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Lipid droplet
- dariush
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11 years 2 weeks ago #1500
by dariush
Lipid droplet was created by dariush
Hello,
I have made a system contain 56 triglycerides (TG) as a hydrophobic core and then added about 350 POPC in system to spontaneously get a monolayer on top of that bilayer.
Unfortunately, some of the core molecules (TGs) go on the surface and do not stay in core region.
Any suggestion to optimize the system would be appreciated? I am going to have two separate regions, core and monolayer like:
www.bio.uu.nl/enmeta/burger/Lipid%20Droplet_files/image001.gif
Thanks,
Dariush
I have made a system contain 56 triglycerides (TG) as a hydrophobic core and then added about 350 POPC in system to spontaneously get a monolayer on top of that bilayer.
Unfortunately, some of the core molecules (TGs) go on the surface and do not stay in core region.
Any suggestion to optimize the system would be appreciated? I am going to have two separate regions, core and monolayer like:
www.bio.uu.nl/enmeta/burger/Lipid%20Droplet_files/image001.gif
Thanks,
Dariush
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- djurre
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11 years 2 weeks ago #1502
by djurre
Replied by djurre on topic Lipid droplet
This is not an easy question to answer, but some things come to my mind.
You mention that "some" of the TG go to the outerlayer. It might be that biologically also a small percentage of TGs mixes with the POPC. Second it might be that the ratio of TG/POPC is not exactly right. Then the droplet in equilibrium would need a few TGs to be in the outerlayer to get the right "areas" of the inner and outer layer. Third the partitioning of Martini TG might not be perfect. It might "like" POPC to much compared to itself. In order to reparameterize this, you would need some experimental data to validate against.
You mention that "some" of the TG go to the outerlayer. It might be that biologically also a small percentage of TGs mixes with the POPC. Second it might be that the ratio of TG/POPC is not exactly right. Then the droplet in equilibrium would need a few TGs to be in the outerlayer to get the right "areas" of the inner and outer layer. Third the partitioning of Martini TG might not be perfect. It might "like" POPC to much compared to itself. In order to reparameterize this, you would need some experimental data to validate against.
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- dariush
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11 years 10 hours ago #1553
by dariush
Replied by dariush on topic Lipid droplet
I could figure out the ratio of TGs/POPC and remove those TGs in the monolayer and then let it go for long Eq.
Now I have another problem, the shape of the droplet is not always sphere, and it sometimes get elliptic shape.
By simple reasoning (minimization of surface energy) it should be sphere. Do you know what can cause this problem?
Adding ions can play a role?
In this case also, ratio of TGs/POPC can affect the system shape?
Thanks,
Dariush
Now I have another problem, the shape of the droplet is not always sphere, and it sometimes get elliptic shape.
By simple reasoning (minimization of surface energy) it should be sphere. Do you know what can cause this problem?
Adding ions can play a role?
In this case also, ratio of TGs/POPC can affect the system shape?
Thanks,
Dariush
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- djurre
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10 years 11 months ago #1554
by djurre
Except for the minimization of surface energy, there will also be thermal fluctuations. This will cause a system not always to be in its minimum energy (sphere) but fluctuate (elips). Could that be what is going on?
Replied by djurre on topic Lipid droplet
dariush wrote: By simple reasoning (minimization of surface energy) it should be sphere. Do you know what can cause this problem?
Except for the minimization of surface energy, there will also be thermal fluctuations. This will cause a system not always to be in its minimum energy (sphere) but fluctuate (elips). Could that be what is going on?
Yes, probably this will influence these things as well.dariush wrote: In this case also, ratio of TGs/POPC can affect the system shape?
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