We have to compare two proteins (wild type and mutant) Do we have to first perform protein stability test in water MD simulation and after that for function, protein-ligand simulations? Will protein ligand md simulation be enough to predict the structural and functional stability?
Software GROMACS.
yes, you have to perform md simulation of your mutant protein comparison to normal one, which give you insight of secondary structural changes of both protein.
You have to perform separate MD simulations for Wild and Mutant types of protein (Apo form) along with protein-ligand complex, to check the structural stability/conformation before and after mutation. If you do so, then you will get RMSD values for mutated and wild-type amino acids before and after binding of ligand.
You make two different sets of simulations to compare mutant and wild type, and the influence of the ligand in both. They will be enough to make your predictions - however, keep in mind that you may have to reproduce your results a few times - triplicates, or more, to ensure consistency.
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