Hi all,
I have to do molecular dynamics of a protein. it is trimer of dimer. It has total 6 chains Although in dimer both chains have same amino acids. It has 6 ligands. Ligand interact via hydrgen bonding with 2 amino acids in one chain. It has been reported that one important residue of another chain of dimer is situated in the active site and must be present for the decaroxylase activity of this enzyme. Although distance of this residues from ligand is different in all three dimer i.e. 3.8, to 5.0 A, Active site is not situated at the interface of two chains.
I have attached here the active site figure with each chains, ligand with both chains and ligand residues interactions.
I want to know whether I have to take one chain in molecular dynamics by Gromacs or two chains?
Second thing protein has metal. I want to know that whether I have to retain the metal ion or not? If I have to retain the metal ion in that case which force field i should use in Gromacs?
Thank you in advance.
I think, better to take whole protein including ligands and metal ion. If you will take monomer of that protein, u will not be able to get the effect of rest of the protein.
Regards
Nandan
not only two chain, whole complex u can take including ligands and metal ion.
It could be based on what you most appropriately wish to study. Eg. For protein-protein interactions, you need the chains. For one single domain changes, you can take only one chain. So it differs and there is no readymade anaswer.
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