The sphingolipid, ceramide, self-assembles in phospholipid membranes, forming large channels capable of translocating proteins across said membranes. These channels are believed responsible for protein release from mitochondria, a key, decision-making step in apoptosis. Rather unexpectedly for lipids, ceramide channels reveal a high degree of order and display properties similar to those of protein channels. They contain amide linkages believed to be responsible for organizing individual lipids into columns, a kind of secondary structure. The columns self-assemble into a barrel-stave, essentially quaternary structure, that is so highly-organized that it shows both negative and positive cooperativity in the presence of chemical analogs. Depending on the location of the chemical change, the presence of the analog could favor channel formation or inhibit the formation. Thus the analogs must intercalate into the structure, altering its stability. Furthermore, ceramide channels can be destabilized or stabilized by proteins that regulate apoptosis and these act in a very specific manner. These proteins do not act as catalysts but rather as modulators or allosteric modifiers. They act to shift the stability constants that determine the equilibrium between channels, monomers, and non-channel aggregates. Bcl-xL destabilizes the channels by forming what appears to be a 1:1 complex with the ceramide channel. The stoichiometry of the interaction with oligomeric Bax, the protein that stabilizes the channel, appears to be larger than 1:1 but the variable oligomeric nature of the protein complicates the interpretation. The affinity between oligomeric Bax and the ceramide channel seems to increase with channel size indicating the possibility of a conformation-driven enlargement of the channel. (supported by NSF grant: MCB-0641208 and a Nano-Biotechnology DBED award)