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.
Highlights
Ion channel proteins form structurally dynamic nanoscale pores within cell membranes,[1,2] where they are responsible for regulating the movement of ions across the lipid bilayer
On the basis of these considerations, and building upon our previous studies,[15] we chose to examine the behavior of polarizable water within the transmembrane pore of the 5-HT3 receptor (5HT3R), a pentameric ligand-gated ion channels (pLGICs) that opens upon binding of serotonin (5-HT3) (Figure 1)
We have shown that a reduced protein system focused on these pore-lining M2 helices of the 5HT3R channel, embedded in a phospholipid bilayer, provided an accurate model system; we chose a similar approach
Summary
Ion channel proteins form structurally dynamic nanoscale pores within cell membranes,[1,2] where they are responsible for regulating the movement of ions across the lipid bilayer. Their activity underlies most forms of cellular electrical activity and signaling, and they are an important class of therapeutic targets for the treatment of disease. The typical ion channel transmembrane pore has an internal radius of ∼0.5 nm and length ∼5 nm They are typically filled with water, providing low-energy ion permeation pathways across a membrane. Molecular simulations play a key role in understanding these anomalous properties.[3−5] the rapidly increasing number of high-resolution structures available for ion channel pores demands faster and more accurate computational approaches for predicting their functional properties
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