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Permeation of Organometallic Compounds through Phospholipid Membranes

von Dr. Raycho Yonchev

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[1.] Ry/Fragment 063 01 - Diskussion
Zuletzt bearbeitet: 2016-01-12 21:49:56 WiseWoman
Anézo 2003, Fragment, Gesichtet, KomplettPlagiat, Ry, SMWFragment, Schutzlevel sysop

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Seite: 63, Zeilen: 1 ff. (entire page)
Quelle: Anézo 2003
Seite(n): 143, 144, 145, Zeilen: 143:12-19; 144:13-15,20-32; 145:
[“Conventional” equilibrium MD simulations, starting with solute molecules located at various depths within the membrane (e.g. hydrophobic core, interface, water layer),] directly provide the average distribution of the solute in the membrane. They also allow the direct analysis of a variety of properties, such as hydrogen bonding between the solutes and the water or lipid molecules, specific orientations or conformations of the solutes within the bilayer. Equilibrium MD simulations give thus information on the preferred location of the solutes within the membrane and enable one to get some idea of the shape of the free energy profile across the membrane.

The perturbations of the bilayer structure generated by the presence of solute molecules inside the membrane can also be observed from equilibrium MD simulations by comparison with the properties of the pure bilayer system simulated under the same conditions.

Hence, equilibrium MD simulations of membranes including solute molecules can provide a wealth of information. However, the simulation time scale is simply not long enough to allow the solute molecules to explore the entire range of membrane environments. In the case of a hydrophilic solute molecule, not enough statistical data are collected in the hydrocarbon core of the bilayer, whereas the sampling is poor in the polar headgroup region for a hydrophobic solute. These regions where the probability to find the solute is low determine, however, the rate of permeation and, thus, need to be thoroughly sampled.

II.4.2 Non-equilibrium MD simulations

Umbrella sampling method. Umbrella sampling is a special biased sampling technique, which has been developed by Torrie and Valleau [71,72]. In this approach, the system of interest is simulated in the presence of an artificial biasing potential (also called “umbrella” or “window” potential), introduced to enhance the sampling in the vicinity of a chosen region of configurational space and thus to confine the system around this region. A complete calculation requires a number of separate simulations (or “windows”), each biasing the configurational sampling around a selected region. Ultimately, the information from the various windows must be unbiased and recombined together to obtain the final result.

Applied to the permeation process of a solute molecule across a lipid bilayer, the umbrella sampling method enables one to compute the free energy profile along the [bilayer normal (taken as z-direction).]


71. Torrie, G. M.; Valleau, J. P. J. Comp. Phys. 1977, 23, 187.

72. Torrie, G. M.; Valleau, J. P. Chem. Phys. Lett. 1974, 28, 578.

[page 143]

“Conventional” equilibrium MD simulations, starting with solute molecules located at various depths within the membrane (e.g. hydrophobic core, interface, water layer), directly provide the average distribution of the solute in the membrane. They also allow the direct analysis of a variety of properties, such as hydrogen bonding between the solutes and the water or lipid molecules, specific orientations or conformations of the solutes within the bilayer. Equilibrium MD simulations give thus information on the preferred location of the solutes within the membrane and enable one to get some idea of the shape of the free energy profile across the membrane. [...]

[page 144]

The perturbations of the bilayer structure generated by the presence of solute molecules inside the membrane can also be observed from equilibrium MD simulations by comparison with the properties of the pure bilayer system simulated under the same conditions. [...]

Hence, equilibrium MD simulations of membranes including solute molecules can provide a wealth of information. However, the simulation time scale is simply not long enough to allow the solute molecules to explore the entire range of membrane environments. In the case of a hydrophilic solute molecule, not enough statistical data are collected in the hydrocarbon core of the bilayer, whereas the sampling is poor in the polar headgroup region for a hydrophobic solute. These regions where the probability to find the solute is low determine, however, the rate of permeation and, thus, need to be thoroughly sampled.

5.2.2.2 Non-equilibrium MD simulations

Umbrella sampling method Umbrella sampling is a special biased sampling technique which has been developed by Torrie and Valleau [179,180]. In this approach, the system of interest is simulated in the presence of an artificial biasing potential (also called “umbrella” or “window” potential), introduced to enhance the sampling in the vicinity of a chosen region of configurational space and thus to confine the system around this region. A complete

[page 145]

calculation requires a number of separate simulations (or “windows”), each biasing the configurational sampling around a selected region. Ultimately, the information from the various windows must be unbiased and recombined together to obtain the final result.

Applied to the permeation process of a solute molecule across a lipid bilayer, the umbrella sampling method enables one to compute the free energy profile along the bilayer normal (taken as the z-direction).


[179] G. M. Torrie and J. P. Valleau. Chem. Phys. Lett., 28:578–581, 1974.

[180] G. M. Torrie and J. P. Valleau. J. Comput. Phys., 23:187–199, 1977.

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