Simulation and modelling of the detergent corona around the membrane protein MhsT based on SAXS data

Abstract

For membrane proteins, ab initio modelling based on a single curve of small-angle X-ray scattering (SAXS) is precluded by the presence of detergent molecules bound to the hydrophobic region of the protein. MEMPROT was developed for the modelling of protein–detergent complexes based on the SAXS curve of the complex, and on an a priori representation of the detergent corona by an elliptical semi-torus surrounding the protein. In previous studies, MEMPROT has succeeded in modelling several membrane proteins solubilized in n-dodecyl-β-maltopyranoside (DDM). However, it has never been tested on proteins solubilized in other detergents. To understand whether the geometrical shape currently parametrized in MEMPROT could be applied to a broader catalogue of protein–detergent complexes, here, MEMPROT was used to model the detergent corona around the multi-hydrophobic substrate transporter from Bacillus halodurans solubilized in four different detergents, namely DDM, n-decyl-β-maltopyranoside (DM), 4-cyclohexyl-1-butyl-β-d-maltoside (Cymal4) and decyl-maltose-neopentyl-glycol (DMNG). The study indicates a significant variation in detergent shapes, depending on the type of detergent. The modelling results suggest that the elliptical semi-torus with a circular closure is an excellent approximation for long-tailed detergents (DDM and DM) but leads to a slightly poorer agreement with the data for DMNG and Cymal4, which have a shorter hydrophobic tail, smaller than the half-width of the protein hydrophobic region. Here, for the latter, it is hypothesized that a corona with a flatter closure would be a better shape descriptor.