Proceedings of the Natural Academy of Sciences

Proceedings of the National Academy of Sciences RSS feed -- current issue
  • TtAgo complexes with guide and target DNA [Biochemistry]
    [Jan 2014]

    We report on crystal structures of ternary Thermus thermophilus Argonaute (TtAgo) complexes with 5′-phosphorylated guide DNA and a series of DNA targets. These ternary complex structures of cleavage-incompatible, cleavage-compatible, and postcleavage states solved at improved resolution up to 2.2 Å have provided molecular insights into the orchestrated positioning of catalytic...
    Categories: Journal Articles
  • Electron flow in multiheme cytochrome [Biophysics and Computational Biology]
    [Jan 2014]

    The naturally widespread process of electron transfer from metal reducing bacteria to extracellular solid metal oxides entails unique biomolecular machinery optimized for long-range electron transport. To perform this function efficiently, microorganisms have adapted multiheme c-type cytochromes to arrange heme cofactors into wires that cooperatively span the cellular envelope, transmitting electrons...
    Categories: Journal Articles
  • Polyhedral membrane protein proteoliposomes [Biophysics and Computational Biology]
    [Jan 2014]

    We demonstrate that membrane proteins and phospholipids can self-assemble into polyhedral arrangements suitable for structural analysis. Using the Escherichia coli mechanosensitive channel of small conductance (MscS) as a model protein, we prepared membrane protein polyhedral nanoparticles (MPPNs) with uniform radii of ∼20 nm. Electron cryotomographic analysis established that these MPPNs...
    Categories: Journal Articles
  • Design of a pH-sensitive IgG binding protein [Biophysics and Computational Biology]
    [Jan 2014]

    Computational design provides the opportunity to program protein–protein interactions for desired applications. We used de novo protein interface design to generate a pH-dependent Fc domain binding protein that buries immunoglobulin G (IgG) His-433. Using next-generation sequencing of naïve and selected pools of a library of design variants, we generated a...
    Categories: Journal Articles
  • Spatial organization of RNAP II at superresolution [Biophysics and Computational Biology]
    [Jan 2014]

    Superresolution microscopy based on single-molecule centroid determination has been widely applied to cellular imaging in recent years. However, quantitative imaging of the mammalian nucleus has been challenging due to the lack of 3D optical sectioning methods for normal-sized cells, as well as the inability to accurately count the absolute copy...
    Categories: Journal Articles
  • Matrix assembly by cells in three dimensions [Cell Biology]
    [Jan 2014]

    Cell-directed deposition of aligned collagen fibrils during corneal embryogenesis is poorly understood, despite the fact that it is the basis for the formation of a corneal stroma that must be transparent to visible light and biomechanically stable. Previous studies of the structural development of the specialized matrix in the cornea...
    Categories: Journal Articles
  • PTP{sigma} regulates intestinal epithelial barrier [Cell Biology]
    [Jan 2014]

    Protein tyrosine phosphatase (PTP)σ (PTPRS) was shown previously to be associated with susceptibility to inflammatory bowel disease (IBD). PTPσ−/− mice exhibit an IBD-like phenotype in the intestine and show increased susceptibility to acute models of murine colitis. However, the function of PTPσ in the intestine is uncharacterized. Here, we show...
    Categories: Journal Articles
  • Roles of common subunits within distinct complexes [Cell Biology]
    [Jan 2014]

    Currently, there is no method to distinguish between the roles of a subunit in one multisubunit protein complex from its roles in other complexes in vivo. This is because a mutation in a common subunit will affect all complexes containing that subunit. Here, we describe a unique method to discriminate...
    Categories: Journal Articles
  • Observation time and the free-energy landscape [Chemistry]
    [Jan 2014]

    When structures that interconvert on a given time scale are lumped together, the corresponding free-energy surface becomes a function of the observation time. This view is equivalent to grouping structures that are connected by free-energy barriers below a certain threshold. We illustrate this time dependence for some benchmark systems, namely...
    Categories: Journal Articles
  • Fenton chemistry at aqueous interfaces [Chemistry]
    [Jan 2014]

    In a fundamental process throughout nature, reduced iron unleashes the oxidative power of hydrogen peroxide into reactive intermediates. However, notwithstanding much work, the mechanism by which Fe2+ catalyzes H2O2 oxidations and the identity of the participating intermediates remain controversial. Here we report the prompt formation of O=FeIVCl3− and chloride-bridged di-iron...
    Categories: Journal Articles
  • Exooceanography and climate of tidal-locking exoplanets [Earth, Atmospheric, and Planetary Sciences]
    [Jan 2014]

    The distinctive feature of tidally locked exoplanets is the very uneven heating by stellar radiation between the dayside and nightside. Previous work has focused on the role of atmospheric heat transport in preventing atmospheric collapse on the nightside for terrestrial exoplanets in the habitable zone around M dwarfs. In the...
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  • Lack of splash singularities for SQG and Muskat [Mathematics]
    [Jan 2014]

    In this paper, for both the sharp front surface quasi-geostrophic equation and the Muskat problem, we rule out the “splash singularity” blow-up scenario; in other words, we prove that the contours evolving from either of these systems cannot intersect at a single point while the free boundary remains smooth. Splash...
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  • Tunable non-eq. dynamics in spin ice field quench [Physics]
    [Jan 2014]

    We present nonequilibrium physics in spin ice as a unique setting that combines kinematic constraints, emergent topological defects, and magnetic long-range Coulomb interactions. In spin ice, magnetic frustration leads to highly degenerate yet locally constrained ground states. Together, they form a highly unusual magnetic state—a “Coulomb phase”—whose excitations are point-like...
    Categories: Journal Articles
  • Root microbiota in Arabidopsis thaliana relatives [Plant Biology]
    [Jan 2014]

    Plants host at the contact zone with soil a distinctive root-associated bacterial microbiota believed to function in plant nutrition and health. We investigated the diversity of the root microbiota within a phylogenetic framework of hosts: three Arabidopsis thaliana ecotypes along with its sister species Arabidopsis halleri and Arabidopsis lyrata, as...
    Categories: Journal Articles
  • Bodily maps of emotions [Psychological and Cognitive Sciences]
    [Jan 2014]

    Emotions are often felt in the body, and somatosensory feedback has been proposed to trigger conscious emotional experiences. Here we reveal maps of bodily sensations associated with different emotions using a unique topographical self-report method. In five experiments, participants (n = 701) were shown two silhouettes of bodies alongside emotional...
    Categories: Journal Articles
  • Satellites and psychology for improved forest monitoring [Opinion]
    [Jan 2014]

    Forests are changing faster today than at any time since the Ice Age. The human enterprise has driven vast forest losses and a mounting wake of forest regrowth that defies historical biogeography. As the pace of change accelerates, so does the demand to monitor forests for conservation and resource policy....
    Categories: Journal Articles
  • Conservation genomics [Core Concepts]
    [Jan 2014]

    The Tasmanian devil, a carnivorous marsupial that prowls the scrublands of the Australian island of Tasmania at night in search of small prey, is often seen as a face of imminent species extinction. Faced with the threat of wipeout, the devils have dwindled in number since the mid-1990s, when a...
    Categories: Journal Articles