Garcia Research Group

Encapsulation of Proteins Inside AOT Reverse Micelles

Figure 1. Schematic picture of the positioning of ubiquitin inside a reverse micelle (left). At the center we show the AOT headgroups at the RM interface. At right we show the water an protein content of the RM-protein system. Ubiquitin binds to the RM through its hydrophobic patch (indicated by green amino acids), which is in turn surrounded by positively charged amino acids (in red). Negatively charged amino acids are colored in blue, and water is gray
Figure 2. Animation showing the self-assembly of the RM containing the protein (ubiquitin). The figure shows water molecules, ubiquitin and AOT surfactant molecules. For clarity, the isooctane co-solvent is not shown, but it is the largest component of the system. Other RM are also formed during the simulations

We study the structure and dynamics of proteins and peptides encapsulated in reverse micelles (RM). The highly electrostricted environment of the RM interior is treated as a model of the crowded cell environment. In these studies we performed extensive MD simulations in order to understand the nature of the interactions of the protein with RMs, the location of the protein inside RM under various salt conditions, and to identify the source of the altered protein dynamics in the confined environment. The reverse micelles are self assembled in presence of the folded protein, and the dynamics and hydration of the protein are compared with the corresponding protein in bulk water. We have performed studied of the encapsulation of alpha helices [Tian and Garcia, BJ 2009] and ubiquitin. Here we briefly describe our results for ubiquitin. It is found that the protein in the RM is partially dehydrated relative to bulk conditions. We find that the protein dynamics are similar in both environments, and differences are restricted to specific regions of the protein. Interestingly, we found that the protein prefers to be close to the RM interface at low excess salt and for an idealized neutral head group RM. However, at high excess salt, the protein prefers the water phase of the RM. This result is consistent with free-energy calculations of the position of ubiquitin relative to the center of mass of the RM calculated using the adaptive biasing force algorithm [Henin et al., JCP (2004)]. In unbiased simulations it is found that ubiquitin binds to the AOT surfactants through the hydrophobic patch formed by amino acid chains Leu 8, Ile 44 and Val 70, and which is the same patch region that interacts with ubiquitin-binding-domains in-vivo. In turn, this hydrophobic patch is surrounded by positively charged amino acids Lys 6, Arg 42, Lys 48, His 68, Arg 72 and Arg 74. The positioning of ubiquitin inside a RM is found to be closely related to the behavior of water in the RM environment. Participants: Jianhui Tian and Angel E Garcia

Selected Publications:

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