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  3. Characterizing Structural And Kinetic Ensembles Of Intrinsically Disordered Proteins Using Writhe.

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Characterizing Structural and Kinetic Ensembles of Intrinsically Disordered Proteins Using Writhe.

Thomas R Sisk1, Simon Olsson2, Paul Robustelli1

  • 1Department of Chemistry, Dartmouth College, Hanover, New Hampshire 03755, United States.

Journal of Chemical Theory and Computation
|November 19, 2025

View abstract on PubMed

Summary
This summary is machine-generated.

We introduce writhe, a knot theory measure, to analyze intrinsically disordered proteins (IDPs). This method enhances the study of protein dynamics and conformational ensembles, improving biological function understanding.

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Area of Science:

  • Biophysics
  • Computational Biology
  • Structural Biology

Background:

  • Intrinsically disordered proteins (IDPs) lack stable 3D structures, making their biological functions dependent on dynamic conformational states.
  • Understanding IDP conformational dynamics is crucial for deciphering their roles in cellular processes.

Purpose of the Study:

  • To develop novel computational methods for analyzing IDP conformational ensembles and dynamics.
  • To establish writhe as a powerful tool for characterizing IDP structural landscapes and kinetics.

Main Methods:

  • Application of writhe, a knot-theoretic measure, to analyze 3D protein backbone curves.
  • Development of multiscale writhe-based descriptors to identify slow dynamical motions in IDPs.
  • Construction of Markov state models using writhe descriptors for enhanced accuracy.
  • Design of an equivariant neural network architecture leveraging writhe symmetry for conformational sampling using denoising diffusion probabilistic models.

    • Main Results:

    • Writhe-based descriptors effectively identify slow motions in IDPs.
    • These descriptors provide a superior basis for constructing Markov state models compared to traditional methods.
    • The novel neural network architecture successfully samples IDP conformational ensembles.

    Conclusions:

    • Writhe offers a versatile and powerful framework for studying IDP conformational dynamics and ensembles.
    • This approach enhances our understanding of how IDP structure relates to biological function.
    • The developed methods provide new avenues for computational analysis in structural biology.