Shujie Fan | People | Beckstein Lab

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Shujie Fan

Shujie Fan

Shujie graduated with a PhD in Physics from ASU in May 2023. He joined Beckstein Lab in August 2017. He obtained his B.S.(2017) in Physics from the Department of Physics and Astronomy at Shanghai Jiao Tong University. During his undergraduate years, he worked on the urea channel of Helicobacter pylori using MD simulations in Jakob P. Ulmschneider’s group at SJTU. He has a strong interest in computational biophysics, especially membrane protein systems.

Shujie’s research was centered on the cation diffusion facilitator family, with a specific focus on YiiP, a bacterial homolog of the mammalian Zinc Transporters (ZnTs). He aimed to address crucial mechanistic questions regarding the individual roles of Zn binding sites, investigate the transport process’s role of protons, and study the structural impact of Zn binding on YiiP. To achieve these goals, he parameterized a zinc multisite model using the CHARMM36 force fields and the CHARMM TIP3P water model, reproducing the experimental properties of zinc in water. He then employed molecular dynamics simulation based on the cryo-EM structures obtained by the experimental collaborator at NYU to study the impact of Zn binding on YiiP’s conformational transition1. Shujie also developed a comprehensive thermodynamic model based on experimental microscale thermophoresis data, revealing a transport stoichiometry of 1 Zn to 2-3 protons, depending on the external pH2. His research provided valuable insights into the cation diffusion facilitator family’s structural and functional properties and their role in regulating the homeostasis of transition metal ions.

In addition to his work on membrane protein systems, he has been working on developing protocols to precisely calculate solvation energies of small and drug-like molecules3,4. He has also been involved in the development of the MDPOW library which automates the process of calculating solvation free energies. Furthermore, he has contributed to the development of pmda 5, the parallel algorithms for MDAnalysis”:https://www.mdanalysis.org/ .

Publications

  1. a Lopez-Redondo, M; Fan, S; Koide, A; Koide, A; Beckstein, O; Stokes, D. L. Zinc binding alters the conformational dynamics and drives the transport cycle of the cation diffusion facilitator YiiP. Journal of General Physiology, 153(8), July 2021.
  2. a Hussein, A.; Fan, S.; Lopez-Redondo, M.L.; Kenney, I.; Zhang, X.; Beckstein, O.; Stokes, D.L., 2023. Energy Coupling and Stoichiometry of Zn2+/H+ Antiport by the Cation Diffusion Facilitator YiiP. https://doi.org/10.1101/2023.02.23.529644 (Accepted by eLife)
  3. a Fan, S.; Iorga, B. I.; and Beckstein, O. Prediction of octanol-water partition coefficients for the SAMPL6-logP molecules using molecular dynamics simulations with OPLS-AA, AMBER and CHARMM force fields. Journal of Computer-Aided Molecular Design. January 2020.
  4. a Fan, S.; Nedev, H; Vijayan, H; Iorga, B. I.; and Beckstein, O. Precise force-field-based calculations of octanol-water partition coefficients for the SAMPL7 molecules. Journal of Computer-Aided Molecular Design. July 2021.
  5. a Fan, S; Linke, M.; Paraskevakos, I.; Gowers, R. J.; Gecht, M.; and Beckstein, O. In Calloway, C.; Lippa, D.; Niederhut, D.; and Shupe, D., editor(s). PMDA – Parallel Molecular Dynamics Analysis. Proceedings of the 18th Python in Science Conference, pages 134 – 142, Austin, TX, 2019.

Poster Presentations

  1. Fan, S; Hussein, A. K.; Kenney, I, M; Stokes, D. L.; Beckstein, O. 2023. Inferring the transport stoichiometry of the proton/zinc transporter YiiP from microscale thermophoresis and simulations. The 67th Meeting of the Biophysical Society, San Diego, CA.
  2. Fan, S; Stokes, D. L.; Beckstein, O. 2022. A plausible model for the outward-facing conformation of YiiP and its transport mechanism. The 66th Meeting of the Biophysical Society, Los Angeles, CA.
  3. Fan, S; Lopez-Redondo, M; Stokes, D. L.; Beckstein, O. 2021. Elucidation of Zn2+ Binding in the Zn2+/H+ Antiporter YiiP. The 65th Meeting of the Biophysical Society.
  4. Fan, S.; Iorga, B. I.; Beckstein, O. 2020. Application of a forward and reversed average convergence analysis in the SAMPL6-logP blind prediction challenge. 16th German Conference on Cheminformatics and SAMPL Satellite Workshop, Virtual Edition.
  5. Fan, S; Linke, M.; Paraskevakos, I.; Gowers, R. J.; Gecht, M.; and Beckstein, O. 2019. PMDA – Parallel Molecular Dynamics Analysis. 18th Python in Science Conference, Austin, TX.

Honors and Awards

  1. The College Graduate Excellence Award, 2020. The College of Liberal Arts & Sciences, ASU.
  2. APS Four Corners travel award, 2019. Dept. of Physics, ASU.
  3. APS Four Corners Student Travel Grant, 2019. APS Four Corners Section.