Deciphering the Structure of the Gramicidin A Channel in the Presence of AOT Reverse Micelles in Pentane Using...

Structural studies of proteins and, in particular, integral membrane proteins (IMPs) using solution NMR spectroscopy approaches are challenging due to not only their inherent structural complexities but also the fact that they need to be solubilized in biomimetic environments (such as micelles), which enhances the slow molecular reorientation. To deal with these difficulties and increase the effective rate of molecular reorientation, the encapsulation of IMPs in the aqueous core of the reverse micelle (RM) dissolved in a low-viscosity solvent has been proven to be a viable approach. However, the effect of the reverse micelle (RM) environment on the IMP structure and function is little known. To gain insight into these aspects, this article presents a series of atomistic unconstrained molecular dynamics (MD) of a model ion channel (gramicidin A, gA) with RMs formed with anionic surfactant diacyl chain bis(2-ethylhexyl) sodium succinate (AOT) in pentane at a water-to-surfactant molar ratio (W₀) of 6. The simulations were carried out with different protocols and starting conditions for a total of 2.4 μs and were compared with other MDs used with the gA channel inserted in models of the SDS micelle or the DMPC membrane. We show here that in the presence of AOT RMs the gA dimer did not look like the "dumbbell-like" model anticipated by experiments, where the C-terminal parts of the gA are capped with two RMs and the rest of the dimer is protected from the oil solvent by the AOT acyl chains. In contrast, the MD simulations reveal that the AOT, Na⁺, and water formed two well-defined and elongated RMs attached to the C-terminal ends of the gA dimer, while the rest is in direct contact with the pentane. The initial β^6.3 secondary structure of the gA is well conserved and filled with 6-9 waters, as in SDS micelles or the DMPC membrane. Finally, the water movement inside the gA is strongly affected by the presence of RMs at each extremity, and no passage of water molecules through the gA channel is observed even after a long simulation period, whereas the opposite was found for gA in SDS and DMPC.