Theoretical physicists from Johannes Gutenberg University Mainz have discovered the most complex protein knot for the first time thanks to the help of Google's AI AlphaFold.
How the chemical compositions of a protein and its amino acid sequence determine the molecule's 3D structure has long been a mystery for biophysicists. This knowledge about molecule folding is in great demand and can significantly contribute to further understanding various diseases and treatment options. Because of this, Google's DeepMind research team developed AlphaFold, an AI system that can predict 3D structures.
Google AlphaFold and Complex Protein Knots
A collaboration of researchers from JGU and the University of California took a closer look at the structures of the molecule and examined for knots. Knots naturally occur in our cells. Knotted proteins can be used to assess the quality of structural predictions. Still, they can also raise important questions about the mechanisms at play in molecular folding and the evolution of proteins.
Maarten Brems, a Ph.D. student and co-author of the study, explains that they investigated numerically all, roughly 100,000, predictions of Google's AI AlphaFold for new protein knots. The study aimed to identify rare, high-quality structures containing complex and previously unknown protein knots to give a basis for experimental verification of AlphaFold's predictions.
The study published in the journal Protein Science, titled "AlphaFold predicts the most complex protein knot and composite protein knots." not only discovered the most complex knotted protein in history but was also the first composite knots in proteins.
Robert Runkel, a co-author of the study and theoretical physicist, explains that the discoveries also give insights into the e4voltuionary mechanisms behind the rare proteins. Dr. Peter Virnau, co-author and lead researcher, says that the team has been able to establish a collaboration with colleagues from UCLA to confirm the structures discovered experimentally. Adding that the line of research will shape the biophysics community's view on AI systems, reports ScienceDaily.
Understanding Proteins
Proteins, according to ScienceDirect, are the essence of life. It plays a crucial role in almost all biological processes. Proteins drive and control the body's metabolism; they protect the body from viruses and bacteria while allowing it to breathe, move, and see.
Natural nanobots formed for thousands of years acquire a specific biologically functional structure known as the native state via the folding process. Typically, this state coincides with the protein's tertiary structure, resulting in a three-dimensional packing of secondary structural elements. In unique proteins, the so-called knotted proteins, the native state embeds a knot.
This is why the groundbreaking discovery of the most complex protein knot bears such significance in the field. It will allow experts to investigate further how and why proteins gain specific functions. But, it will also shed light on how the protein structure affects its functionality.
Although the discovery and predictions of Google's AI AlphaFold need further verification, the study's authors are positive that it will give rise to future groundbreaking studies.
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