Hello everyone. I have a question about free energies(delta G). Let's suppose, as an example, that we have following problem. We have PDB structure of complex of 2 proteins(lets say, Spike protein of SARS-CoV-2 and human ACE-2) and we mutate 1 aminoacid in Spike protein. Then we need to evaluate, how much does that mutation affect that complex(calculate delta delta G). As far as I understand, there are 2 different free energies: 1) energy of stability, 2) binding affinity. Roughly speaking, first one shows us how much energy we should spent to unfold a protein. The second one is about how much energy we should spent to unbind 2 molecules and take them apart.
My questions:
- What free energy(the first or the second one) is it correct to calculate in my case(to evaluate how much virus transmissibility would change due to that mutation)?
- Is it correct to calculate delta delta G of stability of a complex(2 proteins)? Or it's okay to do it only with one protein. As far as I know, FoldX can do it with command BuIldModel.
- What is the physical meaning of a free energy of stability in a case of 2 proteins?
- Do energy of stability and binding affinity somehow correlate?
I am newbie in structural bioinformatics, so maybe my questions would seen as stupid by someone. Thanks.
