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Related Concept Videos

Intrinsically Disordered Proteins02:18

Intrinsically Disordered Proteins

Intrinsically disordered proteins are a group of proteins that do not fold into specific three-dimensional structures. Their structural flexibility allows them to complement ordered proteins to perform functions that are inaccessible to rigid structures. They are more common in eukaryotes than prokaryotes and may either be exclusively intrinsically disordered or hybrid proteins, consisting of a mix of ordered and disordered regions. The absence of a rigid structure in these proteins can be...
Intrinsically Disordered Proteins02:18

Intrinsically Disordered Proteins

Intrinsically disordered proteins are a group of proteins that do not fold into specific three-dimensional structures. Their structural flexibility allows them to complement ordered proteins to perform functions that are inaccessible to rigid structures. They are more common in eukaryotes than prokaryotes and may either be exclusively intrinsically disordered or hybrid proteins, consisting of a mix of ordered and disordered regions. The absence of a rigid structure in these proteins can be...
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Protein Folding01:25

Protein Folding

Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...
Protein Folding01:22

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Protein-protein Interfaces02:04

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...

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

Wangfei Yang1, Henry Silvernail2, Debasis Saha1

  • 1College of Integrative Sciences and Arts, Arizona State University, Mesa, Arizona 85212, United States.

The Journal of Physical Chemistry. B
|June 24, 2026
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Summary
This summary is machine-generated.

Entanglement measures from knot theory reveal new insights into intrinsically disordered proteins (IDPs). These topological features connect protein sequence to function and are evolutionarily conserved.

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Area of Science:

  • Biophysics
  • Computational Biology
  • Structural Biology

Background:

  • Intrinsically disordered proteins (IDPs) lack stable structures, complicating the link between their sequence and function.
  • Conventional methods struggle to capture the complex conformational ensembles of IDPs.
  • New descriptors are needed to understand IDP organization and function.

Purpose of the Study:

  • To apply entanglement-based measures from knot theory to characterize IDP conformational ensembles.
  • To investigate the relationship between sequence composition, entanglement, and biological function in IDPs.
  • To establish entanglement as a relevant dimension for understanding IDP behavior.

Main Methods:

  • Analysis of over 28,000 simulated disordered sequences from the human IDRome database.
  • Computation of continuous entanglement descriptors: writhe and the second Vassiliev invariant (V2).
  • Correlation of entanglement measures with sequence composition and ensemble geometry, including ortholog simulations.

Main Results:

  • Entanglement measures (writhe and V2) show structured, low-dimensional variation across IDP sequences.
  • Writhe correlates with compaction and coiling, predictable from basic sequence/structure features.
  • V2 captures higher-order topological organization, less predictable from simple metrics.
  • Functionally enriched regions identified in entanglement space.
  • Entanglement signatures are evolutionarily conserved across orthologs.

Conclusions:

  • Entanglement provides a biologically relevant dimension for characterizing IDP organization.
  • Knot theory-based measures offer a complementary framework for linking IDP sequence, ensemble structure, and function.
  • This approach enhances our understanding of IDP heterogeneity and functional relevance.