normal Martini forcefield parameters for Mg2+ for a glycosylated protein

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2 years 7 months ago #9106 by zmazhar9
Hello Martini FF developers,

I am currently using Martini 2 for a protein which has a glycan on one of its chains that I am interested in. However, the protein also has a metal ion dependent adhesion site which has a Mg2+ important for the protein's activation and ligand binding activity. I was wondering if there are parameters available for Mg2+ as well as a script to convert it to a CG representation. I have been recommended to use Ca2+ but our lab showed how replacement of Mg2+ with Ca2+ can inhibit the protein's activity. I would appreciate the help!

Best regards,
Zahra

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2 years 6 months ago #9135 by riccardo
Hi Zahra. Capturing differences between Mg2+ and Ca2+ is challenging with classical MD and especially with CG models. I doubt Martini 2 will show any difference between Ca2+ and Mg2+ as they would be treated in the same way (I.e., same LJ parameters and same 2+ charge). If I switch to Martini 3 is possible for you, I'd consider it. The ion parametrization is considerably improved. I would first recommend to check the Supp. Information of the Martini 3 (Nat. Methods 2021) paper: there is an extensive description of ion parametrization and models for several ions. If that looks promising enough to you, I would consider switching. For more info (lectures and tutorials) about Martini 3, see the material of the very recent online Martini workshop cgmartini.nl/index.php/2021-martini-online-workshop

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2 years 6 months ago #9137 by xavier
Hi Zahra,

Interesting topic :)). I did spent a few years on it during my PhD. Back in the end 1900. :)).

We’ll simply but, the classic mechanics can not describe systems where partial charge transfer occurs … timely.

In MD the charge transfer is approximated and considered constant. But we and others have found/considered that fixing the contact with restraints was the better solution. So you have flexibility but no change of neighbors. Alternatively changes are difficult to handle.

Have a look at: x. Periole, doi: 10.1021/JP9701855 and associated publications.

Good vibes

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