protein modeling of metalloprotein

Question

[ppnana]

I am very much new to protein modeling and using a tool modeller and chimera.I have a model a protein for which the template has metal ion in the structure.IN modeller I am not able to model it to put the metal in the modelled protein.what shoudl i do?? Also after so many searches got to know that in chimera i can add a metal to the modelled protein.IS that the right approch to do so. Any other suggestions what could be done.Kindly reply

Answer 1

[Joe]

What do you actually want to achieve?

Homology modelling software will not add metal atoms or ligands. They purely try to match the amino acid chains to a homolog in 3D space as best as they are able. They do not know that the template molecule is constrained by a coordinated molecule.

If you are just trying to do this for visualisation purposes, then you can add the atom however you see fit. If you're trying to perform some kind of analyses of the structure, then you probably shouldn't.

If it is the latter you may need to simulate the whole system in the presence of the metal atom with a proper molecular dynamics package to see if there are favourable bond energies for your protein interacting with the atom, but this is nontrivial (I would advise you find someone who actually knows molecular modelling/dynamics very well.

A brief google turns up:

• http://ambermd.org/tutorials/advanced/tutorial20/index.htm
• https://www.sciencedirect.com/science/article/pii/S0959440X14001511
• https://www.ncbi.nlm.nih.gov/pubmed/21318231