Nanomechanical mechanism for lipid bilayer damage induced by carbon nanotubes confined in intracellular vesicles

Understanding the behavior of low-dimensional nanomaterials confined in intracellular vesicles has been limited by the resolution of bioimaging techniques and the complex nature of the problem. Recent studies report that long, stiff carbon nanotubes are more cytotoxic than flexible varieties, but the mechanistic link between stiffness and cytotoxicity is not understood. Here we combine analytical modeling, molecular dynamics simulations, and in vitro intracellular imaging methods to reveal 1D carbon nanotube behavior within intracellular vesicles. We show that stiff nanotubes beyond a critical length are compressed by lysosomal membranes causing persistent tip contact with the inner membrane leaflet, leading to lipid extraction, lysosomal permeabilization, release of cathepsin B (a lysosomal protease) into the cytoplasm, and cell death. The precise material parameters needed to activate this unique mechanical pathway of nanomaterials interaction with intracellular vesicles were identified through coupled modeling, simulation, and experimental studies on carbon nanomaterials with wide variation in size, shape, and stiffness, leading to a generalized classification diagram for 1D nanocarbons that distinguishes pathogenic from biocompatible varieties based on a nanomechanical buckling criterion. For a wide variety of other 1D material classes (metal, oxide, polymer), this generalized classification diagram shows a critical threshold in length/width space that represents a transition from biologically soft to stiff, and thus identifies the important subset of all 1D materials with the potential to induce lysosomal permeability by the nanomechanical mechanism under investigation.The interactions of low-dimensional materials with the external or plasma membrane of living cells have been the subject of prior studies due to their importance in uptake and delivery, antibacterial action, and nanomaterial safety (1–6). Following uptake, nanomaterials may also interact with internal membranes while under confinement in intracellular vesicles (7–10), but the biophysics of these geometrically constrained systems is poorly understood. Low-dimensional materials interact with biological systems in complex ways dictated by their 1D nanofibrous or 2D nanosheet geometries (7, 11–20). These interactions typically begin when materials encounter the plasma membrane and initiate phenomena that can include adhesion, membrane deformation, penetration, lipid extraction, entry, frustrated uptake, or cytotoxicity (4, 11–14, 19–21). Recent experimental data suggest that the cellular response to some 1D materials is governed by their interaction with the internal lipid-bilayer membranes of endosomes and lysosomes following nanomaterial uptake (7–10). The resulting geometry is fundamentally different in that the fibrous materials are confined within a vesicle, imposing geometric constraints and introducing mechanical forces that act bidirectionally––i.e., on both the thin fibrous structure and the inner leaflet of the soft membrane. The fundamental biophysics of this tube-in-vesicle system is virtually unexplored, yet may be critical for understanding the cellular response to nanotubes/fibers, where shape and stiffness are among the known determinants of toxicity (13, 21). The technique of coarse-grained molecular dynamics (MD), demonstrated to be effective in the study of complex biomolecular systems (22, 23), has been applied to whole lipid-bilayer patches to reveal a biophysical mechanism for carbon nanotube interaction with the plasma membranes leading to tip entry and uptake (4, 19, 20). The same technique may also provide insight relevant to internal membrane interactions, although whole vesicle MD is a significant challenge. Here we use a complement of techniques including coarse-grained MD, all-atom MD, in vitro bioimaging, and carbon nanotube length modification to reveal the behavior of vesicle-encapsulated carbon nanotubes and identify the conditions and carbon nanotube (CNT) types that lead to mechanical stress and membrane damage following cellular uptake and packaging in lysosomes (8).