- Posts: 8
Plasmalogen lipids -ether linkage
- satti
-
Topic Author
- Offline
- Fresh Boarder
Less
More
8 years 9 months ago - 8 years 9 months ago #4670
by satti
Plasmalogen lipids -ether linkage was created by satti
Dear everyone,
I would like to simulate membrane mixtures containing Plasmalogens. In this regard, I would like to know :
1. if any one has simulated those, as the literature search did not reveal anything.
2. If I want a C16:0/C18:1 phosphatidylethanolamine (PE) plasmalogen , I think that one of the difference in the martini tip of PE-plasmalogen and POPE would be a change of one of the Na beads at sn-1 position to P1. Further, I would probably need to determine bonded parameters between P1 and Na beads, with P1 and C1 can be copied from ceramics.
So does anyone has P1-Na bond parameters from any related compound.
Or I am on a wrong track. Would appreciate any suggesions?
best wishes,
Satyan
I would like to simulate membrane mixtures containing Plasmalogens. In this regard, I would like to know :
1. if any one has simulated those, as the literature search did not reveal anything.
2. If I want a C16:0/C18:1 phosphatidylethanolamine (PE) plasmalogen , I think that one of the difference in the martini tip of PE-plasmalogen and POPE would be a change of one of the Na beads at sn-1 position to P1. Further, I would probably need to determine bonded parameters between P1 and Na beads, with P1 and C1 can be copied from ceramics.
So does anyone has P1-Na bond parameters from any related compound.
Or I am on a wrong track. Would appreciate any suggesions?
best wishes,
Satyan
Last edit: 8 years 9 months ago by satti.
Please Log in or Create an account to join the conversation.
- satti
-
Topic Author
- Offline
- Fresh Boarder
Less
More
- Posts: 8
8 years 9 months ago - 8 years 9 months ago #4673
by satti
Replied by satti on topic Plasmalogen lipids -ether linkage
Hello lipid experts,
On a closer look, it appeared that it would be reasonable to change P5 bead of C(d18:1/18:1(11c)) (PVSM) sphingolipid to Na to get topology for C(d18:1/18:1(11c)) plasmalogen.
Any suggesitons. A reply is much awaited.
regards,
satti
On a closer look, it appeared that it would be reasonable to change P5 bead of C(d18:1/18:1(11c)) (PVSM) sphingolipid to Na to get topology for C(d18:1/18:1(11c)) plasmalogen.
Any suggesitons. A reply is much awaited.
regards,
satti
Last edit: 8 years 9 months ago by satti.
Please Log in or Create an account to join the conversation.
- siewert
-
- Offline
- Admin
Less
More
- Posts: 61
8 years 9 months ago #4675
by siewert
Replied by siewert on topic Plasmalogen lipids -ether linkage
Hi Satti,
as far as I know, there are no parameters available for plasmologens. But it would be great to have them!
Given the similarity between normal glycerolipids and plasmologens, I would recommend to take as starting point the PE lipids. You are merely replacing a "C-O-C=O" group by a C-O-C=C" group. In fact, I do not even think this changes the polarity very much and you can keep the Na particle type (but please check in the literature to see how the partitioning of small molecules containing this group might change).
The only important change to be made is then the angle potentials involving the GL1-Gl2-C1B and CL2-C1B-C2B beads, to reflect the presence of the trans double bond. I assume the tails would be slightly more straight, and stiffer, at least this is how we incorporate typically the effect of a trans unsaturation in Martini. Ideally, you would use some reference atomistic simulations to get more accurate estimates.
Good luck!
Siewert-Jan
as far as I know, there are no parameters available for plasmologens. But it would be great to have them!
Given the similarity between normal glycerolipids and plasmologens, I would recommend to take as starting point the PE lipids. You are merely replacing a "C-O-C=O" group by a C-O-C=C" group. In fact, I do not even think this changes the polarity very much and you can keep the Na particle type (but please check in the literature to see how the partitioning of small molecules containing this group might change).
The only important change to be made is then the angle potentials involving the GL1-Gl2-C1B and CL2-C1B-C2B beads, to reflect the presence of the trans double bond. I assume the tails would be slightly more straight, and stiffer, at least this is how we incorporate typically the effect of a trans unsaturation in Martini. Ideally, you would use some reference atomistic simulations to get more accurate estimates.
Good luck!
Siewert-Jan
Please Log in or Create an account to join the conversation.
- satti
-
Topic Author
- Offline
- Fresh Boarder
Less
More
- Posts: 8
8 years 9 months ago - 8 years 9 months ago #4676
by satti
Replied by satti on topic Plasmalogen lipids -ether linkage
Dear Prof. Marrink SJ,
Thanks for your suggestions. For parametrization against the experiments, I found some literature on phase transition behavior of these lipids and was planing to reproduce that with martini. Just that I was not sure if that would be worth the effort, if martini experts believe that it would be rather straight forward to modify existing phospholipids.
with kind regards,
satti
Thanks for your suggestions. For parametrization against the experiments, I found some literature on phase transition behavior of these lipids and was planing to reproduce that with martini. Just that I was not sure if that would be worth the effort, if martini experts believe that it would be rather straight forward to modify existing phospholipids.
with kind regards,
satti
Last edit: 8 years 9 months ago by satti.
Please Log in or Create an account to join the conversation.
Time to create page: 0.093 seconds