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normal Martini forcefield parameters for Mg2++ for a glycosylated protein

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2 years 7 months ago #9105 by zmazhar9
Martini forcefield parameters for Mg2++ for a glycosylated protein was created 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 4 months ago #9253 by riccardo
Replied by riccardo on topic Martini forcefield parameters for Mg2++ for a glycosylated protein
Not sure that even atomistic force fields can capture differences between Ca2+ and Mg2+, and, definitely, Martini 2 would not. 

According to Supp. Table 25 of the Martini 3 paper ( www.nature.com/articles/s41592-021-01098-3 ), magnesium is described by a TD (with charge +2) bead, while calcium by a SD or TD (both with charge +2) "depending on the application". Hence, you may try to use Martini 3 and check if you see differences between calcium and magnesium by modelling Mg by a TD bead and Ca by a SD bead. Validation against experimental data is however highly recommended.

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  1. Force Fields
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  5. Martini forcefield parameters for Mg2++ for a glycosylated protein
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