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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

DOI: https://doi.org/10.47836/pjst.30.3.01

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.

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e-ISSN 2231-8534

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