We investigated structural and dynamical properties of nanodiscs comprising dimyristoylphosphatidylcholine (DMPC) lipids and major scaffold protein MSP1Δ(1-22) from human apolipoprotein A-1 using combined all-atom and coarse-grained (CG) molecular dynamics (MD) simulations. The computational efficiency of the Martini-CG force field enables the spontaneous self-assembly of lipids and scaffold proteins into stable nanodisc structures on time scales up to tens of microseconds. Subsequent all-atom and CG-MD simulations reveal that the lipids in the nanodisc have lower configurational entropy and higher acyl tail order than in a lamellar bilayer phase. These altered average properties arise from rather differential behavior of lipids, depending on their location in the nanodisc. Since the scaffold proteins exert constrictive forces from the outer rim of the disc toward its center, lipids at the center of the nanodisc are highly ordered, whereas annular lipids that are in contact with the MSP proteins are remarkably disordered due to perturbed packing. Although specific differences between all-atom and CG simulations are also evident, the results obtained at both levels of resolution are in overall good agreement with each other and provide atomic level interpretations of recent experiments. Thus, the present study highlights the applicability of multiscale simulation approaches for nanodisc systems and opens the way for future applications, including the study of nanodisc-embedded membrane proteins. (Graph Presented). © 2015 American Chemical Society.