The major limitation of real-time imaging of metabolites and proteins was the selective detection of biomaterials that are not naturally occurring or have stable molecular recognition. We present the development of the design of synthetic near-infrared fluorescent nanosensors based on the fluorescence modulation of single-wall carbon nanotubes (SWNTs) by color-selective adsorption of N-substituted glycine peptide polymers. We evaluate the stability of peptide-SWNT nanosensor candidates under ionic strength, protease exposure, and cell culture media and find that the stability of peptide-SWNTs depends on the composition and length of the peptide polymer. From our library, we identify a peptide-SWNT assembly that is able to detect lectin protein in wheat germ agglutinin (WGA) sensitivity, which is comparable to serum protein concentration. To maintain nanosensor-bound protein activity, we show that the WGA on the nanosensor produces additional fluorescent signal modulation upon exposure to the lectin target sugar, suggesting that the lectin protein remains active and selectively binds to its target sugar, the target molecular molecule. Our results inform design considerations for the development of synthetic molecular recognition elements, by assembling peptide polymers at SWNT and also by demonstrating these assemblies can become optical nanostructures of lectin proteins and their target sugars. Together, these data suggest that it is possible to assemble sequences of peptide sequences with SWNTs that will serve as multiple optical zones for the detection of proteins and their molecular substrates.