Using solution X-ray scattering, optical and electron microscopy we studied the interactions between microtubule and charged molecules. Microtubules are net negatively charged hollow cylinders that self-assemble from tubulin protein subunits. We looked at the interaction between microtubules and cationic lipids and discovered (PNAS 2005, Philos. Trans. A Math. Phys. Eng. Sci., 2006, Biophys. J 2007) a new paradigm for lipid self-assembly leading to nanotubule formation in mixed charged systems: Under the appropriate conditions, lipid-protein nanotubules are spontaneously forming. The lipid-protein nanotubules exhibit a rather remarkable architecture with a cylindrical lipid-bilayer sandwiched between a microtubule and an outer tubulin oligomer, forming rings or spirals. The new type of self-assembly arises because of an extreme mismatch between the charge densities of microtubules and cationic lipid membranes. The nanotube consisting of a three-layer wall appears to be the best the system can do in compensating for this charge density mismatch. Very interestingly, we have found that controlling the degree of overcharging of the lipid-protein nanotube enables us to switch between two states of nanotubes with either open ends or closed ends with lipid caps, which forms the basis for controlled chemical and drug encapsulation and release.