Joe wrote:
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.
I use PISA for this. You need to trick it by giving each domain a
different CHAIN ID - and probably omitting the residue which links them!
But then it gives you all the usual useful analysis of the interface..
Eleanor
