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Nanoscale sensing arrays utilizing the unique properties of the optical protein bacteriorhodopsin and colloidal semiconductor quantum dots are being developed for toxin detection applications. This paper describes an innovative method to activate bacteriorhodopsin-based electrodes with the optical output of quantum dots, producing an enhanced electrical response from the protein. Results show that the photonic emission of CdSe/ZnS quantum dots is absorbed by the bacteriorhodopsin retinal and initiates the proton pumping sequence, resulting in an electrical output from a bacteriorhodopsin-based electrode. It is also shown that activated quantum dots in sub-10 nm proximity to bacteriorhodopsin further amplify the photovoltaic response of the protein by approximately 23%, compared to without attached quantum dots, suggesting direct energy transfer mechanisms beyond photonic emission alone. The ability of quantum dots to activate nanoscale regions on bacteriorhodopsin-based electrodes could allow sub-micron sensing arrays to be created due to the ability to activate site-specific regions on the array.