Structure and Dynamics of Glycosphingolipids in Lipid Bilayers: Insights from Molecular Dynamics Simulations
Figure 3
Surface (a) and ribbon + stick (b) rendering of the cholera toxin-GM1 complex, viewed either along (a) or perpendicular (b) to the molecular 5-fold axis (PDB id 3CHB). Surface renderings (panels (c), (d), and (e)) and stick diagram (panel (f)) of GM1 embedded in a DPPC bilayer taken from MD simulations starting with conformation B (panel (c); at 4 ns), G (panel (d); at 10 ns), or C (panels (e) and (f); at 4 ns) [20]. In the snapshots shown in panels (c), (d), and (e)/(f), the SASA of NeuAc3 is comparable to each other and is within the range 182–200 Å2. However, there is a marked difference in the exposure of Gal5, and its SASA varies widely: 101 Å2 (panel (c)), 14 Å2 (panel (d)) and 151 Å2 (panels (e)/(f)). Color code: Glc1, yellow; Gal2, red; NeuAc3, cyan; GalNAc4, magenta; Gal5, green; Ceramide, orange; cholera toxin/DPPC, grey. The molecules were rendered using VMD [35].
