a, Top, cartesian coordinates root mean square deviation (r.m.s.d.) of Q367 relative to the original crystal structure using one of the partly occupied positions as reference. Bottom, difference of distances between a bridging water and the E165 and E165′ residues. The moving average over 10 ps is shown in red. From both graphics, it can be seen that the water oscillates through the symmetry axis. There is a large movement of Q367 between approximately 4.0 ns and 10.2 ns, during which it builds a hydrogen bond to another water molecule, deactivating the bridge. However, Q367 later returns to its original position. b, Density-based spatial clustering of applications with noise (DBSCAN) analysis of the trajectory, using the two quantities as descriptors for the times 0–4.0 ns and 10.2–16.5 ns. The method finds two clusters, pairing the distance difference around 1 Å to a 2.5 Å r.m.s.d., as well as −1 Å to a 1.0 r.m.s.d. approximately. The latter positions correspond to the partially occupied sites found in the crystal, thus confirming the oscillation. The oscillation takes place in the nanosecond regime, much faster than the reaction time of the catalysis. This observation confirms that a shuttling water could be involved in the proton wire. c, Proton positions for the human transketolase proton wire. The dependence of the structural features on an added proton and water molecule next to E165′ (controlled by the variable λ) are demonstrated, considering two different sampled conformations (top and bottom). Left, the dependence of the glutamate proton distances on λ (the blue area highlights the distance range for LBHBs, of around 1.3 Å); right, ball-and-stick representations of the QM/MM optimised structures at λ = 0 and 1. The hydrogens are shown as green balls and are labelled, from left to right, H1, H2 and H3.