The action of calmodulin (CaM) on target proteins is important for a variety of cellular functions. We demonstrate here, however, that the presence of a CaM-binding site on a protein does not necessarily imply a functional effect. The ␣-subunit of the cGMP-gated cation channel of human retinal cones has a CaM-binding site on its cytoplasmic N-terminal region, but the homomeric channel that it forms is not functionally modulated by CaM. Mutational analysis based on comparison to the highly homologous olfactory cyclic nucleotide-gated channel ␣-subunit, which does form a CaMmodulated channel, indicates that residues downstream of the CaM-binding domain on these channels are also important for CaM to have an effect. These findings suggest that a CaM-binding site and complementary structural features in a protein probably evolve independently, and an effect caused by CaM occurs only in the presence of both elements. More generally, the same may be true for other recognized binding sites on proteins for modulators or activators, so that a demonstrated physical interaction does not necessarily imply functional consequence. C almodulin (CaM) plays an important role in a variety of cellular processes. Typically, it acts by first binding Ca 2ϩ , with the Ca 2ϩ -CaM complex then binding to diverse targets such as protein kinase and phosphatase, adenylyl cyclase, cyclicnucleotide phosphodiesterase, nitric oxide synthase, cytoskeletal proteins, ion transporters, and ion channels (1-3). The direct effects of CaM on ion channels have been recognized only recently (4-18). One ion channel that shows very strong Ca 2ϩ -CaM modulation and has been studied quite extensively is the cyclic nucleotide-gated, nonselective cation channel mediating olfactory transduction in olfactory receptor neurons (OLF) (11,12,19). The opening of this channel generates the olfactory receptor potential (20-23). Because of its high Ca 2ϩ permeability (24, 25), the opening of OLF leads to a rise in cytosolic Ca 2ϩ , which in turn strongly inhibits the channel via Ca 2ϩ -CaM to produce negative feedback (11), making the cell adapt to the olfactory stimulus (24,26,27). This inhibition by Ca 2ϩ -CaM consists of a favoring of the closed state of the channel, manifested as an increase in the half-activation constant, K 1/2 , of the channel for cyclic nucleotide (i.e., a shift of the doseresponse relation to higher ligand concentrations) (11, 12). The binding site on OLF for Ca 2ϩ -CaM has been localized to the cytoplasmic N-terminal region of its ␣-subunit (OLF␣) (12). A similar, but far less potent, inhibition by Ca 2ϩ -CaM exists for a homologous cGMP-gated channel mediating phototransduction in retinal rods (ROD) (7-10, 28), but in this case the binding site for Ca 2ϩ -CaM is localized to a corresponding region on the channel's -subunit (ROD) (29,30). Another cGMP-gated channel mediates phototransduction in retinal cones (CONE) (31-33). We report here that human CONE's ␣-subunit (CONE␣) also has a Ca 2ϩ -CaM binding site that is in roughly the same loca...