Proceedings of the Natural Academy of Sciences

Proceedings of the National Academy of Sciences RSS feed -- current issue
  • Protein folding and binding evolve as spandrels [Evolution]
    [Feb 2015]

    Binding interactions between proteins and other molecules mediate numerous cellular processes, including metabolism, signaling, and gene regulation. These interactions often evolve in response to changes in the protein’s chemical or physical environment (such as the addition of an antibiotic). Several recent studies have shown the importance of folding stability in...
    Categories: Journal Articles
  • Optically driven motions of microrods in an LC [Physics]
    [Feb 2015]

    A small amount of azo-dendrimer molecules dissolved in a liquid crystal enables translational and rotational motions of microrods in a liquid crystal matrix under unpolarized UV light irradiation. This motion is initiated by a light-induced trans-to-cis conformational change of the dendrimer adsorbed at the rod surface and the associated director...
    Categories: Journal Articles
  • Cooperate without looking [Psychological and Cognitive Sciences]
    [Feb 2015]

    Evolutionary game theory typically focuses on actions but ignores motives. Here, we introduce a model that takes into account the motive behind the action. A crucial question is why do we trust people more who cooperate without calculating the costs? We propose a game theory model to explain this phenomenon....
    Categories: Journal Articles
  • Reproducible research can still be wrong [Opinion]
    [Feb 2015]

    Reproducibility—the ability to recompute results—and replicability—the chances other experimenters will achieve a consistent result—are two foundational characteristics of successful scientific research. Consistent findings from independent investigators are the primary means by which scientific evidence accumulates for or against a hypothesis. Yet, of late, there has been a crisis of confidence...
    Categories: Journal Articles
  • Many species, one health [News Feature]
    [Feb 2015]

    In the race to save endangered frogs from extinction, disease ecologists are hunting for patterns of infection that could also improve human well-being. Frogs infected with the flatworm Ribeiroia could be extras in a horror movie. Their bodies are a tangled mess, sprouting extra limbs and joints, and covered with...
    Categories: Journal Articles
  • Simple chained guide trees give poorer alignments [Biological Sciences]
    [Jan 2015]

    Multiple sequence aligners typically work by progressively aligning the most closely related sequences or group of sequences according to guide trees. In PNAS, Boyce et al. (1) report that alignments reconstructed using simple chained trees (i.e., comb-like topologies) with random leaf assignment performed better in protein structure-based benchmarks than those...
    Categories: Journal Articles
  • Real and simulated proteins in MSAs [Biological Sciences]
    [Jan 2015]

    Tan et al. (1) comment on our earlier paper regarding the accuracy of multiple sequence alignments (MSAs) using different guide tree topologies (2). We stress that the scope of our result was confined to alignments of very large numbers of protein sequences with known structures, where accuracy was measured against...
    Categories: Journal Articles
  • Should we "reef" obsolete oil platforms? [Biological Sciences]
    [Jan 2015]

    Claisse et al. (1) show that not only do oil platforms produce fish, but they do so at a rate far greater than our most productive marine habitats, such as coral reefs and mangroves. Because this information may be used to justify increased “reefing” of obsolete oil infrastructure worldwide, we...
    Categories: Journal Articles
  • Oxidation-driven surface dynamics on NiAl(100) [Engineering]
    [Jan 2015]

    Atomic steps, a defect common to all crystal surfaces, can play an important role in many physical and chemical processes. However, attempts to predict surface dynamics under nonequilibrium conditions are usually frustrated by poor knowledge of the atomic processes of surface motion arising from mass transport from/to surface steps. Using...
    Categories: Journal Articles
  • Tackling the single molecule counting problem [Biophysics and Computational Biology]
    [Jan 2015]

    Superresolution imaging methods—now widely used to characterize biological structures below the diffraction limit—are poised to reveal in quantitative detail the stoichiometry of protein complexes in living cells. In practice, the photophysical properties of the fluorophores used as tags in superresolution methods have posed a severe theoretical challenge toward achieving this...
    Categories: Journal Articles
  • M. tuberculosis CrgA structure in lipid bilayers [Biophysics and Computational Biology]
    [Jan 2015]

