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
|