There is currently substantial interest in understanding and controlling protein function on nanomaterials. Carbon nanotubes represent a particularly attractive class of nanomaterials for such investigations, given their unique electrical, optical, and mechanical properties, and the numerous applications of carbon nanotube-protein conjugates. We demonstrate the remote and specific nanotube-mediated deactivation of proteins. We have used this phenomenon in multiple contexts: to design nanotube-peptide conjugates that selectively destroy a target biological toxin – anthrax toxin – and to design nanotube-based “self-cleaning” coatings. Nanotube-assisted inactivation represents a facile strategy for the targeted destruction of proteins, pathogens, and cells, with applications ranging from antifouling coatings to proteomics and novel therapeutics.