    The 93-residue transmembrane protein CrgA in Mycobacterium tuberculosis is a central component of the divisome, a large macromolecular machine responsible for cell division. Through interactions with multiple other components including FtsZ, FtsQ, FtsI (PBPB), PBPA, and CwsA, CrgA facilitates the recruitment of the proteins essential for peptidoglycan synthesis to the...
    Categories: Journal Articles
  • {beta}-Helical architecture of cytoskeletal bactofilin [Biophysics and Computational Biology]
    [Jan 2015]

    Bactofilins are a widespread class of bacterial filament-forming proteins, which serve as cytoskeletal scaffolds in various cellular pathways. They are characterized by a conserved architecture, featuring a central conserved domain (DUF583) that is flanked by variable terminal regions. Here, we present a detailed investigation of bactofilin filaments from Caulobacter crescentus...
    Categories: Journal Articles
  • Multifunctional WRM-1 [Developmental Biology]
    [Jan 2015]

    Vertebrate β-catenin has two functions, as a structural component of the adherens junction in cell adhesion and as the T-cell factor (TCF) transcriptional coactivator in canonical Wnt (wingless-related integration site) signaling. These two functions are split between three of the four β-catenin–related proteins present in the round worm Caenorhabditis elegans....
    Categories: Journal Articles
  • Epitope conservation in MTB and beyond [Immunology and Inflammation]
    [Jan 2015]

    A previous unbiased genome-wide analysis of CD4 Mycobacterium tuberculosis (MTB) recognition using peripheral blood mononuclear cells from individuals with latent MTB infection (LTBI) or nonexposed healthy controls (HCs) revealed that certain MTB sequences were unexpectedly recognized by HCs. In the present study, it was found that, based on their pattern...
    Categories: Journal Articles
  • Antigen-specific tolerogenic nanoparticles [Immunology and Inflammation]
    [Jan 2015]

    Current treatments to control pathological or unwanted immune responses often use broadly immunosuppressive drugs. New approaches to induce antigen-specific immunological tolerance that control both cellular and humoral immune responses are desirable. Here we describe the use of synthetic, biodegradable nanoparticles carrying either protein or peptide antigens and a tolerogenic immunomodulator,...
    Categories: Journal Articles
  • Insights and targets for the immunotherapy of CLL [Immunology and Inflammation]
    [Jan 2015]

    The breakthrough development of clinically effective immune checkpoint inhibitors illustrates the potential of T-cell–based immunotherapy to effectively treat malignancies. A remaining challenge is to increase and guide the specificities of anticancer immune responses, e.g., by therapeutic vaccination or by adoptive T-cell transfer. By analyzing the landscape of naturally presented HLA...
    Categories: Journal Articles
  • Antiviral immunity of Anopheles mosquitoes [Microbiology]
    [Jan 2015]

    Arboviruses are transmitted by mosquitoes and other arthropods to humans and animals. The risk associated with these viruses is increasing worldwide, including new emergence in Europe and the Americas. Anopheline mosquitoes are vectors of human malaria but are believed to transmit one known arbovirus, o’nyong-nyong virus, whereas Aedes mosquitoes transmit...
    Categories: Journal Articles
  • MglA regulates polarity of gliding in M. xanthus [Microbiology]
    [Jan 2015]

    Gliding motility in Myxococcus xanthus is powered by flagella stator homologs that move in helical trajectories using proton motive force. The Frz chemosensory pathway regulates the cell polarity axis through MglA, a Ras family GTPase; however, little is known about how MglA establishes the polarity of gliding, because the gliding...
    Categories: Journal Articles
  • Heavy water as a single-cell activity marker [Microbiology]
    [Jan 2015]

    Microbial communities are essential to the function of virtually all ecosystems and eukaryotes, including humans. However, it is still a major challenge to identify microbial cells active under natural conditions in complex systems. In this study, we developed a new method to identify and sort active microbes on the single-cell...
    Categories: Journal Articles
  • Switch in the identity of NMDAR coagonists [Neuroscience]
    [Jan 2015]

    NMDA receptors (NMDARs) require the coagonists d-serine or glycine for their activation, but whether the identity of the coagonist could be synapse specific and developmentally regulated remains elusive. We therefore investigated the contribution of d-serine and glycine by recording NMDAR-mediated responses at hippocampal Schaffer collaterals (SC)–CA1 and medial perforant path–dentate...
    Categories: Journal Articles