I have a dimer protein and I have to insert three amino acid residues in both monomers of the dimer at the same position. So, can anybody please suggest how to conduct this procedure without affecting the interaction between the protein monomer in the crystal structure.
I'm guessing that this 3-amino-acid insertion is in a loop. If so, this could be treated as a loop rebuilding problem and addressed with tools like loopmodel in Rosetta. You would probably need to specify the loop to build as more than just the three new a-a's; in other words, the software must be told to regard flexible flanking regions as part of the loop to be built. In Rosetta this is done through a "Loops File".
That is going to be a little difficult, because it will certainly affect, even if you don't want to. Depending on the location that you want to insert the amino acids (in the middle or at N-/C-terminal), the best thing is to make an homology model. The example is for the monomer, but then you can also make it for the dimer:
- You take out FASTA sequence and insert the aminoacids in the desired place (this will be your template);
- You align your protein with the template. You can use MOE or MODELLER to do this automatically;
- You build homology models (not really homology but similar) of the protein with the added aminoacids. In MOE and MODELLER, the program will test several conformations and secondary structures to see the most favourable;
- The final output will be your protein with the added residues.
Hope it helps.
Thanks for reply I have done it through swiss model, I just gave sequence of my protein having inserted amino acid and gave PDB ID of same protein (wild type) as template. By using same protein as template it gave me model of protein having inserted amino acid.
I am agree with Ricardo Ferreira, the good way is to build model and insert desired amino acid in to it, then their are many software available for interaction studies
you can use the SPDBV software to insert the desired amino acids in theoretical model then go for docking with autodock Vina to find out interactions of compound with protein. All the best
I'm guessing that this 3-amino-acid insertion is in a loop. If so, this could be treated as a loop rebuilding problem and addressed with tools like loopmodel in Rosetta. You would probably need to specify the loop to build as more than just the three new a-a's; in other words, the software must be told to regard flexible flanking regions as part of the loop to be built. In Rosetta this is done through a "Loops File".
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