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normal Lipid peroxidation

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11 years 10 months ago #1012 by dariush
Lipid peroxidation was created by dariush
Hi,

I have a lipid in my CG-MD system and I am going to do peroxidation. There is a C3 type bead in acyl chain of that lipid and now I am going to add -OOH group on that bead (for peroxidation). Could you please let me know what would be the type of that bead? I was thinking it can be P type, but I do not know which one (P1 … P5)?

Thanks,
Dariush

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11 years 10 months ago #1013 by siewert
Replied by siewert on topic Lipid peroxidation
Have a look at Table 3 of the Martini 2007 paper and you should be able to come up with an appropriate particle type ...

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11 years 10 months ago #1014 by dariush
Replied by dariush on topic Lipid peroxidation
I did carefully, but I could not fit those atoms with one of them. Below you can see 2D of the structure: C=C-O-OH
|
C-C

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11 years 10 months ago #1016 by siewert
Replied by siewert on topic Lipid peroxidation
Do you want to map these six heavy atoms into a single CG bead?
Or is it just the C=C-O-OH group you are worried about?

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11 years 10 months ago #1018 by dariush
Replied by dariush on topic Lipid peroxidation
After preoxidation double bond shifted back one bond and -O-OH group should be added. Any suggestions for mapping would be appreciated... (one/two bead).

Many thanks,
Dariush

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11 years 10 months ago #1020 by siewert
Replied by siewert on topic Lipid peroxidation
Well, there are three options (in my view):

1) change the C3 bead into a P2 bead; a C-C-OOH group would be best represented by a P3 bead but you may tune it down a bit because you have an additional C=C functionality.

2) look up partitioning data for your chemical unit and see which bead is most appropriate

3) use two beads to represent this part, with (if possible) additional methylene units of the remainder of the lipid tail added. You may be able to define a C=C-OOH group and a C-C-C or C-C-C-C group which would be modeled as a P4 and C4/C5 bead.

By the way, are you sure you have a C=C-OOH group and not a C=C-COOH group in your peroxidized lipid?

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11 years 10 months ago #1022 by dariush
Replied by dariush on topic Lipid peroxidation
Dear Siewert,

Thank you so much for your useful comments.

For lipid peroxidation you can see below link:
en.wikipedia.org/wiki/Lipid_peroxidation

I am trying your suggestions...

Thank you again.
Dariush

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