This invention provides bioluminescence resonance energy transfer (BRET) system that comprises four parts: 1) a bioluminescent protein that has luciferase activity; 2) an acceptor fluorophore that can accept the energy from the bioluminescent protein when they are associated, in the presence of the appropriate substrate; 3) a modulator that influences the proximity or the orientation of the bioluminescent protein and the fluorophore, and 4) an appropriate substrate to activate the luciferase activity of the bioluminescent protein. The components of this system interact to influence the spatial relationship between the bioluminescent protein and the fluorophore, that is demonstrated by the light emission from the system. The modulator can be a single entity, covalently attached to both the bioluminescent protein and the fluorophore, it can be two separate entities, each linked covalently to either the bioluminescent protein or the fluorophore, or an alternative configuration that falls within the scope of the invention. Thissystem can be used in both in vivo or in vitro assays to detect molecular changes in a wide variety of applications, and is amenable to automation. In particular, it is useful for assaying protein interactions, enzyme activities and the concentration of analytes or signaling molecules in cells or in solution.