Solution structure of a 142-residue recombinant prion protein corresponding to the infectious fragment of the scrapie isoform - PubMed (original) (raw)

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 β-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 β-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.