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Protein knots and fold complexity: some new twists.

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This review explores topological knots in protein structures, focusing on three, four, and five-strand crossings. It proposes that the simplest knot form and specific chain termini positions are key to identifying naturally occurring protein knots.

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Area of Science:

  • Structural Biology
  • Biophysics
  • Computational Biology

Background:

  • Topological knots are increasingly recognized in protein structures, influencing their stability and function.
  • Understanding the complexity and classification of these knots is crucial for predicting protein folding and evolution.

Purpose of the Study:

  • To review and synthesize current knowledge on topological knots in protein structures, specifically those with three, four, and five-strand crossings.
  • To identify characteristics of naturally occurring protein knots, including their topological forms and the positioning of chain termini.
  • To propose criteria for identifying novel and more complex protein knots and explore alternative measures of knottedness.

Main Methods:

  • Review of existing literature on topological knots in protein structures.
  • Analysis of knot characteristics, including strand crossings, topological forms, and chain termini positions.
  • Examination of alternative measures of knottedness and entanglement, such as slip-knots.

Main Results:

  • The most recently identified five-strand crossing knots exhibit two distinct topological forms.
  • Naturally occurring protein knots appear to be the simplest topological form requiring minimal strand crossings for unknotting.
  • Specific chain termini positions are postulated as essential for enabling knotting and unknotting in a single move.

Conclusions:

  • The 'Jelly-roll' fold in all-beta proteins is a likely candidate for hosting complex topological knots.
  • Criteria for identifying potential protein knots can guide the search for new examples and aid in predicting protein structures.
  • Measures of knottedness and entanglement can serve as valuable filters for assessing the complexity of protein folds.