SKM 2023 – wissenschaftliches Programm

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BP: Fachverband Biologische Physik

BP 17: Protein Structure and Dynamics

BP 17.7: Vortrag

Mittwoch, 29. März 2023, 16:45–17:00, BAR 0106

Alphafold predicts the most complex protein knot and composite protein knotsMaarten Brems1, Robert Runkel1, Todd Yeates2, and •Peter Virnau11Institut für Physik, Staudingerweg 9, JGU Mainz — 2UCLA-DOE Institute for Genomics and Proteomics, University of California Los Angeles (USA)

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 71-knot, the most topologically complex knot ever found in a protein, as well as several 6-crossing composite knots comprised of two methyltransferase or carbonic anhydrase domains, each containing a simple trefoil knot [1]. 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 51-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.
[1] M. Brems et al, Protein Science 31(8), e4380 (2022).

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