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GPI anchor with Anchor protein glycosilated
- Nuria
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8 years 8 months ago #4815
by Nuria
GPI anchor with Anchor protein glycosilated was created by Nuria
Hi,
I need to run some CG simulations to study a protein A, but for that I need to parametrize its receptor, which is a glycosylated protein anchored to a GPI anchor.
So, to parametrize this receptor, I need in fact to parametrize the following: The GPI anchor, formed by a phosphatidylinositol (PI, which is parametrized for Martini), but in my case it will be substituted by both a palmitate and a chain of sugars. Then, I need to parametrize the link between that chain of sugars and the protein B, and then the second chain of sugars substituted on the protein B.
Any suggestion of an approximated way to parametrize that system? Even just parametrizing the GPI anchor would be a great help.
Thanks,
Nuria
I need to run some CG simulations to study a protein A, but for that I need to parametrize its receptor, which is a glycosylated protein anchored to a GPI anchor.
So, to parametrize this receptor, I need in fact to parametrize the following: The GPI anchor, formed by a phosphatidylinositol (PI, which is parametrized for Martini), but in my case it will be substituted by both a palmitate and a chain of sugars. Then, I need to parametrize the link between that chain of sugars and the protein B, and then the second chain of sugars substituted on the protein B.
Any suggestion of an approximated way to parametrize that system? Even just parametrizing the GPI anchor would be a great help.
Thanks,
Nuria
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- Pim
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8 years 8 months ago #4826
by Pim
Replied by Pim on topic GPI anchor with Anchor protein glycosilated
Hi Nuria,
I can't quite visualise your system from your description, but if I understand your question correctly, you found the parameters for the individual parts, but you are mainly looking for the parameters for the link.
I then assume the dynamics of the linker are important to your research. In that case, it sounds like the best strategy would be to run an all-atom simulation on the linker connected to part of the rest of your system (i.e. leave out the protein, sugar moieties and other groups that are far away). If the link is small and you don't need to introduce you can then fit easily fit the distance distribution to a bond distance between the beads of the parts (e.g. using the inverse Boltzmann method), and you're probably fine, even with using automatically generated parameters for the AA simulation (using e.g. CHARMM paramchem, GROMOS ATB or AMBER antechamber. If you need to introduce extra bead types, it is a little bit more tricky, but certainly possible. In both cases, cgmartini.nl/cgmartini/index.php/parametrzining-new-molecule shows you the way!
It sounds like you found these, but here are the links to the parameters anyway:
Phosphatidylinositols:
cgmartini.nl/cgmartini/index.php/force-f...hosphatidylinositols
Palmitate:
cgmartini.nl/cgmartini/index.php/force-f...tml?dir=FA&lipid=PCA
Sugars:
cgmartini.nl/cgmartini/index.php/force-field-parameters/sugars
I can't quite visualise your system from your description, but if I understand your question correctly, you found the parameters for the individual parts, but you are mainly looking for the parameters for the link.
I then assume the dynamics of the linker are important to your research. In that case, it sounds like the best strategy would be to run an all-atom simulation on the linker connected to part of the rest of your system (i.e. leave out the protein, sugar moieties and other groups that are far away). If the link is small and you don't need to introduce you can then fit easily fit the distance distribution to a bond distance between the beads of the parts (e.g. using the inverse Boltzmann method), and you're probably fine, even with using automatically generated parameters for the AA simulation (using e.g. CHARMM paramchem, GROMOS ATB or AMBER antechamber. If you need to introduce extra bead types, it is a little bit more tricky, but certainly possible. In both cases, cgmartini.nl/cgmartini/index.php/parametrzining-new-molecule shows you the way!
It sounds like you found these, but here are the links to the parameters anyway:
Phosphatidylinositols:
cgmartini.nl/cgmartini/index.php/force-f...hosphatidylinositols
Palmitate:
cgmartini.nl/cgmartini/index.php/force-f...tml?dir=FA&lipid=PCA
Sugars:
cgmartini.nl/cgmartini/index.php/force-field-parameters/sugars
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- Nuria
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8 years 8 months ago #4827
by Nuria
Replied by Nuria on topic GPI anchor with Anchor protein glycosilated
Hi Pim,
Thanks a lot for your answer. In fact, I am trying to connect the parts with distance restraints. It's working, but I am still refining it, as some bonds are flexible while others are quite rigid...so I'm just trying to guess which distance restraints to use. But I think it will more or less work :)
Ciao,
Nuria
Thanks a lot for your answer. In fact, I am trying to connect the parts with distance restraints. It's working, but I am still refining it, as some bonds are flexible while others are quite rigid...so I'm just trying to guess which distance restraints to use. But I think it will more or less work :)
Ciao,
Nuria
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8 years 8 months ago #4828
by Pim
Replied by Pim on topic GPI anchor with Anchor protein glycosilated
Alright, indeed you may need to play around a bit. I guess a distance restraint is kind of the same as a bond without the corresponding angle parameters. I hope it works for you.
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