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" <[email protected]>:
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
