The CHI molecular dynamics simulation and energy minimization protocol was used to generate structural models of the EBC5-16 homodimer. This technique was used previously by us and others to study homodimerization of the E5 protein and other transmembrane protein activators of the PDGFbR. The structural calculations were performed based on the active Put3 chimera II, using the last four residues of Put3 up to the point of fusion fused to Leu10 to Gln33 of EBC5-16. Six different symmetric,Aloe-emodin lefthanded coiled-coil, low energy clusters were obtained, one of which predicted Ser25 to be in the interface. The plot of the interaction energies of this model shows the energetic contribution of each residue to the stability of the homodimer interface. Importantly, this CHI model is consistent with the interface inferred from the Put3 experiments, in that Ile18, Pro22, Ser25, and Phe29 all lie in the homodimer interface in this model and contribute to the interaction energy of the dimer. The two interfacial glycines predicted by the Put3 experiments did not appear in the CHI interaction energy plot because glycine lacks a side-chain and thus cannot contribute directly to the energy of the dimer. Therefore, the glycines in the GxxxG motif most likely stabilize the dimer by allowing each monomer of EBC5-16 to approach one another more closely and pack more tightly, as has been observed frequently in other homodimeric transmembrane domains,Betulin including the GpA transmembrane dimer. Consistent with this view, inspection of the CHI model revealed that Gly11 and Gly15 are at or near the dimer interface of EBC5-16, as is Val14, which makes a minor contribution to the interaction energy. There are two additional noteworthy observations from the modeling. First, comparison of the models for EBC5-16 and TC23 showed marked re-arrangement of the amino acid side-chains within the interface as a consequence of the isoleucine to serine mutation. This was most dramatic in the case of the Phe29 side-chains, where the aromatic rings are oriented differently in the models of the TC2-3 and the EBC5-16 dimer.