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Topological Entanglement in Intrinsically Disordered Proteins: Sequence, Structural, and Functional Determinants.

Wangfei Yang1,2, Henry Silvernail3,2, Debasis Saha1

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Summary
This summary is machine-generated.

Entanglement measures reveal new insights into intrinsically disordered proteins (IDPs). Knot theory-based descriptors link protein sequence and structure to function, offering a conserved view of IDP organization.

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Area of Science:

  • Biophysics
  • Computational Biology
  • Structural Biology

Background:

  • Intrinsically disordered proteins (IDPs) lack stable structures, making their conformational ensembles hard to analyze.
  • Understanding the link between IDP sequence, structure, and function is a major challenge in molecular biology.

Purpose of the Study:

  • To apply knot theory-based entanglement measures to characterize IDP conformational ensembles.
  • To investigate the relationship between sequence composition, ensemble geometry, and entanglement in IDPs.
  • To establish entanglement as a biologically relevant feature of IDP organization.

Main Methods:

  • Analysis of over 28,000 simulated disordered protein sequences from the human IDRome database.
  • Calculation of two continuous entanglement descriptors: writhe and the second Vassiliev invariant (V2).
  • Correlation analysis of entanglement measures with sequence composition and ensemble structural features.

Main Results:

  • Entanglement measures (writhe and V2) show structured, low-dimensional variation across IDP sequences.
  • Writhe correlates with compaction and is predictable from sequence/structure, while V2 captures complex topology.
  • Functionally enriched regions in entanglement space were identified and shown to be evolutionarily conserved.

Conclusions:

  • Entanglement provides a novel and complementary dimension for understanding IDP organization.
  • Knot theory-based descriptors offer a rigorous framework for linking IDP sequence, ensemble structure, and function.
  • Entanglement signatures are conserved, highlighting their biological significance in IDP function.