normal developping ornithin lipid parameters

  • vanliefferinge
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3 months 2 weeks ago #7793 by vanliefferinge
vanliefferinge created the topic: developping ornithin lipid parameters
Hi,

I would like to run CG simulations with a ornithine lipid bilayer, but ornithin lipid is not in the Martini force field yet.

I wanted to developped it by analogy with existing parameters. Ornithine is quite similar to lysine (minus a CH2 ) and the carbon chain is classical.

In this picture I present the assignment of the beads type for ornithine lipids with lysine as reference.


https://www.dropbox.com/home/ornithin?preview=ornithine.jpg


I have mainly two questions:

1) concerning the side chain of ornithine. It is one CH2 shorter than the one for lysine. Will the C3 bead be affected? Should I change the type of the bead or remove it?

2) I'm not sure about the P1 bead. It is not a classical lipid junction between the polar head and the carbon chains, so by comparison I decide for a P1. Do you have any advises regarding this?

thank you in advance

Fran├žois

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2 months 1 week ago #7821 by riccardo
riccardo replied the topic: developping ornithin lipid parameters
Sorry for the late reply. I am not able to see the figure you linked via dropbox.
Maybe you can post it in some other way if you are still interested.

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2 months 1 day ago #7833 by vanliefferinge
vanliefferinge replied the topic: developping ornithin lipid parameters
Hello,

thank you for your reply.

You can find the picture in the following link:

ibb.co/k2Azaf

regards

francois

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2 months 23 hours ago #7834 by peterkroon
peterkroon replied the topic: developping ornithin lipid parameters
Hey Francois,

As far as molecules and mappings go, this is a hard one. If you want to keep your mapping mostly as is, I'd drop the C3 bead. Also, I expect P1 to be too polar for a ketone group, but see the original Martini paper.

As an alternative, you can deviate from the Lysine mapping (it's not Lysine anyway, with the missing CH2 and all). In that case, I propose something like the following:
H2N-CH2-CH2-CH2;
HC-COOH;
HN-(C=O)-CH2;
rest.
This has the advantage that it keeps functional group together better, and it very nicely follows 4-1 atoms per bead. The disadvantage is that it looks less like Lysine, so you might need to do some extra validation.

I'm also interested to hear what Riccardo has to add to this :)

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2 months 25 minutes ago #7836 by vanliefferinge
vanliefferinge replied the topic: developping ornithin lipid parameters
Thank you Peterkroon for your reply,
Your mapping look much better than mine but which type of bead would you assign to these 3 beads?

H2N-CH2-CH2-CH2;
HC-COOH;
HN-(C=O)-CH2;

thank you

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1 month 4 weeks ago #7837 by riccardo
riccardo replied the topic: developping ornithin lipid parameters
I would go for the mapping proposed by Peter:

H2N-CH2-CH2-CH2; (Qd as in Lys)
HC-COOH; (P3?)
HN-(C=O)-CH2; (P4? P5?)
rest.

as it nicely follows the 4-1 mapping scheme + keeps functional groups together.

Regarding the bead types, I put some guesses based on Table 3 of Marrink et al 2007 JPCB. Ideally, if you had partitioning data on the fragment you are attaching to the lipid chains you could validate these bead choices by computing free energies of transfer for the fragment and comparing them to the experimental ones. Another option is to look in the literature for other Martini lipids which have a similar head - say, e.g., without the Lys-like piece but with the other two groups - to check how other people mapped those groups (and perhaps you'll find already validated choices).

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1 month 4 weeks ago #7839 by peterkroon
peterkroon replied the topic: developping ornithin lipid parameters
HC-COOH is going to be deprotonated in pH 7, so I'd make it a Qa as first guess.

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