Molecular dynamics simulations of cytochrome c unfolding in AOT reverse micelles: The first steps

Abstract

2This paper explores the reduced form of horse cytochrome c confined in reverse micelles (RM) of sodium bis-(2-ethylhexyl) sulfosuccinate (AOT) in isooctane by molecular dynamics simulation. RMs of two sizes were constructed at a water content of W o = [H 2 O]/[AOT] = 5.5 and 9.1. Our results show that the protein secondary structure and the heme conformation both depend on micellar hydration. At low hydration, the protein structure and the heme moiety remain stable, whereas at high water content the protein becomes unstable and starts to unfold. At W o = 9.1, according to the X-ray structure, conformational changes are mainly localized on protein loops and around the heme moiety, where we observe a partial opening of the heme crevice. These findings suggest that within our time window (10 ns), the structural changes observed at the heme level are the first steps of the protein denaturation process, previously described experimentally in micellar solutions. In addition, a specific binding of AOT molecules to a few lysine residues of the protein was found only in the small-sized RM.3

The Size of AOT Reverse Micelles

“…These systems were included in this study because of previously published on a system of this size. 25 However, their anomalous shape (Figure 2, lower panel) suggests that they are unstable for reasons not reflected in the AOT energy. Fission into smaller systems appears imminent, and this behavior was not observed for any of the smaller systems.…”

“…These water/AOT clusters were placed in the center of a truncated octahedron of sufficient size to contain 2536 molecules of isoO (n ISO ) – a number chosen so that the isoO mass was 83% of the total system mass for the largest RM and thus, within the RM-forming portion of the AOT/water/isoO phase diagram. 25 Compositions of systems are listed in Table 1.…”

“…13,23 Indeed, RM simulations of W 0 = 7.5 have been recently described with as few as 70 AOT molecules per RM, 24 ( n AOT ) and as many as 106. 25 Moreover, the question is a general one, with similar questions arising in studies of reverse micelles made with cetyltrimethylammonium bromide and other surfactants. 14,26 In the case of AOT, One approach to answering the question of RM size via simulation has been to allow RMs to self-assemble from randomly distributed components.…”

Simulations of the confinement of ubiquitin in self-assembled reverse micelles

“…29 Experiments in RM are conducted with different solvents. 14,17,18 However, to maintain consistency in the force field and with previous simulations, 26,29,32,33 we use iso-octane as the organic solvent. Simulations are conducted with the parallel molecular dynamics program NAMD.…”

Conformational Dynamics and Stability Associated with Magnesium or Calcium Binding to DREAM in the Regulation of Interactions between DREAM and DNA or Presenilins

“…The structural properties of encapsulated proteins depend on the water pool size, surfactant charge and interactions between protein and surfactant (Van Horn et al, 2005;Van Horn et al, 2009;Naoe et al, 2004). For example, it has been shown that encapsulation of cytochrome c in AOT RM is associated with a structural destabilization, opening of the heme crevice and dissociation of the Met-80 heme axial ligand (Abel et al, 2010;Brochette et al, 1988). To investigate the conformational dynamics in restricted environment of RM, I have used PAC and transient absorption to characterize the kinetics and thermodynamics associated with CO binding/releasing from horse heart Mb and from microperoxidase-11 (MP-11).…”