Nanoparticle amount, and not size, determines chain alignment and nonlinear hardening in polymer nanocomposites
H. Samet Varol, Fanlong Meng, Babak Hosseinkhani, Christian Malm, Daniel Bonn, Mischa Bonn, Alessio Zaccone, and Sapun H. Parekh
When straining materials (e.g., pulling a rubber band), they initially deform with a certain stiffness; if one pulls harder, some materials strengthen. This phenomenon, known as nonlinear strain hardening, is a critical feature of composite polymer materials—polymers with reinforcing filler particles—used in, e.g., car tires. Engineering properties such as modulus, toughness, and strength of nanocomposites have been traditionally optimized through trial and error by changing the size and amount of fillers. Our work elucidates the molecular origin of strain hardening in polymer nanocomposites, showing that filler amount, but not size, sets the strain-hardening properties based on interfiller chain elongation. The insensitivity to filler size provides a facile concept to independently tune linear and nonlinear mechanics in composites. (See pp. E3170–E3177.)
Structure–metabolism relationships in human-AOX: Chemical insights from a large database of aza-aromatic and amide compounds
Susan Lepri, Martina Ceccarelli, Nicolò Milani, Sara Tortorella, Andrea Cucco, Aurora Valeri, Laura Goracci, Andreas Brink, and Gabriele Cruciani
The metabolism of xenobiotics is a critical aspect of drug discovery; nowadays, aldehyde oxidase (AOX) has emerged as a key metabolic enzyme having a pivotal role in the failures of several clinical candidates. The lack of homogenous data on possible substrates and not substrates of this enzyme represents a serious limit for the development of an in silico model for metabolism prediction. Here, we present a database of 270 chemically diverse compounds containing aza-aromatic and/or amide moieties (susceptible to human AOX), experimentally tested in vitro. The results herein reported should be useful in the development of a reliable prediction model, which should be of wide interest in chemistry, biology, biotechnology, and medicine. (See pp. E3178–E3187.)
Delivering strong 1H nuclear hyperpolarization levels and long magnetic lifetimes through signal amplification by reversible exchange
Peter J. Rayner, Michael J. Burns, Alexandra M. Olaru, Philip Norcott, Marianna Fekete, Gary G. R. Green, Louise A. R. Highton, Ryan E. Mewis, and Simon B. Duckett
The study of molecules and materials is of great significance to both science and human welfare. The noninvasive techniques of NMR and MRI reflect two of the most important methods to study them. However, both of these approaches are insensitive, and hyperpolarization methods to improve sensitivity are needed to access new applications. The hyperpolarization approach signal amplification by reversible exchange is used to produce a signal that is 100,000 times larger than that which would be seen on a routine clinical MRI scanner under Boltzmann equilibrium conditions. By revealing the broad scope of this approach we demonstrate its potential for the future diagnostic detection of metabolites, drugs, and many other small molecules. (See pp. E3188–E3194.)
Quantitative criticism of literary relationships
Joseph P. Dexter, Theodore Katz, Nilesh Tripuraneni, Tathagata Dasgupta, Ajay Kannan, James A. Brofos, Jorge A. Bonilla Lopez, Lea A. Schroeder, Adriana Casarez, Maxim Rabinovich, Ayelet Haimson Lushkov, and Pramit Chaudhuri
Famous works of literature can serve as cultural touchstones, inviting creative adaptations in subsequent writing. To understand a poem, play, or novel, critics often catalog and analyze these intertextual relationships. The study of such relationships is challenging because intertextuality can take many forms, from direct quotation to literary imitation. Here, we show that techniques from authorship attribution studies, including stylometry and machine learning, can shed light on inexact literary relationships involving little explicit text reuse. We trace the evolution of features not tied to individual words across diverse corpora and provide statistical evidence to support interpretive hypotheses of literary critical interest. The significance of this approach is the integration of quantitative and humanistic methods to address aspects of cultural evolution. (See pp. E3195–E3204.)
