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A deeply knotted protein structure and how it might fold

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  • William R. Taylor

    (National Institute for Medical Research)

Abstract

The search for knots in protein has uncovered little that would cause Alexander the Great to reach for his sword. Excluding knots formed by post-translational crosslinking, the few proteins considered to be knotted form simple trefoil knots with one end of the chain extending through a loop by only a few residues1,2, ten in the ‘best’ example3. A knot in an open chain (as distinct from a closed circle) is not rigorously defined and many weak protein knots disappear if the structure is viewed from a different angle. Here I describe a computer algorithm to detect knots in open chains that is not sensitive to viewpoint and that can define the region of the chain giving rise to the knot. It characterizes knots in proteins by the number of residues that must be removed from each end to abolish the knot. I applied this algorithm to the protein structure database and discovered a deep, figure-of-eight knot in the plant protein acetohydroxy acid isomeroreductase4. I propose a protein folding pathway that may explain how such a knot is formed.

Suggested Citation

  • William R. Taylor, 2000. "A deeply knotted protein structure and how it might fold," Nature, Nature, vol. 406(6798), pages 916-919, August.
    • Handle: RePEc:nat:nature:v:406:y:2000:i:6798:d:10.1038_35022623
    DOI: 10.1038/35022623
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    Citations

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    Cited by:

    1. Miguel A Soler & Patrícia F N Faísca, 2012. "How Difficult Is It to Fold a Knotted Protein? In Silico Insights from Surface-Tethered Folding Experiments," PLOS ONE, Public Library of Science, vol. 7(12), pages 1-13, December.
    2. Nick Kinney & Molly Hickman & Ramu Anandakrishnan & Harold R Garner, 2020. "Crossing complexity of space-filling curves reveals entanglement of S-phase DNA," PLOS ONE, Public Library of Science, vol. 15(8), pages 1-20, August.
    3. Michael C Prentiss & David J Wales & Peter G Wolynes, 2010. "The Energy Landscape, Folding Pathways and the Kinetics of a Knotted Protein," PLOS Computational Biology, Public Library of Science, vol. 6(7), pages 1-12, July.
    4. Lindsey A. Doyle & Brittany Takushi & Ryan D. Kibler & Lukas F. Milles & Carolina T. Orozco & Jonathan D. Jones & Sophie E. Jackson & Barry L. Stoddard & Philip Bradley, 2023. "De novo design of knotted tandem repeat proteins," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    5. Ye Lei & Zhaoyong Li & Guangcheng Wu & Lijie Zhang & Lu Tong & Tianyi Tong & Qiong Chen & Lingxiang Wang & Chenqi Ge & Yuxi Wei & Yuanjiang Pan & Andrew C.-H. Sue & Linjun Wang & Feihe Huang & Hao Li, 2022. "A trefoil knot self-templated through imination in water," Nature Communications, Nature, vol. 13(1), pages 1-7, December.
    6. Rhonald C Lua & Alexander Y Grosberg, 2006. "Statistics of Knots, Geometry of Conformations, and Evolution of Proteins," PLOS Computational Biology, Public Library of Science, vol. 2(5), pages 1-8, May.
    7. Miguel A Soler & Patrícia F N Faísca, 2013. "Effects of Knots on Protein Folding Properties," PLOS ONE, Public Library of Science, vol. 8(9), pages 1-10, September.
    8. Alexander Begun & Sergei Liubimov & Alexander Molochkov & Antti J Niemi, 2021. "On topology and knotty entanglement in protein folding," PLOS ONE, Public Library of Science, vol. 16(1), pages 1-17, January.
    9. Zhiwen Li & Jingjing Zhang & Gao Li & Richard J. Puddephatt, 2024. "Self-assembly of the smallest and tightest molecular trefoil knot," Nature Communications, Nature, vol. 15(1), pages 1-6, December.
    10. Tatjana Škrbić & Cristian Micheletti & Pietro Faccioli, 2012. "The Role of Non-Native Interactions in the Folding of Knotted Proteins," PLOS Computational Biology, Public Library of Science, vol. 8(6), pages 1-12, June.

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