I have tried to model its location in the fibril.
The interface between beta sheets is composed primarily of
threonine and valine residues.
Each subunit contributes 3 strands to the central beta sheet.
The 3 strands are linked by hairpin loops.
2) The fundamental building block of the fibril is a domain-swapped dimer.
The first domain swapped dimer is colored purple and violet, the second dimer is
colored yellow and cream.
The 2 dimers of the asymmetric unit differ only in the
conformation of the hinge loop at either end of the central beta sheet.
Two types of interactions were preserved from the crystal structure of
the human prion protein (pdb1i4m.ent): the domain swapping interaction
(within the same asymmetric unit)
and the packing of dimers side by side (between asymmetric units).
3) Look at disulfides between one set of dimers. Purple and violet subunits are domains swapped. Disulfide
bonds are colored yellow.
The disulfide bonds link together subunits
situated across the central beta strands and translated one unit along the
fibril axis. This set of subunits form one half of the fibril.
The entire length of this half of the fibril is
covalently linked through disulfide bonds.
4) Look at disulfides between the other set of dimers.
Yellow and cream subunits are domains swapped. Disulfide
bonds are colored purple. The disulfide bonds link together subunits
situated across the central beta strands and translated one unit along the
fibril axis. This set of subunits form one half of the fibril.
The entire length of this half of the fibril is
covalently linked through disulfide bonds.
5) Look at one sheet.
6) Look at other sheet.