Publication: Influence of water models on water movement through AQP1
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2021-10-21
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American Institute of Physics
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Abstract
Water diffusion through membrane proteins is a key aspect of cellular function. Essential processes of cellular metabolism are driven by osmotic pressure, which depends on water channels. Membrane proteins such as aquaporins (AQPs) are responsible for enabling water permeation through the cell membrane. AQPs are highly selective, allowing only water and relatively small polar molecules to cross the membrane. Experimentally, estimation of water flux through membrane proteins is still a challenge, and hence, accurate simulations of water permeation are of particular importance. We present a numerical study of water diffusion through AQP1 comparing three water models: TIP3P, OPC, and TIP4P/2005. Bulk diffusion, diffusion permeability, and osmotic permeability are computed and compared among all models. The results show that there are significant differences between TIP3P (a particularly widespread model for simulations of biological systems) and the more recently developed TIP4P/2005 and OPC models. We demonstrate that OPC and TIP4P/2005 reproduce protein-water interactions and dynamics in very good agreement with experimental data. From this study, we find that the choice of the water model has a significant effect on the computed water dynamics as well as its molecular behavior within a biological nanopore.</p>
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This work was performed under the Project HPC-EUROPA3 (No. INFRAIA-2016-1-730897), with the support of the EC Research Innovation Action under the H2020 Programme; in particular, the authors gratefully acknowledge the support of M. S. P. Sansom and the computer resources and technical support provided by ARCHER. M.A.G. acknowledges the support of Ayuda Juan de la Cierva-Incorporación (Grant No. IJCI-2016-27497) from Ministerio de Ciencia, innovación y universidades (Spain). M. S. P. Sansom acknowledges the following funding Nos. BBSRC BB/N000145/1, EPSRC EP/R004722/1, and EP/V010948/1. C. Valeriani acknowledges the funding from MINECO No. PID2019-105343GB-I00.