Regarding the stability of a metal ion in a protein

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Hai all,

Suppose if we wish to find the stability of a metal ion (for rg: zinc ion ) in a protein, what are the possible analysis that one can take up ?

I heard about survival probability, preferential binding and binding energy calculations…being a beginner, kindly help me how to assess them using gromacs modules ?



You can monitor the distance between the ion and binding site, the ion and the water, to answer to the question if the ion is bound all the time to the protein or it exchange with the solvent. To evaluate the affinity, you can mutate the ion in another ion type to evaluate relative binding affinity.


Okay thank you for the response