Structure of aryl O-demethylase offers molecular insight into a catalytic tyrosine-dependent mechanism
Amanda C. Kohler, Matthew J. L. Mills, Paul D. Adams, Blake A. Simmons, and Kenneth L. Sale
Modern industrial and agricultural practices generate large quantities of aromatic pollutants; however, these waste products can be converted into fine chemicals, fuels, and plastics through biocatalytic pathways. The bacterial world can inform such utilization strategies as certain strains of soil and marine bacteria metabolize environmentally derived aromatics. Many of these metabolic pathways involve aryl intermediates that require demethylation to facilitate modification and ring opening for assimilation into the tricarboxylic acid (TCA) cycle. Aryl demethylases, which catalyze this reaction, are poorly understood, making their utilization in biotechnology difficult. We provide the structural and mechanistic characterization of a single-domain aryl demethylase, LigM, which employs a tyrosine-dependent mechanism. Insights from this work will inform synthetic biology approaches to convert underutilized aromatics into higher value compounds. (See pp. E3205–E3214.)
Mass spectrometric identification of intermediates in the O2-driven [4Fe-4S] to [2Fe-2S] cluster conversion in FNR
Jason C. Crack, Andrew J. Thomson, and Nick E. Le Brun
The transcriptional regulator Fumarate and Nitrate Reduction is the master switch for the transition between anaerobic and aerobic respiration in many other bacteria. It fulfills this role by controlling the expression of >300 genes in response to O2. It senses O2 through a [4Fe-4S] cluster cofactor, which undergoes conversion to a [2Fe-2S] cluster on reaction with O2, leading to loss of DNA binding. By using time-resolved electrospray ionization mass spectrometry, we gained insight into the reaction through detection of cluster conversion intermediates and products, including a [3Fe-3S] cluster. The data also show that sulfide released from the cluster is oxidized during the conversion reaction and not after it. Our methodology has great potential for broad application to studies of cofactor reactivities. (See pp. E3215–E3223.)
Structural basis of pH-dependent client binding by ERp44, a key regulator of protein secretion at the ER–Golgi interface
Satoshi Watanabe, Manami Harayama, Shingo Kanemura, Roberto Sitia, and Kenji Inaba
The high-resolution structures presented herein explain how ERp44, a multifunctional chaperone cycling in the early secretory pathway, exploits the endoplasmic reticulum (ER)–Golgi pH gradient to bind clients in the acidic Golgi and release them into the neutral ER environment. Protonation of essential cysteine and histidine residues induces conformational changes that simultaneously expose Cys29 in the positively charged client-binding site and the C-terminal KDEL receptor-binding motif, making ERp44 a pH-sensitive molecular machine that controls fidelity of protein secretion. (See pp. E3224–E3232.)
Nit1 is a metabolite repair enzyme that hydrolyzes deaminated glutathione
Alessio Peracchi, Maria Veiga-da-Cunha, Tomiko Kuhara, Kenneth W. Ellens, Nicole Paczia, Vincent Stroobant, Agnieszka K. Seliga, Simon Marlaire, Stephane Jaisson, Guido T. Bommer, Jin Sun, Kay Huebner, Carole L. Linster, Arthur J. L. Cooper, and Emile Van Schaftingen
The genomes of the vast majority of eukaryotes encode a protein [named nitrilase-like protein 1 (Nit1) in humans and mice] whose enzymatic function has long been unknown. We show here that the mammalian Nit1 and the corresponding yeast protein efficiently hydrolyze the deaminated form of the common intracellular antioxidant glutathione. In turn, deaminated glutathione can be produced by a side activity of numerous transaminases. Thus, Nit1 repairs an undesired product, arising from the slow (and erroneous) transformation of an important metabolite by some abundant intracellular enzymes. The importance of this Nit1 function is underscored by the finding that enzymes with the same activity occur in Escherichia coli and in other glutathione-producing bacteria. (See pp. E3233–E3242.)
