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Modeling and Molecular Dynamics of Aquaporin from an Antarctic Pseudomonas sp. Strain AMS3

Muhairil Sulong Tuah, Wahhida Latip, Ainur Yasmin Ahmad Ridzwan, Samyuktha Balakrishnan, Raja Noor Zaliha Raja Abd. Rahman, Noor Dina Muhd Noor and Mohd Shukuri Mohamad Ali

Pertanika Journal of Science & Technology, Volume 30, Issue 3, July 2022


Keywords: Antarctica, aquaporin, homology modeling, molecular dynamics,Pseudomonas sp. AMS3, water gating

Published on: 25 May 2022

Aquaporins, also known as water channels, are a large family of transmembrane channel proteins present throughout all life domains and are implicated in human disorders. The psychrophilic aquaporin comes to attention because of its specialty in adaptive ability to keep on functioning to maintain water homeostasis under low temperatures, which have an optimal temperature for growth at about 15ºC or lower. However, studies regarding aquaporin isolated from psychrophilic Pseudomonas sp. are still scattered. Recently, the genome sequence of an Antarctic Pseudomonas sp. strain AMS3 revealed a gene sequence encoding for a putative aquaporin designated as PAqpZ2_AMS3. In this study, structure analysis and molecular dynamics (MD) simulation of a predicted model of a fully hydrated aquaporin monomer was embedded in a lipid bilayer and was performed at different temperatures for structural flexibility and stability analysis. The MD simulation results revealed that the predicted structure could remain stable and flexible at low to medium temperatures. In addition, the important position of water gating amino acids, Phe36 and Asn180 residues were rearranged in -5ºC MD simulation, leading to changes in the aquaporin water column size. The information obtained from this psychrophilic aquaporin, PAqpZ2_AMS3, provides new insights into the structural adaptation of this protein at low temperatures and could be a useful tool for low-temperature industrial applications and molecular engineering purposes in the future.

  • Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990). Basic local alignment search tool. Journal of Molecular Biology, 215(3), 403-410.

  • Aponte-Santamaría, C., Fischer, G., Båth, P., Neutze, R., & de Groot, B. L. (2017). Temperature dependence of protein-water interactions in a gated yeast aquaporin. Scientific Reports, 7(1), 1-14.

  • Araya-Secchi, R., Garate, J. A., Holmes, D. S., & Perez-Acle, T. (2011). Molecular dynamics study of the archaeal aquaporin AqpM. BioMed Central Genomics, 12(4), 1-13.

  • Bienert, S., Waterhouse, A., de Beer, T. A., Tauriello, G., Studer, G., Bordoli, L., & Schwede, T. (2017). The SWISS-MODEL Repository-new features and functionality. Nucleic Acids Research, 45, 313-319.

  • Brezovsky, J., Chovancova, E., Gora, A., Pavelka, A., Biedermannova, L., & Damborsky, J. (2013). Software tools for identification, visualization and analysis of protein tunnels and channels. Biotechnology Advances, 31(1), 38-49.

  • Brown, D. (2017). The discovery of water channels (aquaporins). Annals of Nutrition and Metabolism, 70(1), 37-42.

  • Cho, C. H., Urquidi, J., Singh, S., Park, S. C., & Robinson, G. W. (2002). Pressure Effect on the density of water. The Journal of Physical Chemistry A, 106(33), 7557-7561.

  • Cohen, E. (2012). Roles of aquaporins in osmoregulation, desiccation and cold hardiness in insects. Entomology, Ornithology & Herpetology, 1, 1-17.

  • Colovos, C., & Yeates, T. O. (1993). Verification of protein structures: Patterns of nonbonded atomic interactions. Protein Science, 2(9), 1511-1519.

  • De Maayer, P., Anderson, D., Cary, C., & Cowan, D. A. (2014). Some like it cold: Understanding the survival strategies of psychrophiles. European Molecular Biology Organization Reports, 15(5), 508-517.

  • Donkor, E. S., Dayie, N. T., & Adiku, T. K. (2014). Bioinformatics with basic local alignment search tool (BLAST) and fast alignment (FASTA). Journal of Bioinformatics and Sequence Analysis, 6(1), 1-6.

  • Finn, R. N., & Cerda, J. (2015). Evolution and functional diversity of aquaporins. The Biological Bulletin, 229, 6-23.

  • Gomes, D., Agasse, A., Thiébaud, P., Delrot, S., Gerós, H., & Chaumont, F. (2009). Aquaporins are multifunctional water and solute transporters highly divergent in living organisms. Biochimica et Biophysica Acta (BBA)-Biomembranes, 1788(6), 1213-1228.

