David Baker, born in Seattle in 1962, is an American professor of biochemistry and computational biology at the University of Washington, Seattle, and Howard Hughes Medical Institute. He has received the Nobel Prize in Chemistry for his pioneering research methods in protein design, and NLS asked him about his career, being a scientist, and of course, a lot about proteins.
December 10, 2024
How did you initially react to winning a Nobel Prize and how has it influenced your life and your work so far?
“I was thrilled! Honestly, I think I was too sleepy to fully process it when I got the call, but I was absolutely excited. Things have become incredibly busy. On the bright side, I’ve reconnected with many people I hadn’t heard from in years. The downside is I haven’t had time for proper conversations with them. Professionally, it’s made things a bit more hectic. I already lead a very active research group with a lot going on, so adding the Nobel Prize on top has increased our workload.”
I now plan to focus more on what matters the most to me.
“I now plan to focus more on what matters the most to me, like collaborating closely with my students and postdocs and dedicating myself to the most meaningful and exciting research projects. I hope to use the Nobel Prize to elevate my research even further.”
How did your career path to becoming a scientist begin?
“I started to study philosophy. I guess I've always been interested in big questions. When there’s not a lot of new things being discovered, there’s a new territory to explore. Then I came across biology and realized it offered endless opportunities for exploration and discovery, which truly fuels my passion.”
“Initially, in college, I only took introductory classes, but then I decided to pursue graduate studies in biology, focusing on understanding how cells function. At that time, I wasn’t working with proteins at all. I didn’t start tackling the kinds of problems I work on now until I became a professor."
How did you first become interested in protein structures?
“Proteins are fascinating because they perform virtually every function in living organisms, yet they’re essentially just large molecules made up of atoms and bonds. At first glance, they might not seem “alive”, but they exhibit remarkable behaviors that make them feel almost life-like. My interest in proteins grew from this paradox – they represent one of the simplest forms of biological self-organization. In nature, proteins accomplish incredible feats, and now, with modern techniques, we can design proteins to achieve equally amazing outcomes, which I find incredibly exciting.”
In nature, proteins accomplish incredible feats, and now, with modern techniques, we can design proteins to achieve equally amazing outcomes, which I find incredibly exciting.
Describe the applications of protein design?
“We create new proteins to break down plastic, treat cancer, treat autoimmune diseases, protect against viruses, or capture solar energy. Additionally, we are designing proteins that can block the key components of snake venom. This means that if someone is bitten by a snake, these proteins could effectively neutralize the venom. The applications for protein design span across fields like medicine, sustainability, and advanced nanotechnology.”
How do you create a new protein?
“There are two main components to our process: computer design and lab synthesis. On the computer we use methods similar to image generation models like DALL-E. For instance, we can input a request to “generate a protein that binds to this component of snake venom” and the program creates a corresponding amino acid sequence (primary structure of proteins). To produce this protein, we first synthesize a gene that encodes this amino acid sequence. While our bodies use natural genes to encode proteins, the antidote we’re designing is a completely new protein, requiring us to create a novel gene from DNA. We then introduce this gene into bacteria, which produce the protein. Finally, we extract the protein and test its effectiveness in blocking snake venom, for example.”
What challenges have you encountered in your research?
“Well, if you give me a specific protein and ask me to create a binder for it, I can certainly do that. However, there are countless proteins to choose from, so the real question is: which proteins should we target to help cure diseases or improve the environment? Right now, the biggest challenge in protein design isn't the methodology itself, but rather deciding on the most impactful applications. With so many possibilities, it's crucial to determine which projects are truly the most important to pursue.”
Is it easier to produce proteins for environmental or medical applications?
“I think it’s different. In the medical field, you have to go through clinical trials but there's a lot of demand, and you don't need so much protein. Whereas in the environmental field, you don't need to go through clinical trials, but you need to make a lot of protein.”
To date, we've started 21 companies to bring our designed proteins into the real world.
“There’s also a sociological aspect to consider, which is somewhat disheartening given the state of the world today. While we can design these proteins, actually deploying them requires resources that typically come from a company. Currently, it’s easier to get funding for medical purposes than environmental. To date, we've started 21 companies to bring our designed proteins into the real world, and it's simply more feasible to focus on cancer-related projects than on those outside the medical field.”
How do you envision the future?
“I'm hoping that there will be a whole new generation of medicines which are designed protein medicines. I expect that in sustainability we have designed proteins that help deal with a lot of the environmental problems that we face. I guess I'm pretty optimistic that in all these areas, we'll be able to come up with better ways of solving the problems than we have currently in the world.”
