Extended Data Fig. 5: Behaviour of BD NTD interface residues in MD simulations.

a, Conformational changes between the NTD dimers seen after 300 ns at pH 5.5 (right panel) but not at pH 8.0 (left panel). b, Downward motion of the H208 side chain is seen in one run at pH 5.5 (red ellipsoid in right panel), approaching the x-ray reference structure (red sticks). This is not the case at pH 8.0 (blue ellipsoid in left panel). Position of the F231 residue is unchanged under both conditions. c, Residue interaction plots, showing standard deviations (STD; side bars) in pairwise residue distances. Top row: standard simulation, pH 5.5 left panel, pH 8.0 right panel. Bottom row: ‘switched protonation’ that is H208 is deprotonated in the pH 5.5 column and protonated in the pH 8.0 column. Boxed regions show changes in residue interactions (STDs) that are strongest between the H208 residues (QTH; red box) but are also seen between F231 (KF) and T204/H208 (QTH; right cyan box). This is not seen at pH 8.0 and is partly reversed in the ‘switched protonation’ panels. d, Interaction plots showing average encounter times between interface residues. Conditions were as described in the above panel c (see Methods for further details).