Divalent metal transporter (DMT1) belongs to the family of Nramp proteins. The fourth transmembrane domain (TM4) housing the disease-causing mutations both in Nramp1 and Nramp2 at the conserved two adjacent glycine residues, was implicated to serve an important biological function. In the present study, we have characterized structurally and topologically a 32-mer synthetic peptide, corresponding to the sequence of the loop 3 and the fourth transmembrane domain of rat DMT1 in membrane-mimetic environments (e.g. TFE, SDS micelles) using both CD and NMR spectroscopic techniques. Solution structures derived from NMR and molecular dynamic/simulated annealing calculation demonstrated that the peptide exhibits a highly defined alpha-helice in the middle portion of the peptide, flanked by a highly flexible N-terminus and a relatively ordered C-terminus. Paramagnetic broadening on peptide signals by spin-labels and Mn2+ suggested that both the N-terminus and helical core of the peptide were embedded into the SDS micelles. The peptide exhibited amphipathic characteristics, with hydrophilic residues (Thr189, Asp192, Thr193 and Asp200) lying in one side of the helix which provides a basis for the formation of water-filled channel architectures through self-associations. Diffusion-ordered spectroscopy (DOSY) indicated that the peptide exhibits mixtures of hexamers, trimers and monomers, in contrast to the fourth transmembrane peptide (24-mer) being aggregated as a trimer only. This appears to be the first report on the effects of loops on aggregation behavior of transmembrane domains in membrane-mimetic environments.