HU, Zixin

HU, Zixin

She/Her

Ph. D. | Computational biophysicist | coarse-grained model | MD simulation | IDP & IDRs | LLPS
* Hope to establish biomolecular modelling empire

Publications

Systematic Investigation of the Liquid–Liquid Phase Separation Propensity of Intrinsically Disordered Proteins by Molecular Simulations Permalink

Published in The Journal of Physical Chemistry B, 2025


This paper is about the relation between liquid-liquid phase separation (LLPS) propensity and multivalency of disordered proteins. It provides a recommended multivalence cutoff for LLPS.

Recommended citation: Zixin Hu, Tiedong Sun, Lars Nordenskiöld, and Lanyuan Lu (2025). "Systematic Investigation of the Liquid–Liquid Phase Separation Propensity of Intrinsically Disordered Proteins by Molecular Simulations." The Journal of Physical Chemistry B. 129, 33, 8299–8317.

Refined Bonded Terms in Coarse-Grained Models for Intrinsically Disordered Proteins Improve Backbone Conformations Permalink

Published in The Journal of Physical Chemistry B, 2024


This paper is about the refined coarse-grained (CG) bonded potentials for disordered proteins. It achieves near-quantitative accuracy with secondary structure propensity estimated by NMR data, and captures the transient secondary structure of p53.
NOTE: This is challenging even in atomistic model!

Recommended citation: Zixin Hu, Tiedong Sun, Wenwen Chen, Lars Nordenskiöld, and Lanyuan Lu (2024). "Refined Bonded Terms in Coarse-Grained Models for Intrinsically Disordered Proteins Improve Backbone Conformations." The Journal of Physical Chemistry B. 128(27).

The intrinsically disordered region of coronins fine-tunes oligomerization and actin polymerization Permalink

Published in Cell Reports, 2023





This paper is about the role of intirnsically disordered regions (IDRs) in the oligomerization of coronin. This trait is observed in yeast but not in murine. The IDR can facilitate the packing of coiled-coil domain, and this effect is strong due to the deficiency of coiled-coil domain in yeast. In murine, the coiled-coil domain adopts perfect packing pattern, which caused selection strength on the length of IDR evolutionally. The coarse-grained model adopts a hybrid strategy, which treats folded domain with Gō-like model and IDRs with adapted Kim-Hummer model.
PS: a very interesting work if you believe in evolution! :)

Recommended citation: Han, X.; Hu, Z.; Surya, W.; Ma, Q.; Zhou, F.; Nordenskiöld, L.; Torres, J.; Lu, L.; Miao, Y. (2023). "The intrinsically disordered region of coronins fine-tunes oligomerization and actin polymerization." Cell Reports. 42(6).