Int J Biol Sci 2012; 8(7):1026-1035. doi:10.7150/ijbs.4703

Research Paper

Molecular Dynamics Simulation and Bioinformatics Study on Yeast Aquaporin Aqy1 from Pichia pastoris

Yubao Cui1, 2, David A. Bastien2✉

1. Department of Laboratory Medicine, Yancheng Health Vocational & Technical College, Jiangsu Yancheng 224006, P. R. China.
2. Department of Physics, University of Texas at San Antonio, San Antonio, Texas 78249, USA.

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Cui Y, Bastien DA. Molecular Dynamics Simulation and Bioinformatics Study on Yeast Aquaporin Aqy1 from Pichia pastoris. Int J Biol Sci 2012; 8(7):1026-1035. doi:10.7150/ijbs.4703. Available from

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In the present study, an equilibrated system for the Aqy1 tetramer was developed, and molecular biophysics modeling showed that the Aqy1 channel was blocked by Tyr-31 in the N-terminus, which was also supported by the free energy profiles. However, bioinformatics analysis of the amino acid sequence of Aqy1 indicated this Tyr-31 is not conserved across all fungi. Analysis of the equilibrated structure showed that the central pore along the four-fold axis of the tetramers is formed with hydrophobic amino acid residues. In particular, Phe-90, Trp-198, and Phe-202 form the narrowest part of the pore. Therefore, water molecules are not expected to translocate through the central pore, a hypothesis that we confirmed by molecular dynamics simulations. Each monomer of the Aqy1 tetramers forms a channel whose walls consist mostly of hydrophilic residues, transporting through the selectivity filter containing Arg-227, His-212, Phe-92, and Ala-221, and the two conserved Asn-Pro-Ala (NPA) motifs containing asparagines 224 and 112. In summary, not all fungal aquaporins share the same gating mechanism by a tyrosine residue in the N-terminus, and the structural analysis in the present study should aid our understanding of aquaporin structure and its functional implications.

Keywords: Fungi, Aquaporin, Diversity, Molecular Dynamics Simulation, Bioinformatics.