Journal
PROTEIN SCIENCE
Volume 31, Issue 8, Pages -Publisher
WILEY
DOI: 10.1002/pro.4380
Keywords
AlphaFold; composite knots; protein knots; protein topology
Categories
Funding
- Deutsche Forschungsgemeinschaft [233630050-TRR 146]
- Johannes Gutenberg University Mainz
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The computer artificial intelligence system AlphaFold has predicted previously unknown three-dimensional structure of thousands of proteins. Among these predictions, it has discovered the most topologically complex knot ever found in a protein, as well as several composite knots formed by gene duplication and interconnection of knotted dimers. Two new five-crossing knots have also been reported. These results provide a basis for future experimental studies to confirm these novel-knotted topologies and explore their folding mechanisms.
The computer artificial intelligence system AlphaFold has recently predicted previously unknown three-dimensional structures of thousands of proteins. Focusing on the subset with high-confidence scores, we algorithmically analyze these predictions for cases where the protein backbone exhibits rare topological complexity, that is, knotting. Amongst others, we discovered a 7(1)-knot, the most topologically complex knot ever found in a protein, as well several six-crossing composite knots comprised of two methyltransferase or carbonic anhydrase domains, each containing a simple trefoil knot. These deeply embedded composite knots occur evidently by gene duplication and interconnection of knotted dimers. Finally, we report two new five-crossing knots including the first 5(1)-knot. Our list of analyzed structures forms the basis for future experimental studies to confirm these novel-knotted topologies and to explore their complex folding mechanisms.
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