In this study we compare major synaptic proteins from Torpedo electric organ to their homologues from mammalian brain. Most of these proteins are members of small gene families. We demonstrate a high degree of evolutionary conservation of most synaptic proteins. However, in the electric organ each gene family is represented only by a single member. We focus on VAT-1, a major protein of the vesicle membrane in Torpedo. VAT-1 is located on the synaptic vesicle membrane and is highly concentrated on the plasma membrane following the application of alpha-latrotoxin. Taking advantage of the relative simplicity of Torpedo synapses, we performed an in vitro study on the properties of VAT-1 affected by changes in Ca2+ levels. VAT-1 is a low affinity Ca2+ binding protein whose ability to bind Ca2+ resides mainly, but not entirely, on the carboxy-terminal domain of the protein. In the presence of Ca2+, the protein is organized in a high molecular mass complex, which is destabilized by depleting Ca2+. This effect occurs only by chelating Ca2+ ions, but not with other divalent ions. VAT-1 is not complexed to any of the proteins which were implicated in the docking/fusion complex such as VAMP, synaptophysin or syntaxin, regardless of Ca2+ levels. Dependence of the stability of protein complexes on Ca2+ levels is also demonstrated on Torpedo n-Sec1. The possible physiological implications of such Ca2+ dependence are discussed.