Results show that fractures in the vault structure are extremely dynamical with respect to aperture, length and number, while average structure can be preserve, when the structure is kept at body temperature (310 K). The time scale of the fluctuations is in the order of tens of nanoseconds and apertures are up to 1.2 nm. Since vaults are considered promising nanomedical delivery systems, the dynamical fractures and consequent ease of permeating the vault are important for the drug delivery process. These simulations would not have been practical without the multiscale algorithm implemented in our custom version of Gromacs 5.0.4, since the atomic fluctuations are Armstrong in scale and the fractures are nanometer in dimension and the atomic vibrations are in femtoseconds, while structural changes are in the nanosecond scale. Simulation results show good correlation with experimental results from AFM, CryoEM and CD spectroscopy at body or room temperature. The multiscale molecular dynamics simulations are up to an order of magnitude faster than conventional MD simulation.

Longtime simulation of dynamical fractures in vault nanoparticles through multiscale molecular dynamics

253rd National Meeting (2017)

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