AlphaFold predicts the most complex protein knot and composite protein knots
| Autor: | Maarten A. Brems, Robert Runkel, Todd O. Yeates, Peter Virnau |
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| Jazyk: | angličtina |
| Rok vydání: | 2022 |
| Předmět: |
Models
Molecular Protein Folding Protein Conformation 530 Physics Proteins FOS: Physical sciences Biomolecules (q-bio.BM) Condensed Matter - Soft Condensed Matter 530 Physik Biochemistry Mathematics::Geometric Topology Quantitative Biology - Biomolecules Artificial Intelligence Biological Physics (physics.bio-ph) FOS: Biological sciences Soft Condensed Matter (cond-mat.soft) Physics - Biological Physics Molecular Biology |
| Popis: | 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, i.e. knotting. Amongst others, we discovered a $7_1$-knot, the most topologically complex knot ever found in a protein, as well several 6-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. This article appeared openly accessible in M. A. Brems et al., Protein Science. 2022; 31( 8):e4380 and may be found at https://doi.org/10.1002/pro.4380 |
| Databáze: | OpenAIRE |
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