Interpretation of solution scattering data from lipid nanodiscs.

Vito Graziano,Lisa Miller,Lin Yang

doi:10.1107/s1600576717018441

Vito Graziano, Lisa Miller + Show 1 more

Open Access

https://doi.org/10.1107/s1600576717018441

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Abstract

The structural information contained in solution scattering data from empty lipid nanodiscs is examined in the context of a multi-component geometric model. X-ray scattering data were collected on nanodiscs of different compositions at scattering vector magnitudes up to 2.0 Å-1. Through the calculation of the partial form factor for each of the nanodisc components before the isotropic average, structural parameters in the model were correlated to the features observed in the X-ray scattering data and to the corresponding distance distribution function. It is shown that, in general, the features at ∼0.3-0.6 Å-1 in the scattering data correlate to the bilayer structure. The data also support the argument that the elliptical shape of nanodiscs found in model fitting is physical, rather than an artefact due to the nanodisc size distribution. The lipid chain packing peak at ∼1.5 Å-1 is visible in the data and reflects the lipid bilayer phase transition. The shape change in the distance distribution function across the phase transition suggests that the nanodiscs are more circular in the fluid phase. The implication of these findings for model fitting of empty and protein-loaded nanodiscs is discussed.

Highlights

Structural studies of membrane proteins are challenging because biophysical and biochemical characterization tools generally require homogenous solution samples
Detergents can complicate the accurate measurement of small-angle X-ray scattering (SAXS) data from solubilized proteins, where the background scattering from the buffer and free detergent micelles must be subtracted before data analysis can proceed
It is well documented that the composition of the lipid–membrane scaffold proteins (MSPs) mixture used for self-assembly is critical for obtaining nanodiscs of uniform size, with non-ideal stoichiometry leading to multiple structural species (Denisov et al, 2004)

Summary

Introduction

Structural studies of membrane proteins are challenging because biophysical and biochemical characterization tools generally require homogenous solution samples. Detergents can complicate the accurate measurement of small-angle X-ray scattering (SAXS) data from solubilized proteins, where the background scattering from the buffer and free detergent micelles must be subtracted before data analysis can proceed. Whether this subtraction is even possible in a three-component system composed of protein– detergent complexes, free micelles and aqueous buffer depends strongly upon the type of detergent (e.g. as discussed on the web site of the SIBYLS beamline at the Advanced Light Source, Berkeley, California, USA; https:// bl1231.als.lbl.gov/). The purpose of this study is to critically evaluate the potential of using solution scattering to determine the low-resolution structures of membrane proteins embedded in lipid nanodiscs

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