Structure and dynamics of a nanodisc by integrating NMR, SAXS and SANS experiments with molecular dynamics simulations

Abstract

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.

Nanodiscs: A toolkit for membrane protein science

“…This observation is in a good agreement with multiple MD simulations of Nanodiscs, starting from our first publication with only 6 ns long trajectories 36 . Subsequently, a variety of Nanodiscs of different sizes were explored both with all‐atom and coarse‐grain modeling, providing a consistent picture of the dynamic bilayer surrounded by two helical belts having distorted circular or elliptical structures 34,89,103,104 . Direct contact with the scaffold protein usually resulted in more disordered and dynamically constrained lipids at the lipid‐protein interface.…”

“…This phase transition can also be monitored by SAXS where the mean area per head group and packing is quantitated 88 . More recent works have also monitored the phase transition and separated the contributions from the central lipid core and those juxtaposed to the MSP belt 89 . Here the core domain has properties similar to those measured for liposomes with 1–2 layers of more perturbed lipids due to their direct interactions with the scaffold protein.…”

“…Here the core domain has properties similar to those measured for liposomes with 1–2 layers of more perturbed lipids due to their direct interactions with the scaffold protein. Recent DSC of the very small DMPC Nanodiscs 89 suggests a significantly perturbed bilayer. Long‐time molecular dynamics studies contributed to a picture of fluctuations of the scaffold protein and internal motion of the Nanodisc 34,90 .…”

Combining Experimental Data and Computational Methods for the Non-Computer Specialist

“…Even though SAXS and SANS share similar principles, neutrons have different scatter properties and therefore can provide complementary information. For instance, it has been shown that the combined use of SAXS and SANS can help in the interpretation of the data [ 69 , 70 ].…”

DEER-PREdict: Software for Efficient Calculation of Spin-Labeling EPR and NMR Data from Conformational Ensembles

“…We present our implementation, distributed as the DEER-PREdict software, and test it against experimental data on HIV-1 Protease, T4 Lysozyme and the Acyl-CoA-Binding Protein. This software has been previously used for the calculation of both intra- and intermolecular DEER and PRE NMR data [28, 29], and has some overlap with the features in RotamerConvolveMD [25] (github.com/MDAnalysis/RotamerConvolveMD). DEER-PREdict is open-source, documented (deerpredict.readthedocs.io) and open to contributions from the community.…”