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© 2010 Bölinger et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Bölinger D, Su?kowska JI, Hsu H-P, Mirny LA, Kardar M, et al. (2010) A Stevedore's Protein Knot. PLoS Comput Biol 6(4): e1000731. doi:10.1371/journal.pcbi.1000731

Abstract

Protein knots, mostly regarded as intriguing oddities, are gradually being recognized as significant structural motifs. Seven distinctly knotted folds have already been identified. It is by and large unclear how these exceptional structures actually fold, and only recently, experiments and simulations have begun to shed some light on this issue. In checking the new protein structures submitted to the Protein Data Bank, we encountered the most complex and the smallest knots to date: A recently uncovered α-haloacid dehalogenase structure contains a knot with six crossings, a so-called Stevedore knot, in a projection onto a plane. The smallest protein knot is present in an as yet unclassified protein fragment that consists of only 92 amino acids. The topological complexity of the Stevedore knot presents a puzzle as to how it could possibly fold. To unravel this enigma, we performed folding simulations with a structure-based coarse-grained model and uncovered a possible mechanism by which the knot forms in a single loop flip.

Details

Title
A Stevedore's Protein Knot
Author
Bölinger, Daniel; Sulkowska, Joanna I; Hsu, Hsiao-Ping; Mirny, Leonid A; Kardar, Mehran; Onuchic, José N; Virnau, Peter
Pages
e1000731
Section
Research Article
Publication year
2010
Publication date
Apr 2010
Publisher
Public Library of Science
ISSN
1553734X
e-ISSN
15537358
Source type
Scholarly Journal
Language of publication
English
ProQuest document ID
1313172609
Copyright
© 2010 Bölinger et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Bölinger D, Su?kowska JI, Hsu H-P, Mirny LA, Kardar M, et al. (2010) A Stevedore's Protein Knot. PLoS Comput Biol 6(4): e1000731. doi:10.1371/journal.pcbi.1000731