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Figure 2.
Fig. 2. NMR structure of SHa rPrP(90-231). (A) Comparison of
the 15 best-scoring structures of rPrP shown with a best-fit
superposition of backbone atoms for residues 113-227
(stereoview). In all figures except C, the color scheme is:
disulfide between Cys179 and Cys214, yellow; sites of
glycosidation in PrPC, i.e., Asn181 and Asn197, gold;
hydrophobic cluster composed of residues 113-126, red; helices,
pink; loops, gray; residues 129-134, green, encompassing strand
S1 and residues 159-165, blue, encompassing strand S2; the
arrows span residues 129-131 and 161-163, as these show a^
closer resemblance to  -sheet. The
structures were generated with the program DIANA (30), followed
by energy minimization with AMBER 4.1 (31). Structure generation
parameters are as follows: 2,401 distance restraints
(intraresidue, 858; sequential (i  i +1), 753;
(i i +2), 195;
(i i +3), 233;
(i i +4), 109;
and (i i +  5), 253 for
amino acid i); hydrogen bond restraints, 44; distance restraint
violations >0.5 Å per structure, 30; AMBER energy,  1,443
± 111 kcal/mol. Precision of structures: atomic^ rms
deviation for all backbone heavy atoms of residues 128-227, <1.9
Å. The distance restraint violations and precision in
some^ molecular moities reflect the conformational heterogeneity
of^ rPrP. (B) Residues 113-132 illustrating (stereoview) in one
representative^ structure the interaction of the hydrophobic
cluster, with van der Waals rendering of atoms in residues
113-127, with the first -strand. (C)
Van der Waals surface of rPrP turned approximately 180° from
A, illustrating the interaction of helix A with helix C. Helices
A, B, and C are colored magenta, cyan, and gold, respectively.
(D) Stereoview, using RIBBONJR, illustrating the proximity of^
helix C to the 165-171 loop and the end of helix B, where
residues Gln168 and Gln172 are depicted with a low-density van
der Waals rendering and helix C residues Thr215 and Gln219 are
depicted with a high-density van der Waals rendering. (E)
Stereoview, highlighting in white the residues corresponding to
point mutations that lead to human prion diseases. Illustrations
were generated with MIDASPLUS. (F) Portion of the
three-dimensional 13C-NOESY spectrum corresponding to 13C planes
of the unresolved Val166 methyl resonances and the Ser222
resonances (a-d) and the 15N plane showing the Tyr225 amide
interaction with Val166 (e). The diagonal peaks and mirrored
crosspeaks for each 1H-1H connectivity are shown. The solid
lines connecting peaks designate^ NOE connectivities.
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