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Authors: Brems, Maarten A.
Runkel, Robert
Yeates, Todd O.
Virnau, Peter
Title: AlphaFold predicts the most complex protein knot and composite protein knots
Online publication date: 2-Feb-2023
Year of first publication: 2022
Language: english
Abstract: 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 71-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 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.
DDC: 530 Physik
530 Physics
Institution: Johannes Gutenberg-Universität Mainz
Department: FB 08 Physik, Mathematik u. Informatik
Place: Mainz
Version: Published version
Publication type: Zeitschriftenaufsatz
Document type specification: Scientific article
License: CC BY
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Journal: Protein science
Publisher: John Wiley & Sons, Ltd
Publisher place: Hoboken, NJ
Issue date: 2022
ISSN: 1469-896X
Publisher DOI: 10.1002/pro.4380
Appears in collections:DFG-491381577-H

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