The Nuclear Pore Complex as a Flexible and Dynamic Gate

Nuclear pore complexes (NPCs) perforate the nuclear envelope and serve as the primary transport gates for molecular exchange between nucleus and cytoplasm. Stripping the megadalton complex down to its most essential organizational elements, one can divide the NPC into scaffold components and the disordered elements attached to them that generate a selective barrier between compartments. These structural elements exhibit flexibility, which may hold a clue in understanding NPC assembly and function. Here we review the current status of NPC research with a focus on the functional implications of its structural and compositional heterogeneity.National Institutes of Health (U.S.) (Grant R01GM077537)National Institutes of Health (U.S.) (Grant R01AR065484

Neutrino oscillations in matter of varying density

We consider two-family neutrino oscillations in a medium of continuously-varying density as a limit of the process in a series of constant-density layers. We construct analytic expressions for the conversion amplitude at high energies within a medium with a density profile that is piecewise linear. We compare some cases to understand the type of effects that depend on the order of the material traversed by a neutrino beam.Comment: 10 page

Mechanism of arginine sensing by CASTOR1 upstream of mTORC1

The mechanistic Target of Rapamycin Complex 1 (mTORC1) is a major regulator of eukaryotic growth that coordinates anabolic and catabolic cellular processes with inputs such as growth factors and nutrients, including amino acids. In mammals arginine is particularly important, promoting diverse physiological effects such as immune cell activation, insulin secretion, and muscle growth, largely mediated through activation of mTORC1 (refs 4, 5, 6, 7).Arginine activates mTORC1 upstream of the Rag family of GTPases, through either the lysosomal amino acid transporter SLC38A9 or the GATOR2-interacting Cellular Arginine Sensor for mTORC1 (CASTOR1). However, the mechanism by which the mTORC1 pathway detects and transmits this arginine signal has been elusive. Here, we present the 1.8 Å crystal structure of arginine-bound CASTOR1. Homodimeric CASTOR1 binds arginine at the interface of two Aspartate kinase, Chorismate mutase, TyrA (ACT) domains, enabling allosteric control of the adjacent GATOR2-binding site to trigger dissociation from GATOR2 and downstream activation of mTORC1. Our data reveal that CASTOR1 shares substantial structural homology with the lysine-binding regulatory domain of prokaryotic aspartate kinases, suggesting that the mTORC1 pathway exploited an ancient, amino-acid-dependent allosteric mechanism to acquire arginine sensitivity. Together, these results establish a structural basis for arginine sensing by the mTORC1 pathway and provide insights into the evolution of a mammalian nutrient sensor.National Institutes of Health (U.S.) (Grant R01CA103866)National Institutes of Health (U.S.) (Grant AI47389)United States. Department of Defense (Award W81XWH-07-0448)National Institutes of Health (U.S.) (Grant F31 CA180271

Structural basis for leucine sensing by the Sestrin2-mTORC1 pathway

Eukaryotic cells coordinate growth with the availability of nutrients through the mechanistic target of rapamycin complex 1 (mTORC1), a master growth regulator. Leucine is of particular importance and activates mTORC1 via the Rag guanosine triphosphatases and their regulators GATOR1 and GATOR2. Sestrin2 interacts with GATOR2 and is a leucine sensor. Here we present the 2.7 angstrom crystal structure of Sestrin2 in complex with leucine. Leucine binds through a single pocket that coordinates its charged functional groups and confers specificity for the hydrophobic side chain. A loop encloses leucine and forms a lid-latch mechanism required for binding. A structure-guided mutation in Sestrin2 that decreases its affinity for leucine leads to a concomitant increase in the leucine concentration required for mTORC1 activation in cells. These results provide a structural mechanism of amino acid sensing by the mTORC1 pathway.United States. Department of Defense (W81XWH-07- 0448)Damon Runyon Cancer Research Foundation (DRG-112-12)National Institutes of Health (U.S.) (Predoctoral Training Grant T32GM007287)National Institutes of Health (U.S.) (Grants R01CA103866, AI47389, T32 GM007753, F30 CA189333, F31 CA180271, and F31 CA189437)United States. Dept. of Defense. Breast Cancer Research Program (Postdoctoral Fellowship BC120208)Massachusetts Institute of Technology. Office of the Dean for Graduate Education (Whitaker Health Sciences Fund Fellowship)Damon Runyon Cancer Research Foundation (Sally Gordon Fellowship DRG-112-12

Pore timing:the evolutionary origins of the nucleus and nuclear pore complex

The name “eukaryote” is derived from Greek, meaning “true kernel”, and describes the domain of organisms whose cells have a nucleus. The nucleus is thus the defining feature of eukaryotes and distinguishes them from prokaryotes (Archaea and Bacteria), whose cells lack nuclei. Despite this, we discuss the intriguing possibility that organisms on the path from the first eukaryotic common ancestor to the last common ancestor of all eukaryotes did not possess a nucleus at all—at least not in a form we would recognize today—and that the nucleus in fact arrived relatively late in the evolution of eukaryotes. The clues to this alternative evolutionary path lie, most of all, in recent discoveries concerning the structure of the nuclear pore complex. We discuss the evidence for such a possibility and how this impacts our views of eukaryote origins and how eukaryotes have diversified subsequent to their last common ancestor

Structural and biophysical characterization of membrane-coating proteins from the nuclear pore and the primary cilium

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biology, 2016.Cataloged from PDF version of thesis.Includes bibliographical references.A hallmark of eukaryotes is an endomembrane system that spatially separates cellular processes into discrete compartments. Macromolecular transport between these compartments canonically involves the fission and fusion of membrane-bound vesicles. Transport to and from the nucleus is a notable exception to this vesicular pathway. Additionally, transport to the primary cilium is not well characterized and is therefore of interest. The nuclear envelope comprises a double membrane that fuses at points to produce pores, which link the nucleoplasm with the cytoplasm. Coating these openings are nuclear pore complexes (NPCs), which regulate all nucleocytoplasmic trafficking by anchoring barrier forming FG-repeat proteins. At 60-120 MDa, the NPC is the largest macromolecular complex in the cell. However, it is a modular assembly formed by -30 different nucleoporins (Nups) arranged into stable subassemblies. One such module is the -600 kDa Y complex, which forms a Y shape and is the best characterized NPC subcomplex with crystal structures accounting for -90% of its total mass. The molecular details of how the short arms of the Y contact the long stem, in a region called the 'hub', were not known. We solved the structure of this last major missing piece of the Y complex to 4.1 A. This hub structure revealed unexpected curvature, allowed us to build the first atomic resolution composite of the mostly complete Y, and led to a novel higher order assembly model of the Y complex in the intact NPC. The ciliary membrane is topologically contiguous with the plasma membrane yet functionally distinct, due to a unique complement of integral membrane proteins. The Bardet- Biedl syndrome protein complex (BBSome) functions in the establishment or maintenance of this unique composition. The BBSome is -500 kDa octamer comprising BBS1, 2, 4, 5, 7, 8, 9, and BBIP10. To date, only the N-terminal domain of BBS1 had been structurally determined. In order to more completely characterize this complex, we have solved the structure of the BBS9 N-terminal [beta]-propeller to 1.8 A and determined its oligomeric state in solution. This structure has allowed us to identify a putative interaction site and characterized a disease relevant mutation on BBS9.by Kevin E. Knockenhauer.Ph. D