About the Author
Paula Pérez González-Anguiano, M.Sc. in Scientific, Medical and Environmental Communication, is a Science Journalist and Illustrator based in Barcelona, Spain.
How did you initially react to winning a Nobel Prize and how has it influenced your life and your work so far?
“I was thrilled! Honestly, I think I was too sleepy to fully process it when I got the call, but I was absolutely excited. Things have become incredibly busy. On the bright side, I’ve reconnected with many people I hadn’t heard from in years. The downside is I haven’t had time for proper conversations with them. Professionally, it’s made things a bit more hectic. I already lead a very active research group with a lot going on, so adding the Nobel Prize on top has increased our workload.”
I now plan to focus more on what matters the most to me.
“I now plan to focus more on what matters the most to me, like collaborating closely with my students and postdocs and dedicating myself to the most meaningful and exciting research projects. I hope to use the Nobel Prize to elevate my research even further.”
How did your career path to becoming a scientist begin?
“I started to study philosophy. I guess I’ve always been interested in big questions. When there’s not a lot of new things being discovered, there’s a new territory to explore. Then I came across biology and realized it offered endless opportunities for exploration and discovery, which truly fuels my passion.”
“Initially, in college, I only took introductory classes, but then I decided to pursue graduate studies in biology, focusing on understanding how cells function. At that time, I wasn’t working with proteins at all. I didn’t start tackling the kinds of problems I work on now until I became a professor.”
How did you first become interested in protein structures?
“Proteins are fascinating because they perform virtually every function in living organisms, yet they’re essentially just large molecules made up of atoms and bonds. At first glance, they might not seem “alive”, but they exhibit remarkable behaviors that make them feel almost life-like. My interest in proteins grew from this paradox – they represent one of the simplest forms of biological self-organization. In nature, proteins accomplish incredible feats, and now, with modern techniques, we can design proteins to achieve equally amazing outcomes, which I find incredibly exciting.”
In nature, proteins accomplish incredible feats, and now, with modern techniques, we can design proteins to achieve equally amazing outcomes, which I find incredibly exciting.
Describe the applications of protein design?
“We create new proteins to break down plastic, treat cancer, treat autoimmune diseases, protect against viruses, or capture solar energy. Additionally, we are designing proteins that can block the key components of snake venom. This means that if someone is bitten by a snake, these proteins could effectively neutralize the venom. The applications for protein design span across fields like medicine, sustainability, and advanced nanotechnology.”
How do you create a new protein?
“There are two main components to our process: computer design and lab synthesis. On the computer we use methods similar to image generation models like DALL-E. For instance, we can input a request to “generate a protein that binds to this component of snake venom” and the program creates a corresponding amino acid sequence (primary structure of proteins). To produce this protein, we first synthesize a gene that encodes this amino acid sequence. While our bodies use natural genes to encode proteins, the antidote we’re designing is a completely new protein, requiring us to create a novel gene from DNA. We then introduce this gene into bacteria, which produce the protein. Finally, we extract the protein and test its effectiveness in blocking snake venom, for example.”
What challenges have you encountered in your research?
“Well, if you give me a specific protein and ask me to create a binder for it, I can certainly do that. However, there are countless proteins to choose from, so the real question is: which proteins should we target to help cure diseases or improve the environment? Right now, the biggest challenge in protein design isn’t the methodology itself, but rather deciding on the most impactful applications. With so many possibilities, it’s crucial to determine which projects are truly the most important to pursue.”
Is it easier to produce proteins for environmental or medical applications?
“I think it’s different. In the medical field, you have to go through clinical trials but there’s a lot of demand, and you don’t need so much protein. Whereas in the environmental field, you don’t need to go through clinical trials, but you need to make a lot of protein.”
To date, we’ve started 21 companies to bring our designed proteins into the real world.
“There’s also a sociological aspect to consider, which is somewhat disheartening given the state of the world today. While we can design these proteins, actually deploying them requires resources that typically come from a company. Currently, it’s easier to get funding for medical purposes than environmental. To date, we’ve started 21 companies to bring our designed proteins into the real world, and it’s simply more feasible to focus on cancer-related projects than on those outside the medical field.”
How do you envision the future?
“I’m hoping that there will be a whole new generation of medicines which are designed protein medicines. I expect that in sustainability we have designed proteins that help deal with a lot of the environmental problems that we face. I guess I’m pretty optimistic that in all these areas, we’ll be able to come up with better ways of solving the problems than we have currently in the world.”
About the Author
Paula Pérez González-Anguiano, M.Sc. in Scientific, Medical and Environmental Communication, is a Science Journalist and Illustrator based in Barcelona, Spain.
Updated: January 23, 2025, 10:34 am
Published: December 10, 2024
