Nanodiscs are binary discoidal complexes of a phospholipid bilayer
circumscribed by belt-like helical scaffold proteins. Using coarse-grained and
all-atom molecular dynamics simulations, we explore the stability, size, and
structure of nanodiscs formed between the N-terminal domain of apolipoprotein
E3 (apoE3-NT) and variable number of
1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) molecules. We study both
parallel and antiparallel double-belt configurations, consisting of four
proteins per nanodisc. Our simulations predict nanodiscs containing between 240
and 420 DMPC molecules to be stable. The antiparallel configurations exhibit an
average of 1.6 times more amino acid interactions between protein chains and 2
times more ionic contacts, compared to the parallel configuration. With one
exception, DMPC order parameters are consistently larger in the antiparallel
configuration than in the parallel one. In most cases, the root mean square
deviation of the positions of the protein backbone atoms is smaller in the
antiparallel configuration. We further report nanodisc size, thickness, radius
of gyration, and solvent accessible surface area. Combining all investigated
parameters, we hypothesize the antiparallel protein configuration leading to
more stable and more rigid nanodiscs than the parallel one