Fig. 6

Molecular dynamics simulations of SiaT. a Heavy-atom RMSD of the substrate with respect to the X-ray structure for four MD simulations with different combinations of Na⁺ ions in the Na2 and Na3 sites (see legend, upper right). Snapshots compare the instantaneous configuration of Neu5Ac, Arg135, Na2 (when present), and unwound residues in Tm1 (Thr58, Leu59 and Ser60) with the X-ray structure (ghost). Solid lines are smoothed over an 800 ps window, while the original full data set saved every 40 ps is transparent. b–e Dependence of Leu59 backbone motion on Na⁺ ion occupancy. ϕ and ψ angles for Leu59 from all four simulations with Neu5Ac bound and different combinations of Na⁺ ions in the Na2 and Na3 sites. Both Na2 and Na3 bound (b), Na2 bound only (c), Na3 bound only (d) and no ions bound (e). In each panel, the instantaneous angle pairs are plotted every 40 ps over the entire 200 ns simulation (light blue), and the data set is contoured at values of 100 (black), 50 (red) and 10 (yellow). The ϕ and ψ values in the X-ray structure are represented as a black dot. The distributions in panels d and e, which lack an ion in the Na2 site, are so broad that the black high-density contour does not exist. f, g Ion stability in the Na2 and Na3 sites. Simultaneous distance of bound Na⁺ ions to the Na2 site and the Na3 site from 200 ns MD simulations in the presence or absence of Neu5Ac with both Na⁺ ions bound (f), only the Na2 ion bound (g) and only the Na3 ion bound (h). In all panels, every point represents a simulation frame saved every 40 ps, the Na2 ion position is blue (with substrate) or green (without substrate), and the Na3 ion position is red (with Neu5Ac) or yellow (without Neu5Ac)