To do this, the electron density distribution of two states of amino acids (single and charged) has been calculated using density functional theory (DFT). Taking into account that charges in the ionic channel pore may play a key role in the conductance and selectivity of the channel, we decided to calculate the charge of amino acid residues with pinpoint accuracy from ab initio methods of quantum chemistry. In some other works (for example, ref 28), the charge of amino acids residues is approximated as ☐.5 e, but there is no evidence to use this estimate. Figure 1Īfter that, we have to know the charges of these residues. Taking into account that in various types of biological cells the thickness W m of the lipid bilayer is different, we decided to describe the position of the channel in the membrane as a distance from outer vestibule to the center of the membrane H m (in most cases there are some α-helix domains in protein, which permeate the lipid bilayer). The inner volume of this tube consists of three simple parts (Figure 1): outer vestibule, inner vestibule (truncated cones with major diameters and heights d out, d in and h out, h in, respectively) and the transmembrane domain (cylindrical with diameter d p). The geometric structure of the ion channel is represented as a cylindrical tube with major diameter D r and height H r.
Like in other previous studies and researches, (22, 28-30) protein and lipid bilayers are represented as rigid bodies. The model of the ionic pore in the membrane suggests three compartments: the ionic pore itself in the bilayer (area of MD simulation), and intra- and extracellular areas (diffusion areas, BD simulation). (7-9) Therefore, understanding of these ionic channels is a very important issue in modern biophysics. (6) Activation of P2X 7 receptors induces the apoptosis mechanism. (5) P2X 5 receptors are likely to be involved in differentiation and growth. (4) P2X 2 and P2X 3 receptors take part in mediating taste transduction. P2X 1 receptors are located mainly in smooth muscles, where they mediate their contractile responses. P2X receptors play a number of important roles in living cells. The channels of that type usually consist of three subunits, forming an ionic pore. The most interesting are P2X receptors these are in fact ion channels, permeable to the passage of cations (2) Na +, K +, and Ca 2+. (1-3) Three families of such receptors are distinguished. The corresponding receptors are called purinergic receptors. In recent years, it has become known that purine nucleotides and nucleosides can possibly act as neuromediators. Uric acid is the final product of human purine degradation elevated levels of uric acid in the blood are the cause of gout. Purine derivatives such as theophylline and caffeine are drugs used for treatment of respiratory diseases. ATP is the energy currency of the cell it provides the energy for many energy-consuming activities. It is known that adenosine takes part in DNA and RNA replication. Purines play many important roles in a great number of biochemical processes that are essential for life.
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