Structure of the MeCP2–TBLR1 complex reveals a molecular basis for Rett syndrome and related disorders
Valdeko Kruusvee, Matthew J. Lyst, Ceitidh Taylor, žygimantė Tarnauskaitė, Adrian P. Bird, and Atlanta G. Cook
Methyl-CpG–binding protein 2 (MeCP2) links epigenetics, brain function, and neurological disease. Mutations in the MeCP2 protein cause Rett syndrome (RTT), making it imperative to determine its mechanism of action. One domain of MeCP2 targets it to methylated DNA, but little was known about a second essential domain except that it recruits a gene-silencing complex. We determined that transducin-beta like (TBL) subunits of the silencing complex bind MeCP2 and solved the structure of the binary complex. Strikingly, amino acids mutated in RTT are precisely those amino acids that intimately contact the TBL subunits. Furthermore, mutations in TBL proteins that cause intellectual disability block interaction with MeCP2. Our data suggest that the TBL–MeCP2 interaction is essential for brain function. (See pp. E3243–E3250.)
Facilitated dissociation of transcription factors from single DNA binding sites
Ramsey I. Kamar, Edward J. Banigan, Aykut Erbas, Rebecca D. Giuntoli, Monica Olvera de la Cruz, Reid C. Johnson, and John F. Marko
Transcription factors (TFs) control biological processes by binding and unbinding to DNA. Therefore, it is crucial to understand the mechanisms that affect TF binding kinetics. Recent studies challenge the standard picture of TF binding kinetics by showing cases of proteins in solution accelerating TF dissociation rates through a facilitated dissociation (FD) process. Our study shows that FD can occur at the level of single binding sites without the action of large protein clusters or long DNA segments. Our results quantitatively support a model of FD in which competitor proteins invade partially dissociated states of DNA-bound TFs. FD is expected to be a general mechanism for modulating gene expression by altering the occupancy of TFs on the genome. (See pp. E3251–E3257.)
Membrane fission by protein crowding
Wilton T. Snead, Carl C. Hayden, Avinash K. Gadok, Chi Zhao, Eileen M. Lafer, Padmini Rangamani, and Jeanne C. Stachowiak
The division of membrane-bound compartments into smaller, separate volumes is essential to cells. The process of membrane fission is required for the separation of two membrane compartments. The prevailing view has been that to drive fission, proteins must contain specific structural features such as curved scaffolds and wedge-like membrane insertions. In contrast, this work demonstrates a more general mechanism, in which crowding among membrane-bound proteins drives fission. Like a compressed gas, collisions among crowded proteins generate pressure that can stretch, bend, and ultimately disrupt membrane surfaces, leading to fission. The discovery of this mechanism broadens our perspective on membrane fission by demonstrating how any protein, independent of its structure, can assist in this essential cellular process. (See pp. E3258–E3267.)
Conformational equilibria of light-activated rhodopsin in nanodiscs
Ned Van Eps, Lydia N. Caro, Takefumi Morizumi, Ana Karin Kusnetzow, Michal Szczepek, Klaus Peter Hofmann, Timothy H. Bayburt, Stephen G. Sligar, Oliver P. Ernst, and Wayne L. Hubbell
The existence of multiple conformational substates of G-protein–coupled receptors in equilibrium may provide for the interaction with multiple partners at the same interface. Here we provide evidence that photoactivated rhodopsin exists in a manifold of conformational substates in a lipid environment, but not in the extensively studied dodecyl maltoside detergent micelles. Moreover, the photoactivated state decays spontaneously to the inactive state on a timescale of minutes. Remarkably, binding of the activated receptor to the cognate G protein strongly biases the receptor to an interacting state that retains more than one conformation, suggesting flexibility in the complex. (See pp. E3268–E3275.)
Climate change both facilitates and inhibits invasive plant ranges in New England
Cory Merow, Sarah Treanor Bois, Jenica M. Allen, Yingying Xie, and John A. Silander Jr.
