Deciphering the Structure of the Gramicidin A Channel in the Presence of AOT Reverse Micelles in Pentane Using Molecular Dynamics Simulations

Abstract

Structural studies of proteins and in particular integral membrane proteins (IMPs) using solution NMR spectroscopy approaches is challenging due not only to their inherent structural complexities, but also to 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, encapsulation of the IMPs in the aqueous core of the reverse micelle (RM) dissolved in a low viscosity solvent has been proved to be a viable approach. However, the effect of the reverse micelle (RM) environment on the IMPs structure and function is little known. To gain insights into these aspects, this paper presents a series of atomistic unconstrained molecular dynamics (MD) of a model ion channel (gramicidin A, gA) with RMs formed with the anionic surfactant di-acyl 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 and for a total of 2.4 µs and were compared with other MDs performed with the gA channel inserted in models of SDS micelle or DMPC membrane. We show here that in presence of AOT RMs, the gA dimer did not look like the "dumbbell-like" model anticipated by experiments, where the C-term parts of the gA are capped with two RMs and the rest of the dimer 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-term 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 micelle or DMPC membrane. Finally, the water movements 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.