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Permeation of Organometallic Compounds through Phospholipid Membranes

von Dr. Raycho Yonchev

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[1.] Ry/Fragment 071 01 - Diskussion
Zuletzt bearbeitet: 2016-01-22 20:45:22 WiseWoman
Anézo 2003, Fragment, Gesichtet, Ry, SMWFragment, Schutzlevel sysop, Verschleierung

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Untersuchte Arbeit:
Seite: 71, Zeilen: 1 ff.
Quelle: Anézo 2003
Seite(n): 157, 158, 159, Zeilen: 157:10ff; 158:1-4,21ff; 159:1-3
III.1.4 Non-equilibrium MD simulations

To construct the free energy profile along the membrane normal (z-direction) corresponding to the transfer of the solute from the water layer into the membrane hydrocarbon core, a series of biased simulations is carried out, where an average force method is used to maintain the solute molecules at different positions in the DPPC membrane. This method allows computation of the local diffusion coefficient at the same time, so that permeability coefficients of the solutes in the membrane should be obtained. In order to follow the complete permeation pathway across the membrane, initial configurations are generated by introducing the solute molecules at different depths into the membrane, applying the growing procedure described above. 67 positions along the bilayer normal 1Å apart, are investigated from z0 = – 3.3 to z0=3.3 nm. The solute center of mass is restrained in the z-direction. To limit computational cost, four solute molecules (two per leaflet) are incorporated into the membrane in each starting structure, which reduces the number of simulations from 67 to 17.

Simulation conditions are the same as those for the equilibrium MD simulations and a tolerance of constraint 1 x 10-10 nm is used. This leads to using of double precision for calculating of atom coordinates, which rapidly slows down the simulations. Again all bond lengths are kept constant. Each window is equilibrated for 2.5 ns, after which a production trajectory of 12.5 ns is generated.

III.2. Results

III.2.1 Equilibrium MD simulations

Figure 3.3 shows the distribution of the twelve solute molecules in the DPPC membrane at the start and after 35 ns MD simulation for each type of solute. In the final ensemble dimathylarsinic acid molecules are not found in the hydrophobic membrane core anymore and are essentially located in the water layers and at the water/membrane interfaces. The trimethylbismuthane molecules leave the aqueous phase and the membrane interior to adsorb at the water/membrane interface.

[page 157]

5.4.4 Umbrella sampling MD simulations

To construct the free energy profile along the membrane normal (z-direction) corresponding to the transfer of the solute from the water layer into the membrane hydrocarbon core, a series of biased simulations is carried out, where an umbrella potential is added to the system to maintain the solute molecules at different positions in the DPPC membrane.

In order to follow the complete permeation pathway across the membrane, initial configurations for the umbrella sampling windows are generated by introducing the solute molecules at different depths into the membrane, applying the growing procedure described in the previous section. 67 positions along the bilayer normal, 1 Å apart, are investigated from z0 = —3.3 to z0 = 3.3 nm (the position of the solute COM is defined relative to the position of the DPPC bilayer COM, taken as reference). The solute COM is restrained in the z-direction by a harmonic umbrella potential with a force constant k of 3000 kJ/mol.nm2 (see Equation 5.5), which allows sufficient overlap between adjacent windows. To limit the computational cost, four solute molecules (two per leaflet) are incorporated into the membrane in each starting structure, which reduces the number of simulations from 67 to 17.

Simulation conditions are identic to those for the equilibrium MD simulations, with the exception of the type of pressure coupling. [...] Each window is equilibrated for 2.5 ns, after which a production trajectory of 12.5 ns is generated for the umbrella sampling calculations. [...]

[page 158]

5.4.5 Constrained MD simulations

Constrained simulations allow for the computation of free energy profiles and local diffusion coefficients at the same time, so that permeability coefficients of the solutes in the membrane should be obtained.

[...]

5.5.1 Equilibrium MD simulations

5.5.1.1 Time course of solute position

Figure 5.9 shows the distribution of the twelve solute molecules in the DPPC membrane at the start (uniform distribution) and after 30 ns MD simulation for each type of solute. In the final ensemble, the polar methylglucose and mannitol molecules are not found in the hydrophobic membrane core anymore and are essentially located in the water layers and at the water/membrane interfaces. At first sight, however, mannitol seems to penetrate somewhat deeper into the membrane than methylglucose does. The salicylic acid molecules leave the aqueous phase and the membrane interior to adsorb, owing to their amphiphilic

[page 159]

character, at the water/membrane interface, with the polar carboxyl and hydroxyl groups of the molecule interacting with the DPPC headgroups and the hydrophobic benzene ring protruding into the bilayer core.

Anmerkungen

No source is given.

Sichter
(Klgn), WiseWoman


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