Journal article
Induced polarization in molecular dynamics simulations of the 5-HT3 receptor channel
- Abstract:
- Ion channel proteins form water-filled nanoscale pores within lipid bilayers, and their properties are dependent on the complex behavior of water in a nanoconfined environment. Using a simplified model of the pore of the 5-HT3 receptor (5HT3R) which restrains the backbone structure to that of the parent channel protein from which it is derived, we compare additive with polarizable models in describing the behavior of water in nanopores. Molecular dynamics simulations were performed with four conformations of the channel: two closed state structures, an intermediate state, and an open state, each embedded in a phosphatidylcholine bilayer. Water density profiles revealed that for all water models, the closed and intermediate states exhibited strong dewetting within the central hydrophobic gate region of the pore. However, the open state conformation exhibited varying degrees of hydration, ranging from partial wetting for the TIP4P/2005 water model to complete wetting for the polarizable AMOEBA14 model. Water dipole moments calculated using polarizable force fields also revealed that water molecules remaining within dewetted sections of the pore resemble gas phase water. Free energy profiles for Na+ and for Cl– ions within the open state pore revealed more rugged energy landscapes using polarizable force fields, and the hydration number profiles of these ions were also sensitive to induced polarization resulting in a substantive reduction of the number of waters within the first hydration shell of Cl– while it permeates the pore. These results demonstrate that induced polarization can influence the complex behavior of water and ions within nanoscale pores and provides important new insights into their chemical properties.
- Publication status:
- Published
- Peer review status:
- Peer reviewed
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(Preview, Version of record, 6.6MB, Terms of use)
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- Publisher copy:
- 10.1021/jacs.0c02394
Authors
- Publisher:
- American Chemical Society
- Journal:
- Journal of the American Chemical Society More from this journal
- Volume:
- 142
- Issue:
- 20
- Pages:
- 9415-9427
- Place of publication:
- United States
- Publication date:
- 2020-04-27
- Acceptance date:
- 2020-04-26
- DOI:
- EISSN:
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1520-5126
- ISSN:
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0002-7863
- Pmid:
-
32336093
- Language:
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English
- Keywords:
- Pubs id:
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1103613
- Local pid:
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pubs:1103613
- Deposit date:
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2021-07-22
Terms of use
- Copyright holder:
- Klesse et al.
- Copyright date:
- 2020
- Rights statement:
- © 2020 American Chemical Society. This is an open access article published under a Creative Commons Attribution (CC-BY) License, which permits unrestricted use, distribution and reproduction in any medium, provided the author and source are cited.
- Licence:
- CC Attribution (CC BY)
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