We present an integrated device, which enables cell lysis, protein extraction, purification, and activity assay for the genetically engineered protein, F1-ATPase. Evaluations of individual functions for cell lysis and assay proved that the device provides a compatible platform to perform a single molecule assay. In addition to these functions, the effective dilution of the eluted protein was necessary to achieve molecular system for the assay. The comparison of experimental results and numerical study reveals that F1-ATPase concentration is optimized in a certain range. © 2008 CBMS.