Molecular dynamics of water transport through membranes: Water from solvent to solute

Abstract

Abstract

Discover natural compounds as potential phosphodiesterase-4B inhibitors via computational approaches

“…(Hornak et al, 2006;Jorgensen, Chandrasekhar, Madura, Impey, & Klein, 1983;Pronk et al, 2013) The system was simulated under the periodic boundary condition with a dodecahedron periodic box also solvated by tip3p water molecules, setting the surface of the protein covered with a water shell of 1.0 nm. (Berendsen & Marrink, 1993) The number of sodium and chloride ions needed to balance the system charge was placed in the solvated system with salt concentration of 0.15 mol/L. The energy minimization was performed to relax the complex system under 1000 kcal/mol/nm by using the steepest descent method.(J.…”

Statistical thermodynamics of biomembranes

“…The method of constrained particles constructs a potential of mean force by restricting the molecules to different regions within the biomembrane (and measures the average force, in the direction of the constraint, required to keep the molecule within the proscribed region). When the diffusion constant profile of the solute D ( Z ) is also determined (e.g., by the force correlation method which relates the time fluctuations in the instantaneous force from the constrained particle method to the local time dependent friction coefficient and to the diffusion constant profile), the experimentally accessible permeability coefficient of the solute, P, can also be calculated using the inhomogeneous solubility-diffusion model of Marrink and Berendsen [103], as: $\frac{1}{P}={\int }_{Z_1}^{Z_2}\frac{\exp (A\left(Z\right)∕k_{B}T)}{D\left(Z\right)}dZ$, where A(Z) is the free energy profile along the membrane normal axis, Z; k B is the Boltzmann constant [13,102,105,181]. The inhomogeneous solubility-diffusion model is valid as long as the thermodynamic gradients remain small.…”

“…Briefly, these studies describe the effect of cholesterol [29,40,68,86,126,127,140,141,158,172], of dimethylsulfoxide (Me 2 SO) [27,122,157,179,182], of methanol [79,135,139], of ions [54,60,96,119,125,155], of proteins [37,58,76,94,107] and of disaccharides [130,131,163], on lipid bilayers; others describe the permeability coefficients of small organic molecules through lipid bilayers [7–10,103], the water/bilayer interface [14,41,73,104,106,111], the permeation of water across a lipid bilayer [13,30,81,102,188], lipid-DNA complexes [6,36,56], porating electric fields for various lipid bilayers [59,189], as well as the aquaporin-1 water channel in a lipid bilayer [30,58,62,63,73,187]. Clearly, a detailed description of all these studies is beyond the scope of this communication!…”

Permeation of cisplatin through the membranes of normal and cancer cells: a molecular dynamics study

“…All-atom MD simulations are able to provide accurate quantitative results on permeability coefficients and diffusion constants of the studied compounds in the membranes. Permeability is usually estimated using inhomogeneous solubilitydiffusion (ISD) formalism (43,44), which accounts for transversal heterogeneity of the membrane along its normal. The ISD model was used successfully in many studies (45,46) (see (47) for extensive review).…”