I am not very familiar with the theoretical foundations of protein interaction,
but it seems possible to me that PD1 can interact better with alpha helices
by forming part of an alpha-helical bundle (as it forms a bundle with itself
in the crystal structure). Since PD1 was designed to form a flat hydrophobic
surface this surprises me a bit: interhelical interactions are usually
accounted for by interactions between the bulges and grooves of helices.
As long as the structure of PD1 is not deposited one can probably only
speculate if there is also a bulge-groove interaction in the four helix
bundle.
A transmembrane beta barrel might possibly form another pattern of
grooves on its surface. One could control this by looking at the published
structure for OmpF which is said to resemble PhoE most. There is also
the structure for the porin from Rhodobacter capsulatus which forms a beta-
barrel as well.
Just speculating,
Cornelius.
--
/* Cornelius Krasel, Abt. Lohse, Genzentrum, D-82152 Martinsried, Germany */
/* email: krasel at alf.biochem.mpg.de, krasel at vms.biochem.mpg.de */
/* "People are DNA's way of making more DNA." (R. Dawkins/anonymous) */
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