Fig. 3: Motions in M during MD simulations.
From: Pathogenic mutation impairs functional dynamics of Hsp60 in mono- and oligomeric states
a Projection of MD metatrajectories of MWT (top; blue) and MV72I (bottom; orange) onto the principal components PC1 and PC2 derived from MD metatrajectories of MWT (left panels) and MV72I (right panels). b Structural variables best describing the main collective motions and reactivity of M, marked on its starting structure with their respective values (atoms defining these are reported in the main text). Green: angle γ (apical domain opening in PC1); blue: dihedral χ (apical domain counterclockwise rotation in PC2); red: distance δ between catalytically relevant aspartates. Moreover, the secondary structures involved have been highlighted in black. c Distribution of δ and γ across MD metatrajectories of MWT (top; blue) and MV72I (bottom; orange). In panels (a) and (c), round dots represent values of plotted quantities in the CryoEM structure of S (M); square dots values in the structure of D; triangular dots values in the structure of F. Colour intensity is proportional to the probability density function, which is directly proportional to the number of MD frames with a given set of values. On the bars in (c), the relative free energy value for the ith contour in kcal mol–1, ∆Gi, is obtained from its probability density, Ρi, using the formula ∆Gi = –kBT ln(ρi / ρ0).
