Molecular Dynamics Simulations of Ion Transport through Protein Nanochannels in Peritoneal Dialysis

Abstract
In recent decades, the development of dialysis techniques has greatly improved the survival rate of renal failure patients, and peritoneal dialysis is gradually showing dominance over hemodialysis. This method relies on the abundant membrane proteins in the peritoneum, avoiding the use of artificial semipermeable membranes, and the ion fluid transport is partly controlled by the protein nanochannels. Hence, this study investigated ion transport in these nanochannels by using molecular dynamics (MD) simulations and an MD Monte Carlo (MDMC) algorithm for a generalized protein nanochannel model and a saline fluid environment. The spatial distribution of ions was determined via MD simulations, and it agreed with that modeled via the MDMC method; the effects of simulation duration and external electronic fields were also explored to validate the MDMC algorithm. The specific atomic sequence within a nanochannel was visualized, which was the rare transport state during the ion transport process. The residence time was assessed through both methods to represent the involved dynamic process, and its values showed the temporal sequential order of different components in the nanochannel as follows: H2O > Na+ > Cl−. The accurate prediction using the MDMC method of the spatial and temporal properties proves its suitability to handle ion transport problems in protein nanochannels.

Citation
Liu, J., Zhang, T., & Sun, S. (2023). Molecular Dynamics Simulations of Ion Transport through Protein Nanochannels in Peritoneal Dialysis. International Journal of Molecular Sciences, 24(12), 10074. https://doi.org/10.3390/ijms241210074

Acknowledgements
This research was funded by the National Natural Scientific Foundation of China (grant no. 51936001) and King Abdullah University of Science and Technology (KAUST) through the grants BAS/1/1351-01 and URF/1/5028-01.For computing time, this research used the resources of the Supercomputing Laboratory at King Abdullah University of Science & Technology (KAUST) in Thuwal, Saudi Arabia.

Publisher
MDPI AG

Journal
International Journal of Molecular Sciences

DOI
10.3390/ijms241210074

Additional Links
https://www.mdpi.com/1422-0067/24/12/10074

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