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International Journal Of Bilogical Sciences

.: Home > International Journal Of Bilogical Sciences > 2012 > Volume 8 Number 7 > Yubao Cui1, 2, David A. Bastien2✉

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.
Abstract :

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.

Date Deposited : 09 Apr 2015 14:02

Last Modified : 09 Apr 2015 14:02

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Volume 8, Number 7, - 2012 , ISSN 1545-1003

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