A Stevedore's Protein Knot
Name
Bolinger-2010-A Stevedore's Protei.pdf
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Author(s)
Bölinger, Daniel
Sułkowska, Joanna I.
Hsu, Hsiao-Ping
Mirny, Leonid A.
Kardar, Mehran
Onuchic, José N.
Virnau, Peter
Date Issued
April 2010
Journal
PLoS Computational Biology
Publisher
Public Library of Science
Citation
Bölinger, Daniel et al. “A Stevedore's Protein Knot.” PLoS Comput Biol 6.4 (2010): e1000731.
Version
Final published version
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.
MIT Department
Harvard University--MIT Division of Health Sciences and Technology
Massachusetts Institute of Technology. Department of Physics
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Creative Commons Attribution
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DOI of Published Version
https://doi.org/10.1371/journal.pcbi.1000731
