Publication List

Journal Articles

  1. Repulsive interaction and secondary structure of highly charged proteins in regulating biomolecular condensation.
    Cheng Tan, Ai Niitsu, and Yuji Sugita.
    bioRxiv 10.1101/2022.11.16.516834

  2. Role of water-bridged interactions in metal ion coupled protein allostery.
    Xingyue Guan,$^{\star}$ Cheng Tan,$^{\star}$ Wenfei Li, Wei Wang, and D. Thirumalai.
    PLoS Computational Biology 18, 6 (2022): e1010195.

  3. Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations.
    Cheng Tan, Jaewoon Jung, Chigusa Kobayashi, Diego Ugarte La Torre, Shoji Takada, and Yuji Sugita.
    PLoS Computational Biology 18, 4 (2022): e1009578.

  4. Testing mechanisms of DNA sliding by architectural DNA-binding proteins: dynamics of single wild-type and mutant protein molecules in vitro and in vivo.
    Kiyoto Kamagata, Yuji Itoh, Cheng Tan, Eriko Mano, Yining Wu, Sridhar Mandali, Shoji Takada, and Reid C. Johnson.
    Nucleic Acids Research 49, 15 (2021): 8642-8664.

  5. The kinetic landscape of nucleosome assembly: A coarse-grained molecular dynamics study.
    Giovanni B. Brandani, Cheng Tan, and Shoji Takada.
    PLoS Computational Biology 17, 7 (2021): e1009253.

  6. New parallel computing algorithm of molecular dynamics for extremely huge scale biological systems.
    Jaewoon Jung, Chigusa Kobayashi, Kento Kasahara, Cheng Tan, Akiyoshi Kuroda, Kazuo Minami, Shigeru Ishiduki et al.
    Journal of Computational Chemistry 42, 4 (2021): 231-241.

  7. The HMGB chromatin protein Nhp6A can bypass obstacles when traveling on DNA.
    Kiyoto Kamagata, Kana Ouchi, Cheng Tan, Eriko Mano, Sridhar Mandali, Yining Wu, Shoji Takada, Satoshi Takahashi, and Reid C. Johnson.
    Nucleic Acids Research 48, 19 (2020): 10820-10831.

  8. Nucleosome allostery in pioneer transcription factor binding.
    Cheng Tan, and Shoji Takada.
    Proceedings of the National Academy of Sciences 117, 34 (2020): 20586-20596.

  9. A singularity-free torsion angle potential for coarse-grained molecular dynamics simulations.
    Cheng Tan, Jaewoon Jung, Chigusa Kobayashi, and Yuji Sugita.
    The Journal of Chemical Physics 153, 4 (2020): 044110.

  10. Nucleosomes as allosteric scaffolds for genetic regulation.
    Shoji Takada, Giovanni B. Brandani, and Cheng Tan.
    Current Opinion in Structural Biology 62 (2020): 93-101.

  11. Dynamic and structural modeling of the specificity in protein–DNA interactions guided by binding assay and structure data.
    Cheng Tan, and Shoji Takada.
    Journal of Chemical Theory and Computation 14, 7 (2018): 3877-3889.

  12. DNA sliding in nucleosomes via twist defect propagation revealed by molecular simulations.
    Giovanni B. Brandani, Toru Niina, Cheng Tan, and Shoji Takada.
    Nucleic Acids Research 46, 6 (2018): 2788-2801.

  13. Sequence-dependent nucleosome sliding in rotation-coupled and uncoupled modes revealed by molecular simulations.
    Toru Niina, Giovanni B. Brandani, Cheng Tan, and Shoji Takada.
    PLoS Computational Biology 13, 12 (2017): e1005880.

  14. Dynamic coupling among protein binding, sliding, and DNA bending revealed by molecular dynamics.
    Cheng Tan, Tsuyoshi Terakawa, and Shoji Takada.
    Journal of the American Chemical Society 138, 27 (2016): 8512-8522.

  15. Modeling structural dynamics of biomolecular complexes by coarse-grained molecular simulations.
    Shoji Takada, Ryo Kanada, Cheng Tan, Tsuyoshi Terakawa, Wenfei Li, and Hiroo Kenzaki.
    Accounts of Chemical Research 48, 12 (2015): 3026-3035.

  16. Atomistic picture for the folding pathway of a hybrid-1 type human telomeric DNA G-quadruplex.
    Yunqiang Bian, Cheng Tan, Jun Wang, Yuebiao Sheng, Jian Zhang, and Wei Wang.
    PLoS Compututational Biology 10, 4 (2014): e1003562.

  17. Localized frustration and binding-induced conformational change in recognition of 5S RNA by TFIIIA zinc finger.
    Cheng Tan, Wenfei Li, and Wei Wang.
    The Journal of Physical Chemistry B 117, 50 (2013): 15917-15925.

  18. Specific Binding of a Short miRNA Sequence by Zinc Knuckles of Lin28: A Molecular Dynamics Simulation Study.
    Cheng Tan, Wenfei Li, and Wei Wang.
    Journal of Theoretical and Computational Chemistry 12, 08 (2013): 1341015.

  19. Low folding cooperativity of HP35 revealed by single-molecule force spectroscopy and molecular dynamics simulation.
    Chunmei Lv, Cheng Tan, Meng Qin, Dawei Zou, Yi Cao, and Wei Wang.
    Biophysical Journal 102, 8 (2012): 1944-1951.

Book Sections

  1. 分子シミュレーションで理解する相分離のメカニズム.
    Cheng Tan, Ai Niitsu, Takao Yoda, and Yuji Sugita.
    実験医学別冊 相分離プロトコール, 発展編5, 235-241. 羊土社 (2022).