Conclusions

In general this simple study has shown that the binding of up to 10 magnesium ions is highly feasible using the simple binding motif of two acid residues. The exact nature and energetics of this binding are really outside the bounds of this simple analysis.

The main problem with the proposed binding modes is the following. We have found no evidence of acidic residues binding magnesium in proteins in a bi-dentate manner. Whilst we have allowed this type of co-ordination here it is generally thought that the Magnesium is too small to support this. Indeed in Ca bound Calmodulin, it is noted that even the larger Ca atoms are never co-ordinated by more that one bi-dentate acid.

The other most likely contribution to the magnesium co-ordination comes from the solvent waters which are very difficult to model. These waters are under almost no geometric constraints and could bind from any angle in any position and are thus extremely difficult to predict.

Further study would probably involve the use of waters and maybe also modelling of conformational change throughout the protein upon co-ordination of these extra metal atoms. Judging from the Electrostatic surface generated without the magnesium atoms, some of the pockets are so deep and well formed that the magnesium atoms could easilly be almost entirely enclosed by the rest of the protein. In fact the metal atom in site 10 is invisible through the surface. This implies that just the two residues, in most cases, would be more than enough to envelope and satisfy the Magnesium atoms.

Another avenue of investigation would be the use of the full CHARMm forcefield. This would use more complex algorithms to model the potentials and a more detailed and logical conformational search of potential metal binding locations. This would be far more accurate but would be computationally expensive to set up and perform. This would however probably enable sensible suggestions to be made as to the preferred affinities for Calcium or Magnesium binding at various locations.

I hope that you will find this document of some interest and use and please note that while further analysis would be possible, that this would require more directed discussion of objectives and more precise techniques.