Hi, Recently we determined two structures of the same protein in complex with different molecules. The protein contains two domains (called domain A and B here). In the two structures, domain A and B have different arrangements relative to each other, resulting different interaction interface. I want to know which inter-domain interaction is stronger. Is there a way to quantatively compare the "interaction energy or intensity" between the two domains? I have calculated the buried surface area. However, just comparing the buried surface does not provide definitive answer, given that the interacting residues on the interface are also different.
BTW, we were not able to purify individual domains, so we cannot measure the binding affinity by wet lab approaches (so far). Thank you in advance for your inputs. -- Best regards, Joe
