Water nanoconfined in a hydrophobic pore: molecular dynamics simulations of transmembrane protein 175 and the influence of water models
Water molecules within biological ion channels are in a nanoconfined environment and therefore exhibit behaviors which differ from that of bulk water. Here, we investigate the phenomenon of hydrophobic gating, the process by which a nanopore may spontaneously dewet to form a “vapor lock” if the pore...
| Main Authors: | , , , , |
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| Format: | Journal article |
| Language: | English |
| Published: |
American Chemical Society
2021
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| _version_ | 1797108164524507136 |
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| author | Lynch, CI Klesse, G Rao, S Tucker, S Sansom, MSP |
| author_facet | Lynch, CI Klesse, G Rao, S Tucker, S Sansom, MSP |
| author_sort | Lynch, CI |
| collection | OXFORD |
| description | Water molecules within biological ion channels are in a nanoconfined environment and therefore exhibit behaviors which differ from that of bulk water. Here, we investigate the phenomenon of hydrophobic gating, the process by which a nanopore may spontaneously dewet to form a “vapor lock” if the pore is sufficiently hydrophobic and/or narrow. This occurs without steric occlusion of the pore. Using molecular dynamics simulations with both rigid fixed-charge and polarizable (AMOEBA) force fields, we investigate this wetting/dewetting behavior in the transmembrane protein 175 ion channel. We examine how a range of rigid fixed-charge and polarizable water models affect wetting/dewetting in both the wild-type structure and in mutants chosen to cover a range of nanopore radii and pore-lining hydrophobicities. Crucially, we find that the rigid fixed-charge water models lead to similar wetting/dewetting behaviors, but that the polarizable water model resulted in an increased wettability of the hydrophobic gating region of the pore. This has significant implications for molecular simulations of nanoconfined water, as it implies that polarizability may need to be included if we are to gain detailed mechanistic insights into wetting/dewetting processes. These findings are of importance for the design of functionalized biomimetic nanopores (e.g., sensing or desalination) as well as for furthering our understanding of the mechanistic processes underlying biological ion channel function. |
| first_indexed | 2024-03-07T07:25:39Z |
| format | Journal article |
| id | oxford-uuid:59203b4d-5644-4a00-8300-67613c6713ab |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-07T07:25:39Z |
| publishDate | 2021 |
| publisher | American Chemical Society |
| record_format | dspace |
| spelling | oxford-uuid:59203b4d-5644-4a00-8300-67613c6713ab2022-11-17T08:55:26ZWater nanoconfined in a hydrophobic pore: molecular dynamics simulations of transmembrane protein 175 and the influence of water modelsJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:59203b4d-5644-4a00-8300-67613c6713abEnglishSymplectic ElementsAmerican Chemical Society2021Lynch, CIKlesse, GRao, STucker, SSansom, MSPWater molecules within biological ion channels are in a nanoconfined environment and therefore exhibit behaviors which differ from that of bulk water. Here, we investigate the phenomenon of hydrophobic gating, the process by which a nanopore may spontaneously dewet to form a “vapor lock” if the pore is sufficiently hydrophobic and/or narrow. This occurs without steric occlusion of the pore. Using molecular dynamics simulations with both rigid fixed-charge and polarizable (AMOEBA) force fields, we investigate this wetting/dewetting behavior in the transmembrane protein 175 ion channel. We examine how a range of rigid fixed-charge and polarizable water models affect wetting/dewetting in both the wild-type structure and in mutants chosen to cover a range of nanopore radii and pore-lining hydrophobicities. Crucially, we find that the rigid fixed-charge water models lead to similar wetting/dewetting behaviors, but that the polarizable water model resulted in an increased wettability of the hydrophobic gating region of the pore. This has significant implications for molecular simulations of nanoconfined water, as it implies that polarizability may need to be included if we are to gain detailed mechanistic insights into wetting/dewetting processes. These findings are of importance for the design of functionalized biomimetic nanopores (e.g., sensing or desalination) as well as for furthering our understanding of the mechanistic processes underlying biological ion channel function. |
| spellingShingle | Lynch, CI Klesse, G Rao, S Tucker, S Sansom, MSP Water nanoconfined in a hydrophobic pore: molecular dynamics simulations of transmembrane protein 175 and the influence of water models |
| title | Water nanoconfined in a hydrophobic pore: molecular dynamics simulations of transmembrane protein 175 and the influence of water models |
| title_full | Water nanoconfined in a hydrophobic pore: molecular dynamics simulations of transmembrane protein 175 and the influence of water models |
| title_fullStr | Water nanoconfined in a hydrophobic pore: molecular dynamics simulations of transmembrane protein 175 and the influence of water models |
| title_full_unstemmed | Water nanoconfined in a hydrophobic pore: molecular dynamics simulations of transmembrane protein 175 and the influence of water models |
| title_short | Water nanoconfined in a hydrophobic pore: molecular dynamics simulations of transmembrane protein 175 and the influence of water models |
| title_sort | water nanoconfined in a hydrophobic pore molecular dynamics simulations of transmembrane protein 175 and the influence of water models |
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