Hello RG community!
I'd like to try modeling binding of a ligand to a few proteins in a family with a few published crystal structures. One of the crystal structures bindings a soluble small molecule, the others bind fatty acids (FA'ss) deeper in the protein core, so I'm hypothesizing that these proteins actually bind some sort of glycerolipid in vivo (in vitro binding assays for the FA binding proteins were only tested with free FA's based on the occurrence of FA's in the crystals from heterologous expression).
So, in short, there are three really nice crystal structures available; how can I test the potential binding of a glycerolipid in silico before trying anything in vivo?
Thank you for any suggestions!
I'd like to try model binding of a ligand to di oxime in a family with a few published crystal structures
Hi Evan,
You can make some initial models using your chemical intuition. Then, if the size of system is not too large, you can perform density functional theory (DFT) calculations implemented in softwares such as VASP and SIESTA to geometrically relax the system. From the DFT calculations output, you can compare the binding energies for different models and determine the thermodynamically most stable structure.
If the system is too large, you can use Molecular dynamics (MD) simulations. For that you can use the lammps package. It gives you an idea about the atoms movements and final structures.
Hope you find this helpful.
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