington biotech spinout". GeekWire. Archived from the original on July 15, 2024. Retrieved October 1, 2024.
  31. ↑ "2002 Overton Prize Winner – David Baker". iscb.org. International Society for Computational Biology. Retrieved September 30, 2024.
  32. ↑ Leila Gray (November 24, 2008). "University of Washington biochemist David Baker to receive 2008 Sackler International Prize in Biophysics for discoveries in protein folding". University of Washington. Retrieved April 29, 2013.
  33. ↑ "The Wiley Prize in Biomedical Sciences". wiley.com. Archived from the original on March 14, 2023. Retrieved September 30, 2024.
  34. ↑ "BBVA Foundation Frontiers of Knowledge Award 2022". Archived from the original on September 21, 2021. Retrieved January 25, 2023.
  35. ↑ "Newcomb Cleveland Prize Recipients". aaas.org. Archived from the original on December 11, 2023. Retrieved September 30, 2024.
  36. ↑ "Winners of the 2004 Feynman Prizes in Nanotechnology". foresight.org. Archived from the original on October 9, 2024. Retrieved September 30, 2024.
  37. ↑ "Breakthrough Prize – Winners Of The 2021 Breakthrough Prizes In Life Sciences, Fundamental Physics And Mathematics Announced". breakthroughprize.org. Archived from the original on January 26, 2021. Retrieved December 13, 2021.
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