When Crystallographic file of the protein contains more than 1 part , in interaction with each other while they are of two different conformer of same protein , what can be the optimal approach? By knowing that the aim is operating Molecular Dynamic simulation.
1) Docking separately and recombining the compound in order to operate MD
or
2) running MD for all proteins separately,too.
Thank you in advance
If the aim of the study is to investigate the interaction of the ligand with the compound protein, it would be best to dock each component of the compound protein separately and then recombine them to operate MD. This approach would allow for a more accurate representation of the interactions between the ligand and each component of the protein.
However, if the aim of the study is to investigate the dynamics of the protein and the effect of the conformations on ligand binding, it would be best to run MD simulations for all proteins separately. This approach would allow for a more detailed analysis of the differences in the protein conformations and how they affect ligand binding.
Is the crystallographic complex a native or artificial dimer? If native, where is the ligand binding site: at the interface of the two monomers or at a site not affected by complex formation?
Martin Klvana
It is natural one.
Actually each protein embeds a Ligand trough its inner structure , also each binding site is away from the others meaning there is no interaction between them, at least not strongly.
The only thing to note is the partial interaction of proteins , back to back seemingly , which doesn't show any ligand shared interaction.
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