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Lipid simulation results

Lipotoxicity due to accumulation of lipid simulation results 300 2 200-400 U/L >5 weeks... [Pg.119]

Figure 8 (Plate 4). Typical snapshot of DPD simulation results [64]. The hydrophobic part of mixed bilayers of DPPC-like lipids and up to 0.8 mole-fraction of the non-ionic surfactant Ci2E6 (left) and 0.9 (right). The surfactant C]2 chains are represented by grey curves, and the lipid C15 chains are black. The hole in the left conformation is transient on the right they are stable. Reproduced by permission of the Biophysical Society... Figure 8 (Plate 4). Typical snapshot of DPD simulation results [64]. The hydrophobic part of mixed bilayers of DPPC-like lipids and up to 0.8 mole-fraction of the non-ionic surfactant Ci2E6 (left) and 0.9 (right). The surfactant C]2 chains are represented by grey curves, and the lipid C15 chains are black. The hole in the left conformation is transient on the right they are stable. Reproduced by permission of the Biophysical Society...
The most popular technique to deal with lipid systems has by far been classical molecular dynamics (MD) (28, 30). In MD, all interactions are classic, and the time evolution of the system is described by integrating Newton s equations of motion. The particles can represent atoms or clusters of atoms the most typical choice is the full-atom description in which all atoms including hydrogens are described explicitly, and the united-atom description in which each methyl and methylene group is described by a single particle. The particle-particle interactions are usually determined from QM calculations and tuned even more in an iterative manner by fitting system properties to experiments until simulation results and experimental data match sufficiently well. Usually, the largest system sizes are hundreds... [Pg.2240]

Moreover, the predicted ALT increases did not occur until after 4-6 weeks of dosing, as was observed in the ERGO trial. It is reasonable to conclude from the comparison of the DILIsym simulation results with the clinical data that etomoxir caused an accumulation of lipids due to the FAO inhibition properties of the compound and lipotoxicity for the LFTs in the ERGO trial. [Pg.119]

While the experimental results are suggestive, simulation results are conclusive in their support for Lieb and Stein s hypothesis. Further, the simulations suggest refinement of their hypothesis. MD simulations of the passive diffusion within the bilayer of molecules of a range of sizes, including methane, benzene, adamantane, and nifedipine clearly show that small molecule (methane and benzene) movement includes discrete rapid jumps between voids within the bilayer. These voids are often as much as the volume of benzene, but seldom much larger. These jumps have been observed to be moderated by the torsional isomerization of the lipid hydrocarbon chains, whose motion creates passages between existing voids [4, 5,7,21]. These jumps are occasional for benzene, however they are very frequent for the much smaller molecule, methane. The movement of adamantane and nifedipine is... [Pg.123]

Once the significant components of the system have been chosen, a computational domain is then defined to enclose them. The geometry of the simulation box must define a volume that realistically encloses the physics of the system, with boundary conditions mimicking the effects of the larger, real system being modeled. Within the ion channel framework, only a small fraction of the cellular lipid membrane is simulated thus, the dimension of the computational domain is minimized to reduce the computational burden. Consequently, the boundary conditions must be chosen carefully so that unwanted computational artifacts are not introduced into the simulation results. [Pg.261]

Simulation Results Small Nanoparticle Near a Lipid Bilayer... [Pg.325]

Simulations of the size and complexity of a lipid bilayer system need to be tested against available experimental data whenever possible to validate the simulation results. When simulations and experiments agree, one can have some degree... [Pg.1641]

Methylanaline could be transnitrosated with nitrite and S-nitrosocysteine and also by a simulated protein bound nitrite. In the latter case, an important factor was the local concentration of nitrosothiol groups on the matrix. The effects of S-nitrosocysteine as an inhibitor of lipid oxidation, as a color developer, and as an anticlostridial, have been reported recently in a turkey product (31). The Molar concentration of RSNO equating to 25 ppm nitrite gave similar results for color and inhibition of lipid oxidation but had less anti-clostridial activity. Transnitrosation between RSNO and heme protein was demonstrated. [Pg.296]

Studies of the effect of permeant s size on the translational diffusion in membranes suggest that a free-volume model is appropriate for the description of diffusion processes in the bilayers [93]. The dynamic motion of the chains of the membrane lipids and proteins may result in the formation of transient pockets of free volume or cavities into which a permeant molecule can enter. Diffusion occurs when a permeant jumps from a donor to an acceptor cavity. Results from recent molecular dynamics simulations suggest that the free volume transport mechanism is more likely to be operative in the core of the bilayer [84]. In the more ordered region of the bilayer, a kink shift diffusion mechanism is more likely to occur [84,94]. Kinks may be pictured as dynamic structural defects representing small, mobile free volumes in the hydrocarbon phase of the membrane, i.e., conformational kink g tg ) isomers of the hydrocarbon chains resulting from thermal motion [52] (Fig. 8). Small molecules can enter the small free volumes of the kinks and migrate across the membrane together with the kinks. [Pg.817]

Results of parameter optimization and MD simulations of small model compounds have been published, including alcohols [63], alkanes [63], aromatic [64] and heteroaromatic [209] compounds and liquid amides [65], Studies of ions in aqueous solution were also performed [61, 88] and results from an MD simulation on a DPPC lipid monolayer have been reported (Harder, MacKerell, Roux, submitted). Notable from the monolayer study was the reproduction of the dipole potential across the monolayer, a value that cannot be reproduced using non-polarizable models. This exciting, unforeseen observation points to the types of results that may be obtained from polarizable macromolecular force fields that are not accessible to the present additive models. [Pg.243]


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See also in sourсe #XX -- [ Pg.325 , Pg.326 , Pg.327 , Pg.328 , Pg.329 , Pg.330 ]




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