Figure 4.

Structures obtained for SB056 (a–c) and (d–f) βSB056 in a dispersion of mixed dodecylphosphocholine (DPC)/sodium dodecyl sulphate (SDS) 3:1. These two detergents are synergistic and form mixed micelles, with the selected molar ratio being typically employed to mimic a bacterial plasma membrane [11]. First, a computer-simulated annealing was applied in a vacuum (a,d) with the distance restraints derived from experimental NOEs (cross peaks from Nuclear Overhauser Effect spectroscopy). Then, an equilibrium molecular dynamics (MD) simulation was run with the same restraints and in the presence of explicit water and detergent molecules. The last frame after 100 ns is shown in (b,e). Finally, a second 100-ns MD run was performed after releasing all restraints, and the last frame is shown in (c,f). The backbone of the α-and ε-branch is represented with a differently coloured trace, green and purple, respectively. The atoms of the detergents are represented with the corresponding van der Waals spheres. DPC and SDS are coloured in cyan and orange, respectively. From [30]. Reproduced with permission.