Ab initio reconstruction of small angle scattering data for membrane proteins in copolymer nanodiscs

Kerrie A Morrison; Aswin Doekhie; George M Neville; Gareth J Price; Paul Whitley; James Doutch; Karen J Edler

doi:10.1016/j.bbadva.2021.100033

Ab initio reconstruction of small angle scattering data for membrane proteins in copolymer nanodiscs

BBA Adv. 2021 Dec 16:2:100033. doi: 10.1016/j.bbadva.2021.100033. eCollection 2022.

Authors

Kerrie A Morrison^{1

2

3}, Aswin Doekhie¹, George M Neville^{1

3}, Gareth J Price^{1

4}, Paul Whitley², James Doutch⁵, Karen J Edler¹

Affiliations

¹ Department of Chemistry, University of Bath, Bath, UK.
² Department of Biology and Biochemistry, University of Bath, Bath, UK.
³ Centre for Sustainable and Circular Technologies, University of Bath, Bath, UK.
⁴ Department of Chemistry, Khalifa University, Abu Dhabi, UAE.
⁵ ISIS Pulsed Neutron and Muon Source, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0QX. UK.

Abstract

Background: Small angle scattering techniques are beginning to be more widely utilised for structural analysis of biological systems. However, applying these techniques to study membrane proteins still remains problematic, due to sample preparation requirements and analysis of the resulting data. The development of styrene-maleic acid co-polymers (SMA) to extract membrane proteins into nanodiscs for further study provides a suitable environment for structural analysis.

Methods: We use small angle neutron scattering (SANS) with three different contrasts to determine structural information for two different polymer nanodisc-incorporated proteins, Outer membrane protein F (OmpF) and gramicidin. Ab initio modelling was applied to generate protein/lipid structures from the SANS data. Other complementary structural methodologies, such as DLS, CD and TEM were compared alongside this data with known protein crystal structures.

Results: A single-phase model was constructed for gramicidin-containing nanodiscs, which showed dimer formation in the centre of the nanodisc. For OmpF-nanodiscs we were able to construct a multi-phase model, providing structural information on the protein/lipid and polymer components of the sample.

Conclusions: Polymer-nanodiscs can provide a suitable platform to investigate certain membrane proteins using SANS, alongside other structural methodologies. However, differences between the published crystal structure and OmpF-nanodiscs were observed, suggesting the nanodisc structure could be altering the folding of the protein.

General significance: Small angle scattering techniques can provide structural information on the protein and polymer nanodisc without requiring crystallisation of the protein. Additional complementary techniques, such as ab initio modelling, can generate alternative models both the protein and nanodisc system.

Keywords: Ab initio; MONSA; Nanodisc; Outer membrane protein F; SMALP; Small angle neutron scattering.