The interactions between biological substances and carbon nanotubes (CNTs) and their effect on the nanotubes are of significant importance in this emerging era of nanobiotechnology. Consequently, highly stable dispersions of debundled CNTs in aqueous solution are an important prerequisite for their applications and for the development of nanotube-based molecular electronic and nanobiomedical devices. Here, we report that proteins can work as tools to this end if their primary structure and the pH value of the system are chosen appropriately. Proteins containing a large number of basic residues, for example, histone, are found to be the most promising protein tools for the dispersion of nanotubes. Apart from other interactions, the polarity of the protein seems to play a vital role in obtaining high yields of debundled nanotubes. In addition, an enrichment of metallic nanotubes in the products is observed, which offers a facile approach for separating nanotubes according to their electronic properties in the bulk.