Gold nanotube membranes are ideal model systems for exploring how pore size affects the rate and selectivity of protein transport in synthetic membranes. This is because these membranes have cylindrical, monodisperse pores (the nanotubes) with diameters that can be varied at will from tens of nanometers down to less than 1 nm. We report here on the effects of nanotube inside diameter, solution pH, and applied transmembrane potential on the rate and selectivity of protein transport in PEG-thiol-treated gold nanotube membranes. The transport properties of four proteins of differing sizes and pI values--lysozyme, bovine serum albumin, carbonic anhydrase, and bovine hemoglobulin--were investigated. In general, membranes containing larger diameter nanotubes showed higher fluxes and lower selectivities than membranes with smaller diameter nanotubes. Transmembrane electrophoresis can be used to augment the diffusive transport selectivity. For example, for proteins that are oppositely charged, a combination of a large transmembrane potential and a large nanotube diameter can be used to optimize both selectivity and flux. In addition to transmembrane potential and nanotube diameter, solution pH value plays an important role in determining the transport selectivity. This is because pH determines the net charge on the protein molecule and this, in turn, determines the importance of the electrophoretic transport term.