Publications

  1. Liu, C.; Xue, L.; Song, C.* Calcium Binding and Permeation in TRPV Channels: Insights from Molecular Dynamics Simulations. J. Gen. Physiol. 2023, 155 (12), e202213261. Link

  2. Yang, S.; Song, C.* Switching Gō-Martini for Investigating Protein Conformational Transitions and Associated Protein-Lipid Interactions. bioRxiv 2023, https://doi.org/10.1101/2023.08.21.554122.

  3. Wang, D.#; Li, J.#; Wang, L.; Cao, Y.; Li, S.*; Song, C.* Toward Atomistic Models of Intact SARS-CoV-2 via Martini Coarse-Grained Molecular Dynamics Simulations. Quant. Biol. (in press). Link 

  4. He, R.; Zhang, J.; Shao, Y.; Gu, S.; Song, C.; Qian, L.; Yin, W.-B.*; Li, Z.* Knowledge-Guided Data Mining on the Standardized Architecture of NRPS: Subtypes, Novel Motifs, and Sequence Entanglements. PLoS Comput. Biol. 2023, 19, e1011100. Link

  5. Schackert, F. K.#; Biedermann, J.#; Abdolvand, S.; Minniberger, S.; Song, C.; Plested, A. J. R.; Carloni, P.*; Sun, H.* Mechanism of Calcium Permeation in a Glutamate Receptor Ion Channel. J. Chem. Inf. Model. 2023, 63, 1293–1300. Link

  6. Kang, K.#; Wang, L.#; Song, C.* ProtRAP: Predicting Lipid Accessibility Together with Solvent Accessibility of Proteins in One Run. J. Chem. Inf. Model. 2023, 63, 1058-1065. Link

  7. Dong, L.; Yang, S.; Chen, J.; Wu, X.; Sun, D.; Song, C.*; Li, L.* Structural Basis of SecA-Mediated Protein Translocation. Proc. Natl. Acad. Sci. U.S.A. 2023, 120, e2208070120. Link

  8. Liu, C.; Zhong, Q.; Kang, K.; Ma, R.*; Song, C.* Asymmetrical Calcium Ions Induced Stress and Remodeling in Lipid Bilayer Membranes. ChemRxiv 2022, https://doi.org/10.26434/chemrxiv-2022-24qv4.

  9. Li, J.; Wang, L.; Zhu, Z.; Song, C.* Exploring the Alternative Conformation of a Known Protein Structure Based on Contact Map Prediction. bioRxiv 2022, https://doi.org/10.1101/2022.06.07.495232.

  10. Wang, L.; Zhang, J.; Wang, D.; Song, C.* Membrane Contact Probability: An Essential and Predictive Character for the Structural and Functional Studies of Membrane Proteins. PLoS Comput. Biol. 2022, 18, e1009972. Link

  11. Zhang, X.#; Yu, H.#,*; Liu, X.; Song, C.* The Impact of Mutation L138F/L210F on the Orai Channel: A Molecular Dynamics Simulation Study. Frontiers in Molecular Biosciences 2021, 8, 755247. Link

  12. Liu, Y.; Ke, P.; Kuo, Y.-C.; Wang, Y.; Zhang, X.*; Song, C.*; Shan, Y.* A Putative Structural Mechanism Underlying the Antithetic Effect of Homologous RND1 and RhoD GTPases in Mammalian Plexin Regulation. eLife 2021, 10, e64304. Link

  13. Wang, Y.#; Guo, Y.#; Li, G.; Liu, C.; Wang, L.; Zhang, A.; Yan, Z.*; Song, C.* The Push-to-Open Mechanism of the Tethered Mechanosensitive Ion Channel NompC. eLife 2021, 10, e58388. Link

  14. Liu, C.; Zhang, A.; Yan, N.; Song, C.* Atomistic Details of Charge/Space Competition in the Ca2+ Selectivity of Ryanodine Receptors. J. Phys. Chem. Lett. 2021, 12, 4286–4291. Link

