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PMF Protein insertion in membrane
- fmerino
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9 years 1 month ago #4474
by fmerino
PMF Protein insertion in membrane was created by fmerino
Dear all,
I need to calculate the PMF for the insertion of a protein region inside a model membrane. My concern is that the protein is rather conical so it requires different number of lipids in the upper and lower leaftlets of the membrane.
Here is my concern, when if I pull the protein out of the membrane from an equillibrated system I'd get an asymmetric membrane. Since there is a pore temporarily created, do you believe the lipids will flip flop and relax the membrane?
Another possibility is to design a symmetric membrane to begin with. However, in this case I am afraid that the lateral pressure will be artificially high in one leaflet over the other.
Any comments?
There are 9 more lipids in one side than the other.
Best
Felipe
I need to calculate the PMF for the insertion of a protein region inside a model membrane. My concern is that the protein is rather conical so it requires different number of lipids in the upper and lower leaftlets of the membrane.
Here is my concern, when if I pull the protein out of the membrane from an equillibrated system I'd get an asymmetric membrane. Since there is a pore temporarily created, do you believe the lipids will flip flop and relax the membrane?
Another possibility is to design a symmetric membrane to begin with. However, in this case I am afraid that the lateral pressure will be artificially high in one leaflet over the other.
Any comments?
There are 9 more lipids in one side than the other.
Best
Felipe
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- helgi
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8 years 11 months ago #4535
by helgi
Replied by helgi on topic PMF Protein insertion in membrane
Hello, hello,
I don't think there is an easy solution to this. When you pull out the protein some lipid flip flop might occur but not enough to equilibrate the bilayer. To some extend the remaining asymmetry might be small (especially if your bilayer is large) so this might not contribute that much to the PMF. You could also make sure the number of lipids in each leaflet are always equilibrated by maintaining a hole through the bilayer somewhere away from your protein e.g. using a mean-field force approximation (MFFA) boundary potentials. But equilibrating the number of lipids in this way might still take quite long.
Cheers,
- Helgi
I don't think there is an easy solution to this. When you pull out the protein some lipid flip flop might occur but not enough to equilibrate the bilayer. To some extend the remaining asymmetry might be small (especially if your bilayer is large) so this might not contribute that much to the PMF. You could also make sure the number of lipids in each leaflet are always equilibrated by maintaining a hole through the bilayer somewhere away from your protein e.g. using a mean-field force approximation (MFFA) boundary potentials. But equilibrating the number of lipids in this way might still take quite long.
Cheers,
- Helgi
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- mnmelo
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8 years 11 months ago #4538
by mnmelo
Replied by mnmelo on topic PMF Protein insertion in membrane
One approach you could take to have a faster lipid equilibration is to have a bilayer that is discontinuous in x (similarly to the one used to test N-BAR-induced bending; Biophysical Journal Volume 97 November 2009 2727–2735).
I'm not sure, however, how much distance you should allow between the protein and the edges to avoid artifacts. I'd recommend at least following the rule that the protein doesn't see any lipids that can interact with the edge (meaning it should sit some 3.0nm from each edge, defining edge where the lipid normal is no longer aligned with z).
Good luck,
Manel
I'm not sure, however, how much distance you should allow between the protein and the edges to avoid artifacts. I'd recommend at least following the rule that the protein doesn't see any lipids that can interact with the edge (meaning it should sit some 3.0nm from each edge, defining edge where the lipid normal is no longer aligned with z).
Good luck,
Manel
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