Hi everyone!
I wanted to know the effect of a mutation from Threonine to Serine on the interaction of a protein with a lipid bilayer, specifically in terms of energy change. I used the pmx tool to analyze the energy change resulting from this mutation. The result is attached below for the protein-membrane complex:
I would like to know if it is necessary to calculate the double free energy change (ΔΔG) in this case, and if so, could you please guide me on how to perform this calculation?
yes, the value as it is is not very meaningful. Only in relation to a reference value, as part of a thermodynamic cycle, does it become meaningful. Which reference state that should be depends on the question. It seems that you’re interested in the membrane insertion effect of the mutation. In that case one possibility would be do do the same mutation with the protein in water. The free energy difference (ΔΔG) in this case would be the membrane insertion effect of the mutation.
