Brownian Dynamics Simulation of Nucleocytoplasmic Transport: A Coarse-Grained Model for the Functional State of the Nuclear Pore Complex

Abstract

The nuclear pore complex (NPC) regulates molecular traffic across the nuclear envelope (NE). Selective transport happens on the order of milliseconds and the length scale of tens of nanometers; however, the transport mechanism remains elusive. Central to the transport process is the hydrophobic interactions between karyopherins (kaps) and Phe-Gly (FG) repeat domains. Taking into account the polymeric nature of FG-repeats grafted on the elastic structure of the NPC, and the kap-FG hydrophobic affinity, we have established a coarse-grained model of the NPC structure that mimics nucleocytoplasmic transport. To establish a foundation for future works, the methodology and biophysical rationale behind the model is explained in details. The model predicts that the first-passage time of a 15 nm cargo-complex is about 2.6±0.13 ms with an inverse Gaussian distribution for statistically adequate number of independent Brownian dynamics simulations. Moreover, the cargo-complex is primarily attached to the channel wall where it interacts with the FG-layer as it passes through the central channel. The kap-FG hydrophobic interaction is highly dynamic and fast, which ensures an efficient translocation through the NPC. Further, almost all eight hydrophobic binding spots on kap-β are occupied simultaneously during transport. Finally, as opposed to intact NPCs, cytoplasmic filaments-deficient NPCs show a high degree of permeability to inert cargos, implying the defining role of cytoplasmic filaments in the selectivity barrier.

Effect of charge, hydrophobicity, and sequence of nucleoporins on the translocation of model particles through the nuclear pore complex

“…A definitive transport mechanism remains elusive because directly visualizing FG-Nups and the kap-cargo complex within individual NPCs is at the limits of current single-molecule tracking technology (15)(16)(17); therefore, theory (18,19) and computer simulations (20)(21)(22) have been used in an attempt to elucidate the essential features of the translocation process. In a recent coarsegrained molecular dynamics (MD) simulation, the kap-FG interaction was found to be highly dynamic and the FG-Nups formed a layer on the pore walls (20). The kap-cargo complex particle interacts with the FG residues in this layer as it diffuses through the channel.…”

“…Until recently, it was believed that hydrophobic interactions were solely responsible for the selectivity of the translocation process (11,14,20,23,24). According to this view, water-soluble proteins generally present a hydrophilic surface and are repelled by the hydrophobic domains of the FG-Nups, but hydrophobic patches on the surface of kaps interact attractively with the FGNups.…”

Stochastic models of intracellular transport

“…Current models include the Entropic Gate model (Rout et al, 2003;Zilman et al, 2007), Selective Phase models (Bickel and Bruinsma, 2002;Kustanovich and Rabin, 2004;Ribbeck andGorlich, 2001, 2002), Dimensionality Reduction model (Peters, 2005), and the Polymeric Brush model (Lim et al, 2007(Lim et al, , 2006. A number of computational models and molecular-based simulations are also being developed (Grunwald and Singer, 2011;Moussavi-Baygi et al, 2011). Here we will review the first two types of model in a little more detail.…”

Intermolecular disulfide bonds among nucleoporins regulate karyopherin-dependent nuclear transport

“…It has been proposed that the flexible polypeptide chains of FG-Nups form a meshwork via hydrophobic interactions between hydrophobic residues (mainly phenylalanine) (Frey et al, 2006;Mohr et al, 2009;Moussavi-Baygi et al, 2011;Ribbeck and Görlich, 2002). This meshwork prevents the passage of large proteins, but allows diffusion of proteins smaller than the mesh size (Mohr et al, 2009).…”