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Related Experiment Video

Updated: Jan 30, 2026

High and Low Throughput Screens with Root-knot Nematodes Meloidogyne spp.
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Untying a Protein Knot by Circular Permutation.

Ya-Chu Chuang1, I-Chen Hu2, Ping-Chiang Lyu2

  • 1Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan; Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 30013, Taiwan.

Journal of Molecular Biology
|January 15, 2019
PubMed
Summary
This summary is machine-generated.

Protein knots, like SPOUT RNA methyltransferases, evolved from unknotted forms. Circular permutation revealed that knotting enhances folding stability and function, supporting evolutionary selection for these robust protein structures.

Keywords:
SPOUT RNA methyltransferasecircular permutationknotted proteinprotein folding

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Protein Evolution

Background:

  • Topologically knotted proteins demonstrate complex protein folding pathways.
  • The evolutionary origins of protein knots are not well understood.
  • SPOUT RNA methyltransferases are a conserved class of topologically knotted enzymes.

Purpose of the Study:

  • To investigate the evolutionary origins of protein knots in the SPOUT superfamily.
  • To understand the functional and structural implications of the conserved knotted topology.
  • To test the hypothesis that circular permutation played a role in the evolution of protein knots.

Main Methods:

  • Utilized circular permutation to convert a topologically knotted SPOUT RNA methyltransferase into an unknotted variant.
  • Compared the three-dimensional structure, oligomeric state, folding stability, folding kinetics, and ligand binding of the knotted and unknotted variants.
  • Analyzed the functional and structural consequences of removing the topological knot.

Main Results:

  • The unknotted variant maintained the same 3D structure and oligomeric state as the knotted parent.
  • Folding stability was significantly reduced, and folding kinetics were accelerated in the unknotted variant.
  • Ligand binding capability was abrogated in the unknotted form.
  • The knotted topology is crucial for the protein's stability and function.

Conclusions:

  • The universally conserved knotted topology in the SPOUT superfamily likely evolved from unknotted precursors via circular permutation.
  • Evolutionary selection favored knotting for enhanced folding robustness and specific functional requirements.
  • The knotted structural element is essential for the proper function of SPOUT RNA methyltransferases.