Solving Challenges with Speed: Protein Design Beyond Evolution
I view this topic as 'architecture on the molecular level.' There was a time when we were satisfied with structures accumulated randomly over billions of years of evolution. Now, humanity is moving into an era of 'designing' new molecular machines with a clear purpose and blueprint.
At the center of this change is the 2024 Nobel Prize in Chemistry winner, David Baker. His TED tSalk goes beyond simply introducing remarkable scientific achievements. What I want to share today is my interpretation of how this 'protein design' technology aims to solve human problems faster than the speed of evolution and what this powerful tool means for us.
Table of Contents
From an era of 'reading' the code of life to 'writing' it
AI: The accelerator catching up with the speed of evolution
Designed Future: Medicine, Environment, and Opportunities for Korea
Open Innovation and Questions for Us Ahead
1. From Reading the Code of Life to Writing It
For a long time, we have considered nature as merely a subject of awe and observation.
Proteins are the 'workers' of life. They transport nutrients, repair tissues, and trigger immune responses; in fact, almost every function within our bodies is performed by proteins. Historically, biology focused on discovering these proteins existing in nature, aiming to 'understand' their structure and function.
David Baker's receipt of the 2024 Nobel Prize in Chemistry marks a paradigm shift. Alongside fellow laureates John Jumper and Demis Hassabis, who achieved breakthroughs in 'protein structure prediction', he pioneered the field of 'protein design', crafting proteins that don't naturally exist.
"We are in an era where we can not only understand biological systems but also create new ones." — David Baker
The key principle is a shift in approach. While the traditional notion held that the amino acid sequence determines a protein's three-dimensional structure, protein design does the reverse. That is, we first design the three-dimensional structure to perform a specific function (e.g., binding to a virus) and then 'reverse-engineer' the amino acid sequence that can form this structure using computational methods. This signifies the transition of biology from a science of observation to one of creation.
2. AI: The Accelerator Keeping Pace with Evolution
Imagining was easy, but the real-world calculations were immensely complex.
Early protein design research relied on physics-based models, requiring vast computational resources to simulate every possible amino acid combination. This effort mobilized distributed computing projects like Rosetta@home. Success rates were low, and progress was painstakingly slow.
Unexpectedly, the breakthrough came from computer science, specifically AI. With the integration of deep learning into protein design, everything changed. AI models like RFdiffusion from David Baker's Institute for Protein Design (IPD) are leading the charge.
These AI models have learned from hundreds of thousands of known protein structures. Consequently, when given prompts like "We need a protein that performs this function," AI can rapidly and accurately generate blueprints (amino acid sequences) for entirely novel proteins that evolution hasn't produced.
This addresses the 'speed' issue I mentioned earlier. Random evolutionary processes that took billions of years can now be condensed into mere hours or days by AI. Humanity's grand challenges—such as pandemics, climate change, and incurable diseases—no longer afford the luxury of waiting for evolution's slow pace. We required an 'accelerator' to tackle these problems, and AI-based protein design has emerged as that powerful contender.
3. A Designed Future: Medicine, Environment, and Opportunities for Korea
No matter how great a technology is, it is meaningful only if it solves the problems of our lives.
This technology is no longer science fiction. During the COVID-19 pandemic, research teams designed synthetic proteins that bonded strongly and stably to the virus, contributing to the development of vaccines and treatments. This showed more precise and powerful potential than existing antibody drugs.
The future that protein design will open up is vast.
Personalized Medicine: Designing precise anti-cancer treatments that bind only to cancer cells, leaving normal cells untouched, much like 'smart missiles'.
Sustainability: Designing custom enzymes (proteins) that efficiently break down PET plastics, which are difficult to decompose in nature, contributing to solving environmental issues.
Next-Generation Materials: Developing 'smart protein materials' that perform functions previously unseen, such as converting light into electricity or storing information.
This is a particularly significant opportunity in the Korean context. Korea is armed with world-class biologics manufacturing capabilities, with companies like Samsung Biologics and Celltrion. If this is combined with global-level design capabilities, it could create tremendous synergy.
Moreover, Korea is one of the fastest aging societies in the world. Protein design technology, which provides precise solutions for chronic diseases such as cancer or degenerative brain diseases, can be key to solving important social challenges beyond industrial opportunities.
4. Open Innovation and the Questions Ahead
Of course, all powerful technologies come with both light and shadow.
David Baker, supported by the TED Audacious Project, is making this innovative technology and software freely available to researchers worldwide. Just as Linux accelerated development through the open-source model, there is a belief that democratizing technology will hasten innovation through collective intelligence.
But at the same time, we must ask: How can we control the risk of this powerful technology being misused for malicious purposes, such as developing biological weapons? Can the speed of technological advancement be matched by social consensus and ethical regulation?
Designing a balance between accelerating innovation through an open ecosystem, commercializing to recoup massive development costs, and implementing safeguards against technological misuse is another challenge we face.
This is why I call this technology 'architecture at the molecular level.' Humanity, which has marveled at nature’s design (evolution) for billions of years, is now becoming an architect that draws 'purpose-driven blueprints' by itself. It is an invitation not only to make better medicines and develop superior materials but also to fundamentally redesign how we approach life, solve problems, and view our own creativity.
TL;DR
The 'Protein Design' pioneered by David Baker, recipient of the 2024 Nobel Prize in Chemistry, goes beyond analyzing natural proteins to 'designing' new proteins that do not exist in nature using computers and AI. With advancements in AI (like RFdiffusion), proteins with desired functions can be created at a speed faster than evolution, showing potential to solve humanity's challenges in areas like COVID-19 vaccines, personalized cancer treatments, plastic-degrading enzymes, and smart new materials.
Protein design is a technology that involves designing new proteins using computers to perform desired functions. Proteins, crucial to life processes, fold into unique three-dimensional structures based on their amino acid sequences, and this principle is used in reverse. Essentially, after conceptualizing the three-dimensional structure that will implement the target function, the amino acid sequence forming that structure is calculated using AI deep learning models to create new proteins.
People Also Ask:
What is protein design? — Protein design is a technology that uses computers to design and create protein molecules from scratch with new structures and functions that do not exist in nature.
How is protein design used in drug development? — By designing proteins that bind precisely to molecules that cause diseases, it's possible to develop new concepts of vaccines or cancer treatments that minimize side effects and maximize therapeutic effects.
What role does AI play in protein design? — AI, especially deep learning models, learns from vast protein structure data to generate amino acid sequences for new proteins that can perform the desired functions quickly and accurately.
Why did David Baker receive a Nobel Prize? — David Baker was awarded the 2024 Nobel Prize in Chemistry for his groundbreaking work in predicting protein three-dimensional structures and further pioneering the field of 'protein design' to create entirely new proteins using computers.
Can protein design solve the plastic problem? — Yes, by designing new enzymes (proteins) that can efficiently degrade substances like PET plastics, it can contribute to solving the plastic waste problem.
LINKS
💰 60% OFF coupon for new users only Search 2HN43PU or 👉 Click the link to get started!
🌟 Already have a SHEIN account? You can still enjoy up to 40% OFF on top brands — just use code U74EGG2 on the SHEIN App or simply click here to grab your coupon 💕
