if the link between the domains is not part of the interface then perhaps
a good first approximation may be to "cut" the linker and then use a
program such as APBS to compute the binding energy..
> 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
>
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