Can it say anything about changes in domains if the protein ligand interacts with only one domain?
Hello.
It is possible, but will depend on the flexibility of your receptor. With MD, the whole structure will adapt towards the perturbation made by each specific ligand. However, it can be difficult to calculate binding energies. One way is through Gibbs Free Energy: if you simulate ligand and protein alone, and then the complex ligand-protein, you can calculate the difference between energies and extrapolate the binding energy. Another thing that you can search is for evidences of 'induced-fit' mechanism between ligand and receptor.
Best regards.
Hello.
It is possible, but will depend on the flexibility of your receptor. With MD, the whole structure will adapt towards the perturbation made by each specific ligand. However, it can be difficult to calculate binding energies. One way is through Gibbs Free Energy: if you simulate ligand and protein alone, and then the complex ligand-protein, you can calculate the difference between energies and extrapolate the binding energy. Another thing that you can search is for evidences of 'induced-fit' mechanism between ligand and receptor.
Best regards.
For your question,if you want to observe the changes in the entire domain,or changes in the movement of one protein domain with respect to another protein domain,I would suggest you do Normal Mode Analysis instead of MD simulations. MD simulations provide an idea of the local structural changes within the domain but may not be very helpful in answering your particular question.Or else if you insist on doing MD alone,you will need to figure out the timescale. A timescale of 1 microsec would give you some answers but it also depends on the size of the protein-ligand complex.
I think It is possible to use ab inito MD to calculate the vibrational properties of your system and get the dynamics of the interaction.
I hope U have heard about the conformational entropy and free energy. There are lot of papers that can give u a flavor of ur protein conformational change during ligand binding process. U can also do free energy of ligand binding by using several free energy techniques e.g., metadynamics, Umbrella Sampling etc.
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