TOPResearch HighlightsStudying the mathematics and biology of tangles, focusing primarily on knotted proteins
Research Topics

Studying the mathematics and biology of tangles, focusing primarily on knotted proteins

Scientific Questions

  1. What is the functional significance of structural entanglement in proteins, as revealed by knotoid theory and other topological invariants?
  2. What roles do transiently forming protein entanglements play in condensed states, such as in protein droplets?
  3. What mathematical frameworks can be devised to extract functionally relevant knotoid and entanglement structures in proteins, mixtures, and complexes?

Recent Publications & Achievements:

  1. Hsiao, L.-C., Lee, C.-H., Mazmanian, K., Yoshida, M., Ito, G., Murata, T., Utsunomiya‑Tate, N., Haino, T., Tate, S.-i., & Hsu, S.-T. D. (2025). Impacts of D-aspartate on the aggregation kinetics and structural polymorphism of amyloid β peptide 1–42. Journal of Molecular Biology, 437(12), 169092.Link to text
  2. Sugiyama, M., Kosik, K. S., & Panagiotou, E. (2025). Geometry based prediction of tau protein sites and motifs associated with misfolding and aggregation. Scientific reports, 15(1), 10283. Link to text
  3. ​​Hsu, S. T. D. (2023). Folding and functions of knotted proteins. Current Opinion in Structural Biology, 83, 102709. Link to text
  4. Puri, S., Liu, C.-Y., Hu, I.-C., Lai, C.-H., Hsu, S.-T. D., & Lyu, P.-C. (2023). Elucidation of the folding pathway of a circular permutant of topologically knotted YbeA by tryptophan substitutions. Biochemical and Biophysical Research Communications, 672, 81–88. Link to text
  5. Ferreira, S. G. F., Sriramoju, M. K., Hsu, S.-T. D., Faísca, P. F. N., & Machuqueiro, M. (2024). Is there a functional role for the knotted topology in protein UCH-L1? Journal of Chemical Information and Modeling, 64(17), 6827–6837. Link to text

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