Molecular models of nanodiscs

Nanodiscs are discoloidal protein-lipid particles that self-assemble from a mixture of lipids and membrane scaffold proteins. They form a highly soluble membrane mimetic that closely resembles a native-like lipid environment, unlike micelles. Nanodiscs are widely used for experimental studies of membrane proteins. In this work, we present a new method for building arbitrary nanodiscs using a combination of the Martini coarse-grained and all-atom force fields. We model the basic membrane scaffold protein MSP1 and its extended versions, such as MSP1E1 and MSP1E2, using a crystal structure of human apolipoprotein Apo-I. We test our method by generating nanodiscs of different sizes and compositions, including nanodiscs with embedded membrane proteins, such as bacteriorhodopsin, outer membrane protein X, and the glucose transporter. We show that properties of our nanodiscs are in general agreement with experimental data and previous computational studies.