  • Goto, S. G., Lee Jr, R. E., & Denlinger, D. L. (2015). Aquaporins in the Antarctic midge, an extremophile that relies on dehydration for cold survival. The Biological Bulletin, 229(1), 47-57.

  • Hedfalk, K., Törnroth-Horsefield, S., Nyblom, M., Johanson, U., Kjellbom, P., & Neutze, R. (2006). Aquaporin gating. Current Opinion in Structural Biology, 16(4), 447-456.

  • Hospital, A., Goñi, J. R., Orozco, M., & Gelpí, J. L. (2015). Molecular dynamics simulations: Advances and applications. Advances and Applications in Bioinformatics and Chemistry, 8, 37-47.

  • Hub, J. S., Grubmüller, H., & De Groot, B. L. (2009). Dynamics and energetics of permeation through aquaporins. What do we learn from molecular dynamics simulations.? Handbook of Experimental Pharmacology, 190, 57-76.

  • Kleywegt, G. J. (2000). Validation of protein crystal structures. Acta Crystallographica Section D: Biological Crystallography, 56(3), 249-265.

  • Kourghi, M., Nourmohammadi, S., Pei, J. V., Qiu, J., McGaughey, S., Tyerman, S. D., Byrt, C. S., & Yool, A. J. (2017). Divalent cations regulate the ion conductance properties of diverse classes of aquaporins. International Journal of Molecular Sciences, 18(11), Article 2323.

  • Kozono, D., Ding, X., Iwasaki, I., Meng, X., Kamagata, Y., Agre, P., & Kitagawa, Y. (2003). Functional expression and characterization of an archaeal aquaporin: AqpM from Methanothermobacter marburgensis. Journal of Biological Chemistry, 278(12), 10649-10656.

  • Krieger, E., & Vriend, G. (2014). YASARA view - Molecular graphics for all devices from smartphones to workstations. Bioinformatics, 30(20), 2981-2982.

  • Lind, U., Järvå, M., Alm Rosenblad, M., Pingitore, P., Karlsson, E., Wrange, A. L., Kamdal, E., Sundell, K., Andre, C., Jonsson, P. R., Havenhand, J., Eriksson, L. A., Hedfalk, K., & Blomberg, A. (2017). Analysis of aquaporins from the euryhaline barnacle Balanus improvisus reveals differential expression in response to changes in salinity. Public Library of Science One, 12(7), 1-33.

  • Mannige, R. V., Kundu, J., & Whitelam, S. (2016). The Ramachandran number: An order parameter for protein geometry. Public Library of Science One, 11(8), 1-14.

  • Mathai, J. C., Missner, A., Kügler, P., Saparov, S. M., Zeidel, M. L., Lee, J. K., & Pohl, P. (2009). No facilitator required for membrane transport of hydrogen sulfide. Proceedings of the National Academy of Sciences, 106(39), 16633-16638.

  • Németh-Cahalan, K. L., & Hall, J. E. (2000). pH and calcium regulate the water permeability of aquaporin 0. The Journal of Biological Chemistry, 275(10), 6777-6782.

  • Sachdeva, R., & Singh, B. (2014). Insights into structural mechanisms of gating induced regulation of aquaporins. Progress in Biophysics and Molecular Biology, 114(2), 69-79.

  • Salomon‐Ferrer, R., Case, D. A., & Walker, R. C. (2013). An overview of the Amber biomolecular simulation package. Wiley Interdisciplinary Reviews: Computational Molecular Science, 3(2), 198-210.

  • Savage, D. F., Egea, P. F., Robles-Colmenares, Y., O’Connell III, J. D., Stroud, R. M., & Simon, S. (2003). Architecture and selectivity in aquaporins: 2.5 Å X-ray structure of aquaporin Z. Public Library of Science Biology, 1(3), 334-340.

  • Schmidt, V., & Sturgis, J. N. (2017). Making monomeric aquaporin Z by disrupting the hydrophobic tetramer interface. American Chemical Society Omega, 2, 3017-3027.

  • Tong, H., Hu, Q., Zhu, L., & Dong, X. (2019). Prokaryotic aquaporins. Cells, 8(11), Article 1316.

  • Woo, J., Chae, Y. K., Jang, S. J., Kim, M. S., Baek, J. H., Park, J. C., Trink, B., Ratovitski, E., Lee, T., Park, B., Park, M., Kang, J. H., Soria, J. C., Lee, J., Califano, J., Sidransky, D., & Moon, C. (2008). Membrane trafficking of AQP5 and cAMP dependent phosphorylation in bronchial epithelium. Biochemical and Biophysical Research Communications, 366(2), 321-327.

  • Zhou, A. Q., O’Hern, C. S., & Regan, L. (2011). Revisiting the Ramachandran plot from a new angle. Protein Science, 20, 1166-1171.

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