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Post Translational Modifications
- Tocci_89
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9 years 8 months ago #3992
by Tocci_89
Post Translational Modifications was created by Tocci_89
Hi everyone,
I need to set-up a CG model of a GPCR with a palmitoylated CYS in the C-term. I have the parameters for the palmitoyl but I don't know how to combine it to my CYS in CG. I tried to combine them in the AA structure and to convert everything in CG, but martinize.py has problems to coarse-grain it.
If anyone already tried something like this would be helpful for me.
Thanks and best regards.
I need to set-up a CG model of a GPCR with a palmitoylated CYS in the C-term. I have the parameters for the palmitoyl but I don't know how to combine it to my CYS in CG. I tried to combine them in the AA structure and to convert everything in CG, but martinize.py has problems to coarse-grain it.
If anyone already tried something like this would be helpful for me.
Thanks and best regards.
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- Clement
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9 years 8 months ago #3994
by Clement
Replied by Clement on topic Post Translational Modifications
I'd say by hand... Once coarse-grained, shouldn't be too hard to add some palmitoyl at the end of the [atoms], [bonds], etc. sections.
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- Tocci_89
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9 years 8 months ago #3995
by Tocci_89
Replied by Tocci_89 on topic Post Translational Modifications
Ok, I'll try so, thank you.
I'll let you know if it works!
I'll let you know if it works!
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9 years 8 months ago #3996
by siewert
Replied by siewert on topic Post Translational Modifications
Please check out the following paper:
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.
In that paper we describe the addition of palmitoyl anchors to transmembrane peptides in detail.
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.
In that paper we describe the addition of palmitoyl anchors to transmembrane peptides in detail.
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- Clement
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9 years 8 months ago #3997
by Clement
Replied by Clement on topic Post Translational Modifications
Oops... Did not remember that one. My bad!
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- Tocci_89
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9 years 8 months ago - 9 years 8 months ago #3998
by Tocci_89
Replied by Tocci_89 on topic Post Translational Modifications
Thank you for your help.
Finally I've obtained the paper! I'll try to set my PTMs as described in there.
Thank you for the time spent for my issues!
Finally I've obtained the paper! I'll try to set my PTMs as described in there.
Thank you for the time spent for my issues!
Last edit: 9 years 8 months ago by Tocci_89.
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9 years 8 months ago #4015
by xavier
Replied by xavier on topic Post Translational Modifications
The attachment of a palmytoil chain on a GPCR using Martini has been described in the periole-JACS-2007 and periole-JACS-2012.
Tocci_89 wrote: Thank you for your help.
Finally I've obtained the paper! I'll try to set my PTMs as described in there.
Thank you for the time spent for my issues!
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