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Int J Mol Sci. 2019 Sep 1;20(17). pii: E4285. doi: 10.3390/ijms20174285.

Confined Dynamics of Water in Transmembrane Pore of TRPV1 Ion Channel.

Author information

1
M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street, 16/10, 117997 Moscow, Russia.
2
National Research University Higher School of Economics, Myasnitskaya ul. 20, 101000 Moscow, Russia.
3
National Research Nuclear University Moscow Engineering Physics Institute, Kashirskoe Shosse, 31, 115409 Moscow, Russia.
4
M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street, 16/10, 117997 Moscow, Russia. r-efremov@yandex.ru.
5
National Research University Higher School of Economics, Myasnitskaya ul. 20, 101000 Moscow, Russia. r-efremov@yandex.ru.
6
Moscow Institute of Physics and Technology (State University), Dolgoprudny, 141701 Moscow, Russia. r-efremov@yandex.ru.

Abstract

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, the behavior of water in confined volumes of a 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 (Transient Receptor Potential Vanilloid type 1) 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 a 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 to 3 times larger than that observed for similar groups at the protein surface. Presumably, these water "blobs" play an important role in the functional activity of TRPV1. In particular, they take part in hydration of the hydrophobic TRPV1 pore by localizing up to six 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 of the full picture of TRPV1 channel solvation requires thorough atomistic simulations and analysis. It is important that the naturally occurring porous volumes, like ion-conducting protein domains, reveal much more sophisticated and fine-tuned regulation of solvation than, e.g., artificially designed carbon nanotubes.

KEYWORDS:

TRPV1 channel permeability for water; anomalous water diffusion; computer simulations; ion channel gating; molecular dynamics; nano-size water pore; physico-chemical properties of confined water; protein-water interactions; water H-bonding; water dynamics

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