  15. Li, W.#; Gu, X.#; Liu, C.; Shi, Y.; Wang, P.; Zhang, N.; Wu, R.; Leng, L.; Xie, B.; Song, C.; Li, M.* A Synergetic Effect of BARD1 Mutations on Tumorigenesis. Nature Communications 2021, 12, 1243. Link

  16. Zhao, X.#; Tian, J. (Jingxin)#; Yu, H.#; Bryksa, B. C.; Dupuis, J. H.; Ou, X.; Qian, Z.; Song, C.*; Wang, S.*; Yada, R. Y.* Insights into the Mechanism of Membrane Fusion Induced by the Plant Defense Element, Plant-Specific Insert. J. Biol. Chem. 2020, 295 (43), 14548–14562. (Editor's Picks & Cover Story) Link

  17. Dupuis, J. H.; Wang, S.; Song, C.; Yada, R. Y.* The Role of Disulfide Bonds in a Solanum Tuberosum Saposin-like Protein Investigated Using Molecular Dynamics. PLOS ONE 2020, 15 (8), e0237884. Link

  18. Wang, D.; Liu, X.; Liu, J.; Song, C.* Phosphorylation-Dependent Conformational Changes of Arrestin in the Rhodopsin-Arrestin Complex. Phys. Chem. Chem. Phys. 2020, 22, 9330-9338. Link

  19. Zhang, A.; Yu, H.; Liu, C.; Song, C.* The Ca2+ Permeation Mechanism of the Ryanodine Receptor Revealed by a Multi-Site Ion Model. Nature Communications 2020, 11, 922. Link

  20. Song, C.*; de Groot, B. L.; Sansom, M. S. P. Lipid Bilayer Composition Influences the Activity of the Antimicrobial Peptide Dermcidin Channel. Biophys. J. 2019, 116 (9), 1658–1666. Link

  21. Xu, Y.; Lin, K.; Wang, S.; Wang, L.; Cai, C.; Song, C.; Lai, L.; Pei, J.* Deep Learning for Molecular Generation. Future Medicinal Chemistry 2019, 11 (6), 567–597. Link

  22. Vestergaard, M.; Berglund, N. A.; Hsu, P.-C.; Song, C.; Koldsø, H.; Schiøtt, B.*; Sansom, M. S. P.* Structure and Dynamics of Cinnamycin–Lipid Complexes: Mechanisms of Selectivity for Phosphatidylethanolamine Lipids. ACS Omega 2019, 4, 18889–18899. Link

  23. Dupuis, J. H.; Yu, H.; Habibi, M.; Peng, X.; Plotkin, S. S.; Wang, S.; Song, C.; Yada, R. Y.* pH Dependent Membrane Binding of the Solanum Tuberosum Plant Specific Insert: An in Silico Study. BBA – Biomembranes 2018, 1860 (12), 2608–2618. Link

  24. Zhang, M.; Wang, D.; Kang, Y.; Wu, J.-X.; Yao, F.; Pan, C.; Yan, Z.*; Song, C.*; Chen, L.* Structure of the Mechanosensitive OSCA Channels. Nat. Struct. Mol. Biol. 2018, 25 (9), 850–858. Link

  25. Wang, D.; Yu, H.; Liu, X.; Liu, J.; Song, C.* The Orientation and Stability of the GPCR-Arrestin Complex in a Lipid Bilayer. Sci. Rep. 2017, 7 (1), 16985. Link

  26. Trick, J. L.; Song, C.; Wallace, E. J.; Sansom, M. S. P.* Voltage Gating of a Biomimetic Nanopore: Electrowetting of a Hydrophobic Barrier. ACS Nano 2017, 11 (2), 1840–1847. Link

  27. Kutzner, C.; Köpfer, D. A.; Machtens, J.-P.; de Groot, B. L.; Song, C.; Zachariae, U.* Insights into the Function of Ion Channels by Computational Electrophysiology Simulations. Biochim. Biophys. Acta BBA – Biomembr. 2016, 1858 (7, Part B), 1741–1752. Link

