A membrane system with nanometer-scale thick electrodes is able to selectively bind genetically modified proteins and pump them across the membrane with sequential voltage pulses. The electrodes are located at the first 20 nm of pore entrances to specifically capture targeted proteins and block non-specific protein transport through the pores during the binding cycle. During the release cycle, concentration of imidazole is controlled to keep the pore blocked while releasing proteins at the bottom edge of the electrode. A separation factor for GFP:BSA of 16 was achieved with observed GFP electrophoretic mobility of 2.54 × 10−6 cm2 V−1 s−1. This non-optimized system with a membrane area of 0.75 cm2 has the same throughput as 1 mL of commercially available chromatography columns showing viability as a continuous process. This system will enable continuous separation of expressed proteins directly from fermentation broths dramatically simplifying the separation process as well as reducing bio-pharmaceutical production costs.