Unraveling membrane protein localization and stabilization in nanodiscs

Nanodiscs are nanoscale structures consisting of a lipid bilayer surrounded by membrane scaffold proteins (MSPs). They are widely used in the study of membrane proteins (MPs) because they provide a stable lipid environment. However, the precise mechanism governing MP behavior within the nanodisc remains elusive. Here, we examined the cryo-EM structures of various MPs reconstituted in nanodiscs from an electron microscopy database (EMPIAR). By analyzing the heterogeneity and interactions in the nanodiscs, we found that MPs within nanodiscs display a distinct spatial preference toward the edges of the nanodisc shells. Furthermore, we observed that MPs can establish direct, amphipathic interactions with the MSPs, promoting protein stability. These interactions may induce a rearrangement of the MSP-MSP interactions, leading to the formation of MP-MSP interactions Collectively, our study provides structural and biophysical insights into how nanodiscs contribute to MP structural behavior and stability. SIGNIFICANCEBy thoroughly examining multiple deposited datasets of membrane proteins (MPs) reconstituted in nanodiscs, we have gathered compelling evidence that MPs exhibit a clear spatial inclination toward the periphery of the nanodisc shells. Moreover, we have observed that MPs establish direct and amphipathic interactions with membrane scaffold proteins (MSPs). These interactions have the potential to induce a rearrangement of the MSP-MSP interactions, consequently forming MP-MSP interactions. Through quantitative analysis, we have successfully characterized the significant role played by these interactions in ensuring the overall stability of the proteins.