This article is from the WeChat public account: Academic Headline (ID: SciTouTiao) , author: academic Jun, title figure from: The Tonight Show
The important role of protein in life is self-evident, it is the cornerstone of life. The process of protein synthesis in our body is also quite complicated, involving not only a series of processes such as amino acid activation, but also the regulation of various biochemical substances in the receptor. In addition, the complex three-dimensional folding structure of proteins has discouraged scientists who want to synthesize proteins.
On March 17, local time, MIT scientists brought a new result. They turned the complex structure of the protein into a musical score, and then gave the computer a seed sequence, and the artificial intelligence system could design it. A “new” protein never seen in nature.
They found that this “new” protein not only has a folded structure, it is also relatively stable. In addition, this “new” protein has never been found in nature. It can be said that this research provides a unique method for making proteins. The research results are published in APL Bioengineering.
The author of the study, MIT’s Markus J. Buehler, said that such a method paves the way for the creation of entirely new biomaterials. For example, if a protease is found in nature, this method can be used to improve the catalytic efficiency or generate new protein variants.
As we all know, amino acids are the basic units that make up proteins. To artificially make proteins, you must either imitate existing proteins or manually edit the amino acid sequences that make up proteins, but these two processes are very time consuming and change the amino acid sequence It is also difficult to predict what effect the later will have on the structure and function of the entire protein.
“Protein must have its own language.” Buehler said. In view of this, The team tried to translate protein language into another form that is easier for people to understand—music. Like music, the structure of protein is also layered, with different lengths or time scales. Structural hierarchy.
Given the 20 amino acids that make up a protein, each has a unique vibration frequency (calculated by quantum chemical theory) , so the chemical structure of the entire protein Can be described by notes, volume, melody and rhythm in music theory.
The team successfully developed a system that can convert protein molecular structure into sound last June, and the research was published in the journal ACS Nano.
The system can convert 20 amino acids in nature into 20 pitch syllables, that is, the amino acid sequence that makes up any kind of protein can be converted into a string of notes. The complex structural and functional information of proteins is also encoded in the melody’s pitch, volume, and duration dimensions.
Designing a protein composed of amino acids through music
Then researchers used artificial intelligence systems to study the melody produced by many different proteins.The intelligent system introduces small changes in the music sequence, and then translates the sound back to the corresponding amino acid sequence. In the process of protein production, changes in different music can be achieved by controlling temperature parameters.
Through this process, researchers can create variants of existing proteins, for example, based on a protein found in spider silk, one of the strongest materials in nature, to create something different from any More powerful proteins produced by biological evolution.
In this study published today, researchers used specific sounds produced by protein folding to train artificial intelligence systems. When the system learned to understand the complex language of folded proteins, they gave the system a seed sequence, and then artificial intelligence Based on this initial sequence, the system inferred and designed a “new” protein.
Then this “new” protein exists in nature, is it a known protein we know?
The research team compared this “new” protein with a large database of all currently known protein information and analyzed its molecular dynamics and characteristics using common patterns. Finally, the “new” The protein has not been found in nature, and this “new” protein has a stable folding structure.
In addition, researchers have found that by clarifying the rhythm and pitch of proteins, they can also help create new compositional techniques in classical music, a method that Buehler calls materiomusic. He said, “During the evolution of thousands of proteins, nature has also provided us with new ideas on how sounds can be combined.”
You can also listen to some protein music synthesized by researchers: https://soundcloud.com/user-275864738
Reference:
https://www.eurekalert.org/emb_releases/2020-03/aiop-cnp031220.php
https://aip.scitation.org/doi/10.1063/1.5133026
This article comes from WeChat public account: Academic Headline (ID: SciTouTiao) author: studyShujun