What would happen if histines were to be mutated amd made it to be roch in amino acids aspartic and gultamic acid?
Answers
Answer:
For residues in the protein core, the most accurate results will probably come from SCWRL 4.0, as Stephane suggested. Optimize the mutated residues and all contacting residues, leave the rest untouched (fixed =lowercase in sequence, file moveable= Uppercase). Directly minimizing all residues will cause small changes in all the residues, even those not affected by the mutation. While SCWRL is very good, it is not perfect, and it is probably better to use the native structure as much as possible. You can experiment with how many residues must be optimized upon mutation.
Once finished, you can minimize the energy of the SCWRL structure using GROMACS if you'd like, particularly if it is a low resolution or NMR structure. Directly simulating the structure in GROMACS may not find the optimal energy because many of the sidechains must be moved if the residue is in the protein core, therefore you are likely to hit a local minimum that may be difficult to get out of.