normal Mapping for the palmitoyl Cystine

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8 years 9 months ago #5091 by flaviyan
Mapping for the palmitoyl Cystine was created by flaviyan
Dear Moderators,

I am trying to run simulations of peptides containing palmitoylated cysteine, the parameters are already published in the following manuscripts:

Molecular view on protein sorting into liquid-ordered membrane domains mediated by gangliosides and lipid anchors
pubs.rsc.org/en/Content/ArticleLanding/2...D20086D#!divAbstract

NRas slows the rate at which a model lipid bilayer phase separates
pubs.rsc.org/en/Content/ArticleLanding/2...D00131H#!divAbstract


Both the studies report parameters for the DPPC linked with Cysteine "for palmitoyl chains (Na–C1–C1–C1–C1), were connected to cysteine 181 and 184 (H-Ras) or 184 (N-Ras) side chains using a harmonic bond with equilibrium distance r0 = 0.39 nm and force constant fc = 5000 kJ mol−1 nm−2".

My question is regarding the mapping scheme i.e i see two possibilities from the above statements:

MAPPING 1

BB(Nda)-SC1(Na)-SC2(C1)-SC3(C1)-SC4(C1)-SC5(C1)

MAPPING 2

BB(Nda)-SC1(C5)-SC2(Na)-SC3(C1)-SC4(C1)-SC5(C1)–SC6(C1)

The first mapping considers whole of thioester group as one bead that is more ester like (Na-bead)

The second mapping scheme keeps both the thio properties (C5-bead) and the ester (Na-bead), but the mapping is close to 3:1 in which case should I assign different masses than 72?

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8 years 9 months ago #5092 by helgi
Replied by helgi on topic Mapping for the palmitoyl Cystine
Good question,

As for as I can tell in the “D.H. de Jong, C.A. Lopez, S.J. Marrink. Molecular view on protein sorting into liquid-ordered membrane domains mediated by gangliosides and lipid anchors. Farad. Discuss., 161:347-363, 2013” paper this was done according to your Mapping 2.

You are right the underlying density for those x2 beads is then somewhat lower than average Martini (this explains the relatively short stiff linker between the beads). For most problems I would advise using Mapping 2 and not worry about the exact weight of the beads (having 72 for all beads is already a large approximation and this won’t affect that much). Except if you are really carefully exploring the detailed interaction/location of the anchor with respect to the protein and bilayer. Then I would advise you also do some atomistic control simulations for your system and based on those revisit the mapping.

Cheers,
- Helgi

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8 years 9 months ago #5093 by flaviyan
Replied by flaviyan on topic Mapping for the palmitoyl Cystine
Thanks for the replies Dr.Ingólfsson

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8 years 9 months ago #5111 by flaviyan
Replied by flaviyan on topic Mapping for the palmitoyl Cystine
Hi,

I did some atomistic simulations and the distributions of bond distances with 0.39 and 5000 kJ/mol/nm^2 better matches the five bead mapping scheme

BB(Nda)-SC1-SC2(C1)-SC3(C1)-SC4(C1)-SC5(C1)

The mass distribution is also close to the 72 than the 6 bead mapping. But I am now having a question on what bead type should I assign to the thioester bond between the cysteine and acyl chain, I am considering N0 bead type as it is intermediate between C5 and Na (published in the paper).

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