Influence of water models on water movement through AQP1
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 membr...
| Main Authors: | , , , , |
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| Format: | Journal article |
| Language: | English |
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AIP Publishing
2021
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| _version_ | 1797098741656715264 |
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| author | Gonzalez, MA Zaragoza, A Lynch, C Sansom, MSP Valeriani, C |
| author_facet | Gonzalez, MA Zaragoza, A Lynch, C Sansom, MSP Valeriani, C |
| author_sort | Gonzalez, MA |
| collection | OXFORD |
| description | 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. <br /> 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 behaviour within a biological nanopore.
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| first_indexed | 2024-03-07T05:13:58Z |
| format | Journal article |
| id | oxford-uuid:dc822bfa-b12b-4293-83f0-dbe85f9e8650 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-07T05:13:58Z |
| publishDate | 2021 |
| publisher | AIP Publishing |
| record_format | dspace |
| spelling | oxford-uuid:dc822bfa-b12b-4293-83f0-dbe85f9e86502022-03-27T09:18:19ZInfluence of water models on water movement through AQP1Journal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:dc822bfa-b12b-4293-83f0-dbe85f9e8650EnglishSymplectic ElementsAIP Publishing2021Gonzalez, MAZaragoza, ALynch, CSansom, MSPValeriani, CWater 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. <br /> 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 behaviour within a biological nanopore. |
| spellingShingle | Gonzalez, MA Zaragoza, A Lynch, C Sansom, MSP Valeriani, C Influence of water models on water movement through AQP1 |
| title | Influence of water models on water movement through AQP1 |
| title_full | Influence of water models on water movement through AQP1 |
| title_fullStr | Influence of water models on water movement through AQP1 |
| title_full_unstemmed | Influence of water models on water movement through AQP1 |
| title_short | Influence of water models on water movement through AQP1 |
| title_sort | influence of water models on water movement through aqp1 |
| work_keys_str_mv | AT gonzalezma influenceofwatermodelsonwatermovementthroughaqp1 AT zaragozaa influenceofwatermodelsonwatermovementthroughaqp1 AT lynchc influenceofwatermodelsonwatermovementthroughaqp1 AT sansommsp influenceofwatermodelsonwatermovementthroughaqp1 AT valerianic influenceofwatermodelsonwatermovementthroughaqp1 |