Invasive species are often expected to benefit from novel conditions encountered with global change. Our range models based on demography show that invasive Alliaria petiolata (garlic mustard) may have much lower establishment in New England under future climate, despite prolific success under current climate, whereas other invasive and native plants may expand their ranges. Forecasts suggest that management should focus on inhibiting northward spread of A. petiolata into unoccupied areas and understanding source–sink population dynamics and how community dynamics might respond to loss of A. petiolata (it modifies soil properties). Our methods illustrate inadequacy of current approaches to forecasting invasions in progress, which are based on correlations between species’ occurrence and environment and illustrate critical need for mechanistic studies. (See pp. E3276–E3284.)
Intracellular metabolite β-glucosylceramide is an endogenous Mincle ligand possessing immunostimulatory activity
Masahiro Nagata, Yoshihiro Izumi, Eri Ishikawa, Ryoko Kiyotake, Rieko Doi, Satoru Iwai, Zakaria Omahdi, Toshiyuki Yamaji, Tomofumi Miyamoto, Takeshi Bamba, and Sho Yamasaki
Sensing tissue damage is a crucial function of pattern recognition receptors (PRRs). However, endogenous ligand recognition by PRRs is not well documented. Macrophage inducible C-type lectin (Mincle) is a PRR that recognizes both pathogens and damaged cells. In this study, we isolated endogenous glycolipids derived from damaged cells and identified a ubiquitous intracellular metabolite, β-glucosylceramide (GlcCer), as a Mincle ligand. β-GlcCer induced inflammatory and acquired immune responses via Mincle on myeloid cells. Accumulation of β-GlcCer leads to Gaucher disease, a disorder characterized mainly by systemic inflammation. In a Gaucher model in which mice are deficient in the β-GlcCer–degrading enzyme, further deletion of the Mincle gene attenuated inflammatory responses. These results suggest that β-GlcCer is an endogenous Mincle ligand and acts as an immunostimulatory factor upon cell damage. (See pp. E3285–E3294.)
Nimodipine fosters remyelination in a mouse model of multiple sclerosis and induces microglia-specific apoptosis
Andrea Schampel, Oleg Volovitch, Tobias Koeniger, Claus-Jürgen Scholz, Stefanie Jörg, Ralf A. Linker, Erhard Wischmeyer, Marie Wunsch, Johannes W. Hell, Süleyman Ergün, and Stefanie Kuerten
Multiple sclerosis (MS) is the most frequent neurological disease that leads to premature retirement in young adults. Progressive MS currently is not only incurable, but also untreatable. Here we show that the calcium channel antagonist nimodipine significantly attenuated clinical disease and central nervous system degeneration and also fostered remyelination in a mouse model of MS. The effect of nimodipine was microglia specific, inducing apoptosis and decreasing the production of neurotoxic molecules such as nitric oxide and reactive oxygen species both in vitro and in vivo. These results introduce a treatment option for MS and also may have broad therapeutic implications for chronic neuroinflammatory diseases in general. (See pp. E3295–E3304.)
Dynamic neural architecture for social knowledge retrieval
Yin Wang, Jessica A. Collins, Jessica Koski, Tehila Nugiel, Athanasia Metoki, and Ingrid R. Olson
Knowledge about other people is critical for group survival and may have unique cognitive processing demands. Here, we investigate how person knowledge is represented, organized, and retrieved in the brain. We show that the anterior temporal lobe (ATL) stores abstract person identity representation that is commonly embedded in multiple sources (e.g. face, name, scene, and personal object). We also found the ATL serves as a “neural switchboard,” coordinating with a network of other brain regions in a rapid and need-specific way to retrieve different aspects of biographical information (e.g., occupation and personality traits). Our findings endorse the ATL as a central hub for representing and retrieving person knowledge. (See pp. E3305–E3314.)
