Comparative structure-function studies have been carried out for alpha-conotoxin GI acting on nicotinic acetylcholine receptors (AChR) from mammalian muscles and from the electric organ of the Torpedo californica ray and for alpha-conotoxin ImI, which targets the neuronal alpha7 AChR. A series of analogs has been prepared for this purpose: chemically modified derivatives, including a covalently linked dimer of GI, as well as analogs wherein one or several amino acid residues have been changed using solid-phase peptide synthesis. The activity of all compounds was assessed in competition with radioiodinated and/or tritiated alpha-conotoxin GI for binding to the membrane-bound AChR of Torpedo californica. Binding of radioiodinated alpha-conotoxin GI dimer was also monitored directly, revealing the largest, as compared to all other analogues, difference in the affinity between the two binding sites in the receptor (KD approximately 11 and 1200 nM). Comparison of binding data with the results of CD measurements point to important role of the spatial organization of the alpha-conotoxin second loop in manifestation of their "muscle" or "neuronal" specificity.