evaluating the effect of mutation in binding affinity of two proteins

Question

[elmira b]

Hi,

I used Swiss pdb viewer to mutate three polar amino acids in the contact surface of two proteins. First these amino acids are mutated to Alanine in one of the interacting proteins and then the contact surface is recalculated.

I wonder if this is a correct approach in identifying the importance of amino acids in the contact surface?

Which software are extensively used to evaluate mutation of amino acids in the binding sites of two proteins?

Thanks,

[elmira b]

recent update about my question: interface alanine scanning by Rosetta

Answer 1

[Jiyao Wang]

You can use iCn3D to have the estimate of the mutation effect, e.g., https://www.ncbi.nlm.nih.gov/Structure/icn3d/?mmdbid=6M0J&command=scap%20interaction%206M0J_E_484_K. The menu is "Analysis > Mutation". You can download the PDB of the mutant and do further MD simulation if you want to get more accurate interactions.