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
ROR:	https://ror.org/023b0x485
DOI:	http://doi.org/10.25358/openscience-8709
Version:	Published version
Publication type:	Zeitschriftenaufsatz
Document type specification:	Scientific article
License:	CC BY
Information on rights of use:	https://creativecommons.org/licenses/by/4.0/
Journal:	Protein science 31 8
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