To better understand the interaction of alpha-synuclein (alpha Syn) with lipid membranes, we carried out self-assembly molecular dynamics simulations of alpha Syn with monomeric and micellar sodium dodecyl sulfate (SDS), a widely used membrane mimic. We find that both electrostatic and hydrophobic forces contribute to the interactions of alpha Syn with SDS. In the presence of alpha Syn, our simulations suggest that SDS aggregates along the protein chain and forms small-size micelles at very early times. Aggregation is followed by formation of a collapsed protein-SDS micelle complex, which is consistent with experimental results. Finally, interaction of alpha Syn with preformed micelles induces alterations in the shape of the micelle, and the N-terminal helix (residues 3 through 37) tends to associate with micelles. Overall, our simulations provide an atomistic description of the early time scale alpha Syn-SDS interaction during the self-assembly of SDS into micelles.