Publications

Selected articles in recent 3 years

1. Yuxiang Luo, Zhaoyue Yan, Xiakun Chu, Ying Zhang, Yufan Qiu, and Huilin Li*. Binding mechanism and distant regulation of histone deacetylase 8 by PCI-34051. Communications Biology, 8(1), 221, 2025.
2. Chen Wang, Cheng Ma, Yuanyou Xu, Shenghai Chang, Hangjun Wu, Chunlan Yan, Jinghua Chen, Yongping Wu, Shaoya An, Jiaqi Xu, Qin Han, Yujie Jiang, Zhinong Jiang, Xiakun Chu, Haichun Gao*, Xing Zhang*, and Yunjie Chang*. Dynamics of the mammalian pyruvate dehydrogenase complex revealed by in-situ structural analysis. Nature Communications, 16(1), 917, 2025.
3. Chengzhen Xu and Xiakun Chu*. Dissecting the Roles of Electrostatic Interactions in Modulating the Folding Stability and Cooperativity of Engrailed Homeodomain. Biochemistry, 63(24), 3261-3272, 2024.
4. Tao Zhu, Chunhe Li, and Xiakun Chu*. Fluctuating Chromatin Facilitates Enhancer–Promoter Communication by Regulating Transcriptional Clustering Dynamics. The Journal of Physical Chemistry Letters, 15(45), 11428-11436, 2024.
5. Shiqinrui Xu, Chengze Huo, and Xiakun Chu*. Unraveling the Interplay between Stability and Flexibility in the Design of Polyethylene Terephthalate (PET) Hydrolases. Journal of Chemical Information and Modeling, 64(19), 7576-7589, 2024.
6. Guoqing Zhang and Xiakun Chu*. Balancing thermodynamic stability, dynamics, and kinetics in phase separation of intrinsically disordered proteins. The Journal of Chemical Physics, 161(9), 2024.
7. Yongqiang He, Shuai Wang, Junping Wen, Niu Feng, Ruxiang Ma, Hetong Zhang, Guoxun Chen, Xiakun Chu, Yiping Chen*. Redesigned Guide DNA Enhanced Clostridium butyricum Argonaute Activity for Amplification-Free and Multiplexed Detection of Pathogens. Nano Letters, 24(31), 9750-9759, 2024.
8. Xiakun Chu, Cibo Feng, and Jin Wang*. Deciphering the dynamical chromosome structural reorganizations in human neural development. Physical Review Research, 6(2), 023309, 2024.
9. Qiang Zhu, Didi Geng, Jingchao Li, Jinqiu Zhang, Haofan Sun, Zhiya Fan, Jiahui He, Ninghui Hao, Yinping Tian, Liuqing Wen, Tiehai Li, Weijie Qin, Xiakun Chu, Yong Wang*, Wen Yi*. Computational and Chemical Design Strategy for Manipulating Glycan‐Protein Recognition. Advanced Science, 11(24), 2308522, 2024.
10. Xiakun Chu and Jin Wang*. Quantifying the large-scale chromosome structural dynamics during the mitosis-to-G1 phase transition of cell cycle. Open Biology, 13(11), 230175, 2023
11. Cibo Feng, Jin Wang* and Xiakun Chu*. Large-scale data-driven and physics-based models offer insights into the relationships among the structures, dynamics, and functions of the chromosomes. Journal of Molecular Cell Biology, 15(6), mjad042, 2023
12. Xiakun Chu and Jin Wang*. Insights into the cell fate decision-making processes from chromosome structural reorganizations. Biophysics Reviews, 3(4), 041402, 2022
13. Xiakun Chu and Jin Wang*. Quantifying chromosome structural reorganizations during the differentiation, reprogramming and transdifferentiation. Physical Review Letters, 129(6), 068102, 2022
14. Jing Huang+, Xiakun Chu+ (co-first), Yuxiang Luo+, Yong Wang, Ying Zhang, Yu Zhang, and Huilin Li*. Insights into phosphorylation induced protein allostery and conformational dynamics of Glycogen Phosphorylase via integrative structural mass spectrometry and in silico modeling. ACS Chemical Biology, 17(7), 1951-1962, 2022
15. Wenting Chu, Xiakun Chu, and Jin Wang*. Uncovering the quantitative relationships among chromosome fluctuations, epigenetics, and gene expressions of transdifferentiation on Waddington landscape. Advanced Science, 9(10), 2103617, 2022.
16. Xiakun Chu, Zucai Suo and Jin Wang*. Investigating the conformational dynamics of a Y-family DNA polymerase during its folding and binding to DNA and a nucleotide. JACS Au, 2(2), 341-356, 2022.
17. Xiakun Chu and Jin Wang*. Dynamics and pathways of chromosome structural organizations during cell transdifferentiation. JACS Au, 2(1), 116-127, 2022.
18. Xiakun Chu, Suhani Nagpal, Victor Muñoz*. Molecular Simulations of Intrinsically Disordered Proteins and Their Binding Mechanisms. In Protein Folding: Methods and Protocols (pp. 343-362). New York, NY: Springer US, 2021.
19. Xiakun Chu, Yong Wang, Pengfei Tian, Wenfei Li, Davide Mercadante. Advanced Sampling and Modeling in Molecular Simulations for Slow and Large-Scale Biomolecular Dynamics. Frontiers in Molecular Biosciences, 8, 795991, 2021.
20. Wenting Chu, Zhiqiang Yan, Xiakun Chu, Xiliang Zheng, Zuojia Liu, Li Xu, Kun Zhang and Jin Wang*. Physics of biomolecular recognition and conformational dynamics. Reports on Progress in Physics, 84(12), 126601, 2021.
21. Xiakun Chu and Jin Wang*. Deciphering the molecular mechanism of the cancer formation by chromosome structural dynamics. PLoS Computational Biology, 17(11), e1009596, 2021.
22. Qing-Miao Nie, Li-Zhen Sun, Hai-Bin Li, Xiakun Chu∗ (co-corr) and Jin Wang*. Effects of electrostatic interactions on global folding and local conformational dynamics of a multidomain Y-family DNA polymerase. Physical Chemistry Chemical Physics, 23(37), 20841-20847, 2021.
23. Xiakun Chu, Zucai Suo and Jin Wang*. Investigating the trade-off between folding and function in a multidomain Y-family DNA polymerase. eLife, 9, e60434, 2020.
24. Xiakun Chu and Jin Wang*. Microscopic chromosomal structural and dynamical origin of cell differentiation and reprogramming. Advanced Science, 7(20) 2001572, 2020.
25. Xiakun Chu and Jin Wang*. Conformational state switching and pathways of chromosome dynamics in cell cycle. Applied Physics Reviews, 7(3), 031403, 2020.
26. Wenting Chu, Xiakun Chu, and Jin Wang*. Investigations of the underlying mechanisms of HIF-1α and CITED2 binding to TAZ1. Proceedings of the National Academy of Sciences, 117(11), 5595-5603, 2020.
27. Xiakun Chu and Jin Wang*. Theoretical investigations of a multi-domain protein folding under confinements and crowders. Biophysical Journal, 118(3), 510a, 2020.
28. Xiakun Chu, Zucai Suo and Jin Wang*. Confinement and crowding effects on folding of a multidomain Y-Family DNA polymerase. Journal of Chemical Theory and Computation, 16(2), 1319–1332, 2020.