The Flexibility of Unbound Importin-beta studied by Molecular Dynamics

Abstract

The transport of macromolecules between the nucleus and the cytoplasm takes place through nuclear pore complexes (NPC). NPCs act as an barrier against the diffusion of larger molecules. Karyopherins mediate the selective transport of proteins and RNA across this barrier.A particularly well studied and crucial karyopherin is importin-beta. This protein binds in the cytoplasm to a cargo and transports it into the nucleus. Here, the complex is dissociated by RanGTP, which itself binds to importin-beta and is transported back into the cytoplasm, where it dissociates after hydrolysis.All these processes are mediated by different conformations of importin-beta [1]. A number of these conformations have been resolved, revealing an inherent flexibility of importin-beta. Furthermore, recent molecular dynamics studies [2] as well as small angle x-ray scattering data [3] suggested an extended conformation of the free, unbound state of importin-beta. According to the “loaded spring” hypothesis, the elasticity of importin-beta plays a crucial role in this context which, however, is not accessible experimentally so far.In this work, the energetics and the mechanical properties of importin-beta are studied by both force probe and free molecular dynamics simulations. Based on the outcome of the simulations, mechanical models are developed to further gain insight into the large scale motions of importin-beta.[1] Conti, Muller, Stewart, Current Opinion in Structural Biology 16, 237-244 (2006)[2] Zachariae, Grubmuller, Structure 16, 906-915 (2008).[3] Fukuhara et. al., Journal of Biological Chemistry 279, 2176-2181 (2004).