UC Berkeley polymer scientists are working to make artificial fluids made of random heteropolymers with little complexity, but which retain many of the natural proteins' properties (right) such as stabilizing fragile molecular markers.
The majority of life on Earth is dependent on polymers made up of 20 different amino acids, which have evolved into hundreds of thousands of unique proteins. These proteins are capable of many tasks including triggering reactions, forming the spine and muscles, and even facilitating movement.
Is all this variety necessary? Is it possible to have biology working equally well with a reduced number of building blocks and simpler polymers?
Ting Xu, a polymer scientist at the University of California, Berkeley, believes it is possible. She has found that two, four, or six different building blocks — currently used in plastics — perform much better than the real protein and are much simpler to synthesize than trying to recreate nature's design.
She used her design methodology, which is based on machine learning or artificial intelligence, to fabricate polymers that mimic blood plasma. Natural protein biomarkers were kept intact without refrigeration and even enhanced natural proteins' resilience to high temperatures.
Since a lot of effort is now being spent on developing natural proteins to do things they were never intended to do, or attempting to recreate the 3D structure of natural proteins, protein substitutions may be a game changer for biomedical applications.
Instead, AI might select the appropriate number, type, and arrangement of plastic building blocks — similar to those used in dental fillings — to emulate a protein's desired function, and simple polymer chemistry could be employed to accomplish it.
Artificial polymers were developed to dissolve and stabilize natural protein biomarkers in blood. Xu and her colleagues also developed a mixture of synthetic polymers to replace the so-called cytosol in a test tube filled with artificial biological fluid. The cell's nanomachines, the ribosomes, continued to pump out natural proteins as if they didn't care whether the fluid was natural or artificial.
"All of the data suggests that we may utilize this design framework or philosophy to create polymers to a degree that the biological system would not be able to distinguish whether or not it is a polymer or a protein," said Xu, a UC Berkeley professor of chemistry and materials science and engineering. "We basically fool the biology."
The proposed system opens the way for hybrid biological systems, where plastic polymers interact easily with natural proteins to improve a system, such as photosynthesis. And the polymers may be made to degrade naturally, making the system more recyclable and sustainable.
“You begin to think about a completely different future for plastic, rather than all this commodity stuff,” said Xu, who is also a faculty scientist at Lawrence Berkeley National Laboratory.
The research of She and her colleagues was published in the Nature journal on March 8th.
Xu considers living tissue to be a complex collection of proteins that evolved to play together in a flexibly, with less attention paid to the actual amino acid sequence of each protein than to the functional subunits of the protein, the locations where these proteins interact. So like in a lock-and-key mechanism, where it doesn't matter whether the key is aluminum or steel, the actual composition of the functional subunits is less important than what they are.
If you follow the appropriate methods to design and select them, then natural protein mixtures might be possible.
"Nature does not do a lot of bottom-up, molecular, precision-driven research like we do in the lab," said Xu. "Nature requires flexibility in order to get where it is. Nature does not say, let's study the structure of this virus and develop an antigen to attack it. It's going to express a library of antigens and from there choose the one that works."
According to Xu, randomness may be exploited to create synthetic polymers that blend well with natural proteins, enabling them to create biocompatible plastics more easily than today's targeted methods.
Researchers developed deep learning techniques to match natural protein characteristics with plastic polymer properties in order to construct an artificial polymer that functions similarly, but not identically, to the natural protein. For example, the most important properties of the fluid are whether or not the polymer subunits like to interact with water, or whether or not the subunits are hydrophilic or hydrophobic.
Huang and graduate student Shuni Li studied the deep learning technique, also known as a modified variational autoencoder (VAE), on a database of about 60,000 natural proteins. These proteins were broken down into 50 amino acid segments, and the segment properties were compared to those of synthetic polymers made of only four building blocks.
The group was able to chemically synthesize a random number of polymers, RHPs, that resembled natural proteins in terms of charge and hydrophobicity thanks to Xu's lab research.
Xu said: "We examine the sequence space that nature has already created, we analyze it, we make the polymer match to what nature has already evolved, and they work." "How well you follow the protein sequence determines the performance of the polymer you obtain." Extracting information from an established system, such as naturally occurring proteins, is the easiest way to pinpoint the appropriate criteria for designing biologically compatible polymers."
Carlos Bustamante, a UC Berkeley professor of molecular and cell biology, chemistry, and physics, collaborated on single-molecule optical tweezers experiments and demonstrated that RHPs can mimic proteins' behavior.
Xu, Huang, and their colleagues are now attempting to mimic other protein characteristics in order to mimic many of the other functions of natural amino acid polymers in plastic.
Huang said, "Right now, our focus is just stabilizing proteins and mimicking the most basic protein functions." "I think it's natural for us to investigate other functions with a more refined RHP system."
The innovative platform opens the way for natural and synthetic polymers to evolve, but also suggests ways to make biocompatible materials more readily accessible, from artificial tears or cartilage to coatings that are effective in the delivery of drugs.
“You have to be compatible with biological systems,” said Xu. Here are the design guidelines. This is how you should interact with biological fluids.
Because current methods, which primarily aim at mimicking natural protein structures, are inadequate, Amy's ultimate goal is to completely redesign how biomaterials are currently constructed.
"We are not letting the biology dictate how the material should be constructed," said the Food and Drug Administration. "We are not letting the biology dictate how the material should be constructed."
Zhiyuan Ruan, Shuni Li, Alexandra Grigoropoulos, Shayna L. Hilburg, Haotian Chen, Ivan Jayapurna, Tao Jiang, Zhaoyi Gu, Alfredo Alexander-Katz, Carlos Bustamante, Haiyan Huang, and Ting Xu, Nature. DOI: 10.1038/s41586-022-05675-0
The Alfred P. Sloan Foundation's Matter-to-Life initiative supported the Department of Defense, the National Science Foundation, and the Department of Energy's Office of Science.
