PT  - JOURNAL ARTICLE
AU  - Tone Bengtsen
AU  - Viktor L. Holm
AU  - Søren R. Midtgaard
AU  - Nicolai Tidemand Johansen
AU  - Sandro Bottaro
AU  - Lise Arleth
AU  - Kresten Lindorff-Larsen
TI  - Structure and dynamics of a lipid nanodisc by integrating NMR, SAXS and SANS experiments with molecular dynamics simulations
AID  - 10.1101/734822
DP  - 2019 Jan 01
TA  - bioRxiv
PG  - 734822
4099  - http://biorxiv.org/content/early/2019/08/13/734822.short
4100  - http://biorxiv.org/content/early/2019/08/13/734822.full
AB  - Nanodiscs are membrane mimetics that consist of a protein belt surrounding a small lipid bilayer. Nanodiscs are of broad use for solution-based characterization of membrane proteins, but we still lack a full understanding of their structure and dynamics. Recently, NMR and EPR experiments provided a view of the average structure of the nanodisc’s protein component, and small-angle X-ray and neutron scattering experiments have provided insight into the global structural properties of both protein and lipids. Here, we investigate the structure, dynamics and biophysical properties of two small nanodiscs, MSP1D1ΔH5 and ΔH4H5. We use differential scanning calorimetry to compare the melting transition of DMPC in nanodiscs of different sizes with DMPC vesicles, and find that the ordering of the lipids is highly dependent on the nanodisc size. Using combined SEC-SAXS and SEC-SANS experiments, we obtain low-resolution structures of the nanodiscs and find that these have the shape of elliptical discs. These structures are in apparent contrast to the NMR/EPR structure, which showed a more circular conformation. We reconcile these views by using a Bayesian/Maximum Entropy method to combine molecular dynamics simulations of MSP1D1ΔH5 with the NMR and SAXS experiments. We derive a conformational ensemble representing the structure and dynamics of the nanodisc, and find that it displays conformational heterogeneity with various elliptical shapes that explain both the SAXS and NMR data. 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.