Hello
In molecular dynamics simulation, if we want to study enzyme activity, should the enzyme be simulated with the substrate?
If the enzyme is simulated without substrate, it is not possible to check its activity?
Thank you
@Maryam, run MD simulation with as well as without substrate. Consider MD run without substrate as control. And compare it with the simulation of enzyme in the presence of substrate to analyze the effect of substrate binding.
Best,
Dear Maryam,
You have both the option; you can with the complete substrate which will give you better insight.
Molecular dynamics (MD) alone cannot help in studying enzymatic activity. An enzyme is a molecular machine to catalyze a chemical reaction (that is, breaking chemical bonds and making new ones). A reaction cannot occur in MD, where a system's topology is constant during the simulation time. You may need to use hybrid MM/QM simulations to study enzymatic reactions.
You should do even triple calculations:
- enzyme
- enzyme + substrate
- enzyme + substrate + inhibitor.
As Dmitri Kireev wrote, you would find only the proper way of binding in the space, but the reaction would not occur. QM calculations are needed, but you may use them as the last step when the initial MD system is optimized.
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