Nanodiscs are membrane mimetics that consist of a protein belt surrounding a lipid bilayer, and are broadly used for characterization of membrane proteins. Here, we investigate the structure, dynamics and biophysical properties of two small nanodiscs, MSP1D1ΔH5 and ΔH4H5. We combine our SAXS and SANS experiments with molecular dynamics simulations and previously obtained NMR and EPR data to derive and validate a conformational ensemble that represents the structure and dynamics of the nanodisc. We find that it displays conformational heterogeneity with various elliptical shapes, and with substantial differences in lipid ordering in the centre and rim of the discs. Together, our results reconcile previous apparently conflicting observations about the shape of nanodiscs, and paves the way for future integrative studies of larger complex systems such as membrane proteins embedded in nanodiscs.

Nanodiscs are membrane mimetics that consist of a protein belt surrounding a lipid bilayer. Nanodiscs are of broad use for solutionbased characterization of membrane proteins, but we lack a full understanding of their structure and dynamics. Recently, NMR/EPR experiments provided a view of the average structure of the nanodisc's protein component, while small-angle X-ray and neutron scattering have provided insight into the global structure of both protein and lipids. Here, we investigate the structure, dynamics and biophysical properties of two small nanodiscs, MSP1D1∆H5 and ∆H4H5. We combine SEC-SAXS and SEC-SANS to obtain low-resolution structures of the nanodiscs as elliptical discs. These are in apparent contrast to the NMR/EPR structure, which showed a more circular conformation. We reconcile these views using a Bayesian/Maximum Entropy method to combine our molecular dynamics simulations of MSP1D1∆H5 with the NMR and SAXS experiments. We derive a conformational ensemble that represents the structure and dynamics of the nanodisc, and find that it displays conformational heterogeneity with various elliptical shapes. We find substantial differences in lipid ordering in the centre and rim of the discs, and support these observations using differential scanning calorimetry of nanodiscs of various sizes. We find that the order and phase transition of the lipids is highly dependent on the nanodisc size. Together, our results demonstrate the power of integrative modelling and paves the way for future studies of larger complex systems such as membrane proteins embedded in nanodiscs.

No abstract

No abstract