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Article

Confined dynamics of water in transmembrane pore of TRPV1 ion channel

International Journal of Molecular Sciences. 2019. Vol. 20. No. 4285. P. 1-13.
Трофимов Ю. А., Krylov N., Efremov R.

Solvation effects play a key role in chemical and biological processes. The microscopic properties of water near molecular surfaces are radically different from those in the bulk. Furthermore, behavior of water in confined volumes of nanometer scale, including transmembrane pores of ion channels, is especially nontrivial. Knowledge at the molecular level of structural and dynamic parameters of water in such systems is necessary to understand the mechanisms of ion channels functioning. In this work, the results of molecular dynamics (MD) simulations of water in the pore and selectivity filter domains of TRPV1 membrane channel are considered. These domains represent nanoscale volumes with strongly amphiphilic walls, where physical behavior of water radically differs from that of free hydration (e.g., at protein interfaces) or in the bulk. Inside the pore and filter domains, water reveals very heterogeneous spatial distribution and unusual dynamics: it forms compact areas localized near polar groups of particular residues. Residence time of water molecules in such areas is at least 1.5-3 times larger than that observed for similar groups at the protein surface. Presumably, these water “blobs” play an important role in functional activity of TRPV1. In particular, they take a part in hydration of the hydrophobic TRPV1 pore by localizing up to 6 waters near the so-called “lower gate” of the channel and reducing by this way the free energy barrier for ion and water transport. Although the channel is formed by four identical protein subunits, which are symmetrically packed in the initial experimental 3D structure, in the course of MD simulations, hydration of the same amino acid residues of individual subunits may differ significantly. This greatly affects the microscopic picture of the distribution of water in the channel and, potentially, the mechanism of its functioning. Therefore, reconstruction the full picture of the TRPV1 channel solvation requires a thorough atomistic simulations and analysis. It is important that the naturally occurred porous volumes like ion conducting protein domains reveal much more sophisticated and fine-tuned regulation of solvation than, e.g. artificially designed carbon nanotubes.