From: mk_thisisit
Synthetic proteins are novel proteins created in a laboratory, marking a significant departure from all previously known proteins, which originated from natural evolution spanning billions of years [00:00:05]. This field is revolutionizing biology, moving it “out of the Stone Age” [00:00:25], by enabling the creation of entirely new structures to solve specific problems [00:10:44].
The Dawn of Synthetic Proteins: Top 7
The breakthrough moment in the field was the creation of a new protein in the laboratory [00:00:05]. Top 7 is recognized as the first protein designed using a computer [00:00:16] [00:15:35], possessing a completely new structure [00:15:37]. This discovery showed that humans could now create entirely new proteins [00:15:46]. Top 7, created in 2003 [00:16:19], initially had no function [00:15:53] but opened the door for designing proteins with precise structures [00:15:56]. Its name, “Top 7,” was given by Brian Kuhlman because it was the seventh protein topology attempted that proved successful [00:16:42] [00:16:51]. The realization of its success came when experimental confirmation showed its structure matched the computer model [00:05:32] [00:16:03].
The Design Process
The design of synthetic proteins relies on advanced computational methods:
- Understanding Protein Folding: The ability to design proteins from scratch became possible once the principle of protein folding was understood [00:10:39].
- Leveraging Data and AI: The field benefits from an extensive database containing structures of about 200,000 proteins, which serves as ideal material for deep learning methods [00:07:32]. These methods analyze data, identify patterns between amino acid sequences and structures, and accurately predict the structure of new sequences [00:07:41].
- Role of Artificial Intelligence: Recent design methods are based on the use of artificial intelligence [00:03:37]. While companies like DeepMind focus on predicting protein structures, David Baker’s lab focuses on protein design, viewing their activities as complementary [00:11:12] [00:11:33].
Challenges
The space of possible protein combinations is vast. For a protein 100 residues long with 20 amino acids, there are 20 to the power of 100 possible combinations, making the key challenge finding the best solutions within this immense space [00:04:08].
Applications of Synthetic Proteins
The possibilities opened by synthetic protein design are vast, with potential applications in medicine and technology [00:06:12] [00:07:01].
- Medicine:
- Creating precise drugs to effectively treat diseases while minimizing side effects, such as those seen in anti-cancer therapies [00:06:16].
- Designing universal vaccines that strengthen resistance to various threats [00:06:27].
- Developing more effective drugs and progressing in disease treatment [00:13:32].
- Advancements in genetic drugs [00:13:38].
- Ecology:
- Helping break down plastic [00:06:38].
- Neutralizing pollution [00:06:40].
- Removing greenhouse gases from the atmosphere to combat climate change [00:06:43].
- Technology:
- Opening the way for the creation of innovative materials [00:06:54].
- Developing advanced measurement tools [00:06:58].
- Creating new kinds of hybrid materials similar to teeth and bones that involve proteins interacting with inorganic compounds [00:20:08].
- Developing catalysts for various chemical reactions [00:20:26].
- The creation of new biological machines, particularly at the protein level [00:00:41] [00:13:56].
- Synthetic Olfactory Receptors: David Baker’s laboratory created the first synthetic olfactory receptor [00:18:04], which may lead to creating new proteins capable of detecting many different types of molecules [00:18:13]. This research aims to place sensors that detect molecules directly in silicon chips [00:00:33] [00:18:50], cell phones, and connect proteins with electronics [00:00:46] [00:19:01]. The potential of such an electronic nose is to detect many more compounds than a human can [00:00:53] [00:19:43].
From Stone Age to Advanced Engineering
Professor David Baker emphasizes that today’s biological engineering resembles early engineering from 100,000 years ago [00:00:21], when humans only used what they found in the environment or made minor modifications to natural elements [00:10:14] [00:10:30]. This is why he advocates for “taking biology out of the Stone Age” [00:00:25] [00:08:47].
The analogy used is that instead of trying to modify birds to fly, humans discovered aerodynamics to build planes [00:09:42]. Similarly, in biology, instead of solely relying on existing natural proteins and minor modifications, scientists can now design completely new structures from scratch to solve specific problems [00:10:39].
Future Outlook
Predicting the future of science and technology is challenging, as breakthroughs are often unpredictable [00:12:46]. However, the field of synthetic proteins is poised for significant impact. While the concept of super human artificial intelligence (AGI) is a complex topic, computers are expected to become increasingly capable of performing most human tasks [00:23:06]. The internal states of such AGI, or artificial consciousness, remain a mystery given the current lack of understanding of human consciousness itself [00:23:31].
David Baker, a Nobel laureate in Chemistry, believes his achievements will have a substantial impact [00:20:48]. He anticipates that future generations of scientists, including current PhD and master’s students in his group, will achieve even more amazing things [00:21:24].