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birefringence in polarized light in the latter case; that have a high
content of
arrangement, where the hydrogen
bonds between two consecutive sheets are oriented parallel to
the main fibril axis while the constituting
β
-structures in a cross-
β
β
-strands are oriented
50,51
transversely to the main fibril axis.
This type of strongly
hydrogen-bonded structure (Fig. 6.3) that absorbs specifically
infrared light between 1618 and 1623 cm
−1
52
gives rise to a
characteristic pattern of reflections in X-ray diffraction experiments.
This pattern consists of a conserved 4.6 to 4.8 Å meridional spacing
and an equatorial spacing of approximately 10 Å (Fig. 6.3). The 4.6
to 4.8 Å reflection comes from the distance between two hydrogen-
bonded strands, and is invariant as it depends on the geometry of the
polypeptide backbone. It is referred to as the “main chain spacing”.
The equatorial reflection at approximately 10 Å comes from the
packing distance between two juxtaposed
,
53,54
This dis-
tance can vary with the amino acid composition of the polypeptide as
it depends on the orthogonal protrusion of the amino acid side chains
from the plane of the sheet. It is worth noting that this reflection is
not observed when the intersheet spacing is not regular.
Finally, as the sheets forming the backbone of the fibrils are
systematically hydrogen bonded (Fig. 6.3) and are poorly exposed
to the solvent, the backbone amide hydrogen atoms within amyloid
fibrils are extremely resistant to hydrogen/deuterium exchange.
β
-sheets.
55-62
While full-length Ure2p fibrils have been extensively chara-
cterized structurally, full-length Sup35p fibrils have not. The
following section will therefore develop what we learned from the
structural characterization of fibrillar Ure2p without precluding
what a thorough structural characterization of full-length Sup35p
fibrils might reveal. As indicated above, fibrillar Ure2p has
increased resistance to limited proteolytic treatments; however, the
degradation patterns of the soluble and fibrillar forms of the protein
are very similar,
32,63
suggesting that the assembly of Ure2p into
protein fibrils is not accompanied by a major conformational change.
The absence of conformational changes within the compactly folded
helical C-terminal domain of Ure2p upon assembly, of full-length
Ure2p into fibrils, is further supported by the finding that the protein
binds glutathione,
36
37
and exhibits glutathione perroxidase activity
within the fibrils as does the native, soluble form.
-sheet content of
macromolecular assemblies further suggest that Ure2p fibrils are
Two methods ideally suited for analyzing the
β
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