Background: The envelope glycoprotein of the human (HIV) and related simian (SIV) immunodeficiency virus are synthesized as gp160 precursors which are processed into two non-covalently associated glycoproteins: gp120 and gp41. The gp120 mediates viral entry into the host cell by binding to the cellular receptor CD4 and a chemokine co-receptor, both of which are located on the host cell surface. This binding induces conformational changes in the transmembrane gp41, which facilitates membrane fusion between the viral and host membranes. An understanding of these processes at the molecular level may lead to a direct means of inhibiting HIV infection. HIV gp41, and the closely related SIV gp41, are heavily glycosylated transmembrane proteins. The ectodomain region, located on the outer surface of the viral membrane directly mediates membrane fusion events via an N-terminal fusion domain. Both the NMR and X-ray structures of the gp41 ectodomain have been solved. The structure determined by both methods is a rod-like trimer comprising three parallel N-terminal alpha-helices assembled as a coiled-coil in the center with three antiparallel C-terminal alpha-helices packed on the outside with highly flexible loops connecting the inner and outer helices. Results: To gain further insight into gp41 function we have expressed in bacteria regions of the protein for which there is currently no structural information, namely, the extremely hydrophobic N-terminal fusion peptide, the transmembrane region and the long cytoplasmic domain. The proteins produced are being studied by new NMR techniques designed for the structural analysis of membrane proteins and peptides (A.Bax). The structure of a membrane associated region of the cytoplasmic domain was previously determined and the structure of the N-terminal fusion domain has now been determined and has been submitted for publication. We have also prepared site-specific mutants of the helical N-terminal fusion domain which abrogate the fusion process and structural studies indicate corresponding perturbations of the helical structure. These studies will also be submitted for publication soon. In other published studies we have examined mutants of the HIV gp41 ectodomain which are resistant to the new class of peptide inhibitors targeted against membrane fusion. We have shown that the resistance mutations increase the thermodynamic stability of the gp41 ectodomain and these results provides new insight into the potential mechanism of resistance. Significance and future direction: More detailed structure determinations of the whole gp41 protein including the transmembrane region and the large cytoplasmic domain will provide more targets for rational drug design.