Previous Publications

  1. Yang, F.; Yu, X.; Liu, C.; Qu, C.-X.; Gong, Z.; Liu, H.-D.; Li, F.-H.; Wang, H.-M.; He, D.-F.; Yi, F.; et al. Phospho-Selective Mechanisms of Arrestin Conformations and Functions Revealed by Unnatural Amino Acid Incorporation and 19F-NMR. Nat. Commun. 2015, 6, 8202. Link

  2. Köpfer, D. A.#; Song, C.#,*; Gruene, T.; Sheldrick, G. M.; Zachariae, U.*; de Groot, B. L.* Ion Permeation in K+ Channels Occurs by Direct Coulomb Knock-On. Science 2014, 346 (6207), 352–355. Link

  3. Song, C.; Weichbrodt, C.; Salnikov, E. S.; Dynowski, M.; Forsberg, B. O.; Bechinger, B.; Steinem, C.; de Groot, B. L.; Zachariae, U.*; Zeth, K.* Crystal Structure and Functional Mechanism of a Human Antimicrobial Membrane Channel. Proc. Natl. Acad. Sci. U. S. A. 2013, 110 (12), 4586–4591. Link

  4. Song, C.; Corry, B.* Testing the Applicability of Nernst-Planck Theory in Ion Channels: Comparisons with Brownian Dynamics Simulations. PLoS One 2011, 6 (6), e21204–e21204. Link

  5. Song, C.; Corry, B.* Ion Conduction in Ligand-Gated Ion Channels: Brownian Dynamics Studies of Four Recent Crystal Structures. Biophys. J. 2010, 98 (3), 404–411. Link

  6. Song, C.*; Corry, B. Computational Study of the Transmembrane Domain of the Acetylcholine Receptor. Eur. Biophys. J. 2009, 38 (7), 961–970. Link

  7. Song, C.; Corry, B.* Role of Acetylcholine Receptor Domains in Ion Selectivity. BBA-Biomembr. 2009, 1788 (7), 1466–1473. Link

  8. Song, C.; Corry, B.* Intrinsic Ion Selectivity of Narrow Hydrophobic Pores. J. Phys. Chem. B 2009, 113 (21), 7642–7649. Link

  9. Song, C.*; Xia, Y.; Zhao, M.; Liu, X.; Li, J.; Li, L. The Electronic Structure Evolution of DNA during Its Conformation Transition Process. Phys. Chem. Chem. Phys. 2008, 10 (33), 5077–5082.

  10. Song, C.*; Xia, Y.; Zhao, M.; Liu, X.; Li, F.; Ji, Y.; Huang, B.; Yin, Y. The Effect of Salt Concentration on DNA Conformation Transition: A Molecular-Dynamics Study. J. Mol. Model. 2006, 12 (3), 249–254.

  11. Song, C.*; Xia, Y.; Zhao, M.; Liu, X.; Li, F.; Huang, B.; Zhang, H.; Zhang, B. Functionalization of Silicon-Doped Single Walled Carbon Nanotubes at the Doping Site: An Ab Initio Study. Phys. Lett. A 2006, 358 (2), 166–170.

  12. Song, C.*; Xia, Y.; Zhao, M.; Liu, X.; Li, J.; Li, L.; Li, F.; Huang, B. Ab Initio Calculation on the Self-Assembled Base-Functionalized Single-Walled Carbon Nanotubes. Chin Phys Lett 2006, 23, 2210–2212.

  13. Song, C.*; Xia, Y.; Zhao, M.; Liu, X.; Huang, B.; Li, F.; Ji, Y. Self-Assembly of Base-Functionalized Carbon Nanotubes. Phys. Rev. B 2005, 72 (16), 165430.

  14. Song, C.*; Xia, Y.; Zhao, M.; Liu, X.; Li, F.; Huang, B. Ab Initio Study of Base-Functionalized Single Walled Carbon Nanotubes. Chem. Phys. Lett. 2005, 415 (1), 183–187.