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Destabilizing polymorphism in cervid prion protein hydrophobic core determines prion conformation and conversion efficiency

Fig 7

Molecular dynamics simulations.

Comparison of wt and 116G PrP via MD simulations. (a) Cartoon representation of wild type PrP (residues 112 to 233): red spheres represent alanine in position 116. H1, H2 and H3 stand for helix one, two, and three, respectively. S1 and S2 stand for β-strands one and two. (b) Cartoon representation of 116G PrP: red spheres represent glycine in position 116. (c) RMSD plot for the folded domains of both wt (blue) and 116G polymorphism (red). (d) RMSF plot comparing wt (blue) and 116G polymorphism (red). The location of the polymorphism at residue 116 is shown with a black line and a label. The yellow and blue bars highlight the location of individual β-strands and α-helices, respectively. Both graphs show the average of three rounds (R1, R2, R3) of simulation. (e) Radius of gyration (Rg) values for both wt (blue) and the 116G polymorphism (red) as a function of simulation time. Both graphs are the average of three rounds (R1, R2, R3) of simulation. (f) Per-residue percentage of dominant secondary structure for the last 20 ns of production simulation. The blue and red graphs represent wt and the 116G polymorphism, respectively. The location of known secondary structure elements are shown using yellow and blue bars (top), on the crystal structure of deer prion protein (PDB ID: 4yxh [66]. (g) Solvent accessible surface area for both 116G PrP and wt PrP. (h) Hydrophobic surface area for both 116G and wt. (g) and (h) both show the average of three rounds (R1, R2, R3) of simulation and the dashed lines represent the linear fit for the solvent accessible surface area and the hydrophobic surface area values, respectively.

Fig 7