I have a dimer protein. I want to study monomeric conformation changes and see, by using molecular dynamics, how dimer is created. Maybe study transitional conformations. I don't know.
Does anyone know if this is possible? How can I do that?
Regards,
Gabriela
Probably the best docking software available for looking at protein complex formation at the moment is HADDOCK . GROMACS is a molecular modelling software which is primarily used to observe motions and dynamics of proteins, but can be used as a complementary technique for protein docking. Normally, protein docking uses rigid models to decrease the degrees of freedom available (and make the algorithm computationally fast). By using a program like GROMACS, potential models can be allowed to move and adopt more favourable conformations, improving detection of protein-protein interactions .
so you have to dock the monomer to form a dimer using a docking software, then you have to perform the dynamics to study monomeric conformation changes occur if any.
Probably the best docking software available for looking at protein complex formation at the moment is HADDOCK . GROMACS is a molecular modelling software which is primarily used to observe motions and dynamics of proteins, but can be used as a complementary technique for protein docking. Normally, protein docking uses rigid models to decrease the degrees of freedom available (and make the algorithm computationally fast). By using a program like GROMACS, potential models can be allowed to move and adopt more favourable conformations, improving detection of protein-protein interactions .
so you have to dock the monomer to form a dimer using a docking software, then you have to perform the dynamics to study monomeric conformation changes occur if any.
Formation of dimer is computationally demanding. It dependes heavily on the initial configurations and the simulation protocol. I recommend you to simulate some simple systems first before dealing with complex systems.
In order to do that you need yo use enhanced sampling techniques. Vanilla MD doesn't do the trick. If you know the dimeric structure start from this and study the reverse process (maybe with Umbrella Sampling)...then you have an idea of what might be going on. I did something similar here but with a different goal in mind :Article Intrinsic Conformational Preferences and Interactions in α-S...
For studying dimerization you may need REMD and more complex analysis tools.
Hope this helps.
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