this will only give an estimate of *electrostatic* contributions via
poisson boltzmann calculations NOT *binding* energy. certainly one way
to try to estimate those (and hyrdophobics via buried surface area?).
perhaps FEP/MD or something that actually takes into account hydrogen
bonding properly might be better, but perhaps also rather time
consuming (no suggestions).
tommi
Quoting "Chandra Verma" <[log in to unmask]>:
> 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
>>
>
>
--
Tommi Kajander, Ph.D.
Macromolecular X-ray Crystallography
Research Program in Structural Biology and Biophysics
Institute of Biotechnology
P.O. Box 65 (Street address: Viikinkaari 1, 4th floor)
University of Helsinki
FIN-00014 Helsinki, Finland
Tel. +358-9-191 58903
Fax +358-9-191 59940
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