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Tying a true topological protein knot by cyclization.

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Enzymatically closing the open ends of the YibK protein (HiYibK) minimally altered its structure and ligand binding. However, path closure significantly impacted the protein

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Area of Science:

  • Biophysics
  • Structural Biology
  • Protein Science

Background:

  • Knotted proteins exhibit complex 3D structures and enhanced stability.
  • Naturally occurring knotted proteins have open N- and C-termini, unlike true mathematical knots.

Purpose of the Study:

  • To investigate the impact of path closure on the structure-function relationship and folding stability of a knotted protein.
  • To compare a cyclized knotted protein with its naturally occurring counterpart.

Main Methods:

  • Enzymatic cyclization of the 31 knotted YibK protein (HiYibK).
  • Utilized X-ray crystallography, NMR spectroscopy, small-angle X-ray scattering, differential scanning calorimetry, and isothermal calorimetry.

Main Results:

  • Path closure minimally perturbed the native structure and ligand binding of HiYibK.
  • Cyclization altered the folding stability and mechanism of HiYibK, as shown by chemical and thermal unfolding analyses.

Conclusions:

  • Protein path closure has a subtle effect on native structure but significant impact on folding stability.
  • Findings enhance fundamental understanding of protein folding and knotting.
  • Implications for designing more stable proteins.