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Self-assembling a raft
- mferraro
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10 years 11 months ago #1629
by mferraro
Self-assembling a raft was created by mferraro
Hi all,
I would like to obtain a protein-membrane self-assembly within a bilayer composed by an equimolar (1:1:1) ratio of DSPC:POPE:CHOL and 6 water beads for lipid. I generally observe the formation of micelles instead of bilayers (1200 ns)in this system. So I've decided to study the binary equimolar mixture of DSPC and POPE alone and with the protein to understand if the inertia of the system is due to an increasing viscosity that locks water migration and bilayer formation. I interestingly found that self-assembly of my protein in DSPC/POPE bilayer occurs, whereas the bilayer alone remains stacked in micellar states again. Moreover if I increase the number of water beads in DSPC/POPE system alone, I can see the formation of the desired bilayer. My first question is about this behavior: can the assembly be accelerated by the presence of a protein or more solvation waters? Why?
The second question is about the formation of micelles in DSPC/POPE/CHOL mixture: can I appreciate an increased viscosity in such a CG membrane and can this change influence the formation of a bilayer? I'm simulating at 330 K and with a semiisotropic pressure control; my protein structure is conserved with the standard Elastic Network (martini 2.2 FF).
Any suggestion will be appreciated!
Thanks in advance.
Maria.
I would like to obtain a protein-membrane self-assembly within a bilayer composed by an equimolar (1:1:1) ratio of DSPC:POPE:CHOL and 6 water beads for lipid. I generally observe the formation of micelles instead of bilayers (1200 ns)in this system. So I've decided to study the binary equimolar mixture of DSPC and POPE alone and with the protein to understand if the inertia of the system is due to an increasing viscosity that locks water migration and bilayer formation. I interestingly found that self-assembly of my protein in DSPC/POPE bilayer occurs, whereas the bilayer alone remains stacked in micellar states again. Moreover if I increase the number of water beads in DSPC/POPE system alone, I can see the formation of the desired bilayer. My first question is about this behavior: can the assembly be accelerated by the presence of a protein or more solvation waters? Why?
The second question is about the formation of micelles in DSPC/POPE/CHOL mixture: can I appreciate an increased viscosity in such a CG membrane and can this change influence the formation of a bilayer? I'm simulating at 330 K and with a semiisotropic pressure control; my protein structure is conserved with the standard Elastic Network (martini 2.2 FF).
Any suggestion will be appreciated!
Thanks in advance.
Maria.
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- djurre
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10 years 11 months ago #1630
by djurre
Replied by djurre on topic Self-assembling a raft
Let me try to answer your question one by one:
1. Yes, the hydration level will influence to what state your self-assembly simulations goes. I'm not sure if it makes sense that with little water it goes to micelles, while with more water it goes to a bilayer. But it might be...
2. Yes, peptides can influence the state the self assembly will reach. For an example of where this has been studied extensively, see: dx.doi.org/10.1021/ja207290b
3. I'm not sure how the viscosity of this lipid composition will differ in Martini compared to experiment/other forcefields, nor how this will influence the formation of the bilayer. Compared to experiments I would expect the periodic boundaries to be the biggest difference.
(4.) It seems you are not really interested in studying the selfassembly of the bilayer, but you are doing it to obtain a proper starting structure. If this is the case you could also try to start from one of the preformed bilayers (Downloads >> Example Applications) and manipulate them by removing/adding molecules, changing lipid type/removing beads from certain lipids, etc.
1. Yes, the hydration level will influence to what state your self-assembly simulations goes. I'm not sure if it makes sense that with little water it goes to micelles, while with more water it goes to a bilayer. But it might be...
2. Yes, peptides can influence the state the self assembly will reach. For an example of where this has been studied extensively, see: dx.doi.org/10.1021/ja207290b
3. I'm not sure how the viscosity of this lipid composition will differ in Martini compared to experiment/other forcefields, nor how this will influence the formation of the bilayer. Compared to experiments I would expect the periodic boundaries to be the biggest difference.
(4.) It seems you are not really interested in studying the selfassembly of the bilayer, but you are doing it to obtain a proper starting structure. If this is the case you could also try to start from one of the preformed bilayers (Downloads >> Example Applications) and manipulate them by removing/adding molecules, changing lipid type/removing beads from certain lipids, etc.
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