Int J Biol Sci 2012; 8(7):1026-1035. doi:10.7150/ijbs.4703
Molecular Dynamics Simulation and Bioinformatics Study on Yeast Aquaporin Aqy1 from Pichia pastoris
1. Department of Laboratory Medicine, Yancheng Health Vocational & Technical College, Jiangsu Yancheng 224006, P. R. China.
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.
This is an open access article distributed under the terms of the Creative Commons Attribution (CC BY-NC) License. See http://ivyspring.com/terms for full terms and conditions.
How to cite this article:
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 http://www.ijbs.com/v08p1026.htm