normal Post Translational Modifications

  • Tocci_89
  • Tocci_89's Avatar Topic Author
  • Offline
  • Fresh Boarder
More
9 years 11 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.

Please Log in or Create an account to join the conversation.

More
9 years 11 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.

Please Log in or Create an account to join the conversation.

  • Tocci_89
  • Tocci_89's Avatar Topic Author
  • Offline
  • Fresh Boarder
More
9 years 11 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!

Please Log in or Create an account to join the conversation.

More
9 years 11 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.

Please Log in or Create an account to join the conversation.

More
9 years 11 months ago #3997 by Clement
Replied by Clement on topic Post Translational Modifications
Oops... Did not remember that one. My bad!

Please Log in or Create an account to join the conversation.

  • Tocci_89
  • Tocci_89's Avatar Topic Author
  • Offline
  • Fresh Boarder
More
9 years 11 months ago - 9 years 11 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!
Last edit: 9 years 11 months ago by Tocci_89.

Please Log in or Create an account to join the conversation.

More
9 years 11 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!

Please Log in or Create an account to join the conversation.

Time to create page: 0.091 seconds