Structural insights into AQP3 channel closure upon pH and redox changes reveal an autoregulatory molecular mechanism

Some structure files and simulation run files related to the paper:

Huang, P., Venskutonytė, R., Wilson, C.J., Bsharat, S., Prasad, R.B., Gourdon, P., Artner, I., de Groot, B.L., & Lindkvist-Petersson, K. (2025).
Structural insights into AQP3 channel closure upon pH and redox changes reveal an autoregulatory molecular mechanism
Lund University & Copenhagen University & Max Planck Institute for Multidisciplinary Sciences.

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Proposed model of AQP3 gating

The proposed model of AQP3 gating: an equilibrium between the open state (blue), closed state (magenta), and a closed state with bound H2O2 (green) is governed by the changes in pH and the presence of H2O2.

Cryo-EM structures

• pH 8.0 (open): 9QSX.pdb
• pH 5.5 (closed): 9QSY.pdb
• pH 8.0 + H2O2 (closed): 9QSZ.pdb

MD run files

• cphmd: contains initial structures for open/closed, and .mdp required for pH 7 simulation (just change pH value if you want high/low)
• unbiased: contains initial structures for open/closed, and .mdp. Protonation states were fixed to various protonation states, default GROMACS assignment structures are provided
• neq: pKa free energy calculations were initialzed from unbiased trajectories of the various endstates. pmx software was used for .top file generation. See Ref 1 for more discussion on these calculations. [1] J. Chem. Theory Comput. 2023, 19, 21, 7833–7845 https://doi.org/10.1021/acs.jctc.3c00721

Citation

If you are using this data please cite the paper:

@article{Huang2025,
  title = {Structural insights into AQP3 channel closure upon pH and redox changes reveal an autoregulatory molecular mechanism},
  volume = {16},
  url = {http://dx.doi.org/10.1038/s41467-025-67144-2},
  DOI = {10.1038/s41467-025-67144-2},
  number = {1},
  journal = {Nature Communications},
  publisher = {Springer Science and Business Media LLC},
  author = {Huang,  Peng and Venskutonytė,  Raminta and Wilson,  Carter J. and Bsharat,  Sara and Prasad,  Rashmi B. and Gourdon,  Pontus and Artner,  Isabella and de Groot,  Bert L. and Lindkvist-Petersson,  Karin},
  year = {2025},
  month = dec
}

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