Conserved Spatial Organization of FG Domains in the Nuclear Pore Complex

Laboratory of Cellular Biophysics, The Rockefeller University, New York, New York.
Biophysical Journal (Impact Factor: 3.97). 01/2013; 104(1):37-50. DOI: 10.1016/j.bpj.2012.11.3823
Source: PubMed


Selective transport through the nuclear pore complex (NPC) requires nucleoporins containing natively unfolded phenylalanine-glycine (FG) domains. Several differing models for their dynamics within the pore have been proposed. We characterize the behavior of the FG nucleoporins in vivo using polarized fluorescence microscopy. Using nucleoporins tagged with green fluorescent protein along their FG domains, we show that some of these proteins are ordered, indicating an overall orientational organization within the NPC. This orientational ordering of the FG domains depends on their specific context within the NPC, but is independent of active transport and cargo load. For most nups, behavior does not depend on the FG motifs. These data support a model whereby local geometry constrains the orientational organization of the FG nups. Intriguingly, homologous yeast and mammalian proteins show conserved behavior, suggesting functional relevance. Our findings have implications for mechanistic models of NPC transport.

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Available from: Sanford Simon, Dec 23, 2013
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    • "A highly dynamic, fluid state for FG repeats in vivo is in agreement with measurements of the living NPC (Atkinson et al., 2013). FG Nups do not appear to form a molten globule or collapsed state, as has also been proposed (Yamada et al., 2010), instead behaving as a fully disordered IDP (Rout et al., 2003; Lim et al., 2006; Lim and Deng, 2009; Atkinson et al., 2013). Our results also allow us to distinguish their IDP class (Uversky, 2011; van der Lee et al., 2014). "
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    ABSTRACT: Nuclear pore complexes (NPCs) form a selective filter that allows the rapid passage of transport factors (TFs) and their cargoes across the nuclear envelope, while blocking the passage of other macromolecules. Intrinsically disordered proteins (IDPs) containing phenylalanyl-glycyl (FG)-rich repeats line the pore and interact with TFs. However, the reason that transport can be both fast and specific remains undetermined, through lack of atomic-scale information on the behavior of FGs and their interaction with TFs. We used nuclear magnetic resonance spectroscopy to address these issues. We show that FG repeats are highly dynamic IDPs, stabilized by the cellular environment. Fast transport of TFs is supported because the rapid motion of FG motifs allows them to exchange on and off TFs extremely quickly through transient interactions. Because TFs uniquely carry multiple pockets for FG repeats, only they can form the many frequent interactions needed for specific passage between FG repeats to cross the NPC.
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    ABSTRACT: Bioinformatics of disordered proteins is especially challenging given high mutation rates for homologous proteins and that functionality may not be strongly related to sequence. Here we have performed a novel bioinformatic analysis, based on the spatial clustering of physically relevant features such as binding motifs and charges within disordered proteins, on thousands of Nuclear Pore Complex (NPC) FG motif containing proteins (FG nups). The biophysical mechanism by which FG nups regulate nucleocytoplasmic transport has remained elusive. Our analysis revealed a set of highly conserved spatial features in the sequence structure of individual FG nups, such as the separation, localization, and ordering of FG motifs and charged residues along the protein chain. These functionally conserved features provide insight into the particular biophysical mechanisms responsible for regulation of nucleocytoplasmic traffic in the NPC, strongly constraining current models. Additionally this method allows us to identify potentially functionally analogous disordered proteins across distantly related species.
    Preview · Article · Sep 2013 · PLoS ONE
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