Fig. 3: Thermal parameter (B-factor) distribution in human PrP.
From: Structural effects of the highly protective V127 polymorphism on human prion protein
(a) V127/M129 PrP (b) G127/M129 PrP shown as “putty” representation, as implemented by PyMOL. The V127/M129 PrP Cα atom B-factors range from 22.7 Å2 to 96.9 Å2 with average values of 38.3 Å2 for the whole protein, and 30.4 Å2 for the core secondary structure elements (residues 128–131 (β-strand 1), 144–154 (α-helix 1), 160–164 (β-strand 2), 174–186 (α-helix 2) and 202–220 (α-helix 3)). The Cα B-factors are depicted on the structure in dark blue (lowest B-factor) through to red (highest B-factor), with the radius of the ribbon increasing from low to high B-factor. The lowest B-factor is observed in the region of α-helix 2 (α2) and α-helix 3 (α3) where the disulphide bridge links the two α-helices at residues 179 and 214 (dark blue), with the antibody-binding epitope spanning α-helix 1 also displaying lower than average B-factors, consistent with the antibody contacts stabilising this region of PrP relative to the overall structure. The largest B-factors are observed in the loop region linking helices α2 and α3 (red) (α2- α3 loop; residues 191–199), where the electron density clearly shows more disorder than elsewhere in the structure. In contrast, the B-factors for residues in close proximity to the V127 polymorphism are not unusually high, and all of these residues are clearly observed in the electron density (see also Fig. 2).