Parietal neurons encode expected gains in instrumental information
Nicholas C. Foley, Simon P. Kelly, Himanshu Mhatre, Manuel Lopes, and Jacqueline Gottlieb
We examine how the brain guides active sensing in awake, behaving primates using a paradigm in which information sampling is dissociated from reinforcement variables, such as cumulative future reward or reward prediction errors. We show that target selective cells in lateral intraparietal cortex encode decision variables based on expected gains in instrumental information—the extent to which a visual cue, when discriminated, is expected to reduce the uncertainty of a subsequent action. (See pp. E3315–E3323.)
Trk receptor signaling and sensory neuron fate are perturbed in human neuropathy caused by Gars mutations
James N. Sleigh, John M. Dawes, Steven J. West, Na Wei, Emily L. Spaulding, Adriana Gómez-Martín, Qian Zhang, Robert W. Burgess, M. Zameel Cader, Kevin Talbot, Xiang-Lei Yang, David L. Bennett, and Giampietro Schiavo
The mechanisms triggering motor and sensory nerve dysfunction in the genetically diverse Charcot–Marie–Tooth disease (CMT) remain unresolved, as does the reason for the lack of sensory pathology observed in distal hereditary motor neuropathies, which can be associated with CMT genes. To unravel the pathways leading to afferent deterioration, we have studied the sensory nervous system of CMT type 2D (CMT2D) mice. Our work demonstrates that the specific cellular identity of sensory nerves is perturbed in mutant mice prenatally, and that this is likely caused by aberrant interaction of mutant CMT2D protein with Trk receptors impacting their prodifferentiation/development signaling. CMT therefore manifests through malfunctioning of the complex interplay between developmental, maturation, and survival programs, which has important implications for therapeutic timing. (See pp. E3324–E3333.)
Neuroendocrine androgen action is a key extraovarian mediator in the development of polycystic ovary syndrome
Aimee S. L. Caldwell, Melissa C. Edwards, Reena Desai, Mark Jimenez, Robert B. Gilchrist, David J. Handelsman, and Kirsty A. Walters
The cause of polycystic ovary syndrome (PCOS) is unknown, but androgen excess is a key feature. We combined a hyperandrogenized PCOS mouse model with global and tissue- and cell-specific androgen-resistant mouse lines to uncover the sites of androgen action that initiate PCOS. We demonstrate that direct androgen actions, particularly in neurons but less so in granulosa cells, are required for the development of key reproductive and metabolic PCOS features. These data highlight the previously overlooked importance of extraovarian neuroendocrine androgen action in the origins of PCOS. Targeting androgen-driven mechanisms may represent new options for developing a mechanism-based treatment of PCOS. (See pp. E3334–E3343.)
Parathyroid hormone controls paracellular Ca2+ transport in the thick ascending limb by regulating the tight-junction protein Claudin14
Tadatoshi Sato, Marie Courbebaisse, Noriko Ide, Yi Fan, Jun-ichi Hanai, Jovana Kaludjerovic, Michael J. Densmore, Quan Yuan, Hakan R. Toka, Martin R. Pollak, Jianghui Hou, and Beate Lanske
Renal calcium reabsorption is a critical process for maintaining systemic calcium homeostasis. Although the role of parathyroid hormone (PTH) in the regulation of transcellular Ca2+ reabsorption in distal convoluted tubules is well understood, its potential role in controlling the paracellular Ca2+ transport in the thick ascending limb of Henle (TAL) has not been investigated. We now present data demonstrating that PTH/PTHrP receptor (PTH1R) signaling directly and indirectly controls the levels of Claudin14 (CLDN14), a tight-junction protein responsible for paracellular Ca2+ transport in the TAL. Our findings suggest that down-regulation of Claudin14 could provide a potential treatment option to correct urinary Ca2+ loss, particularly in patients with hypoparathyroidism. (See pp. E3344–E3353.)
Phosphatidylinositol 3-phosphate–binding protein AtPH1 controls the localization of the metal transporter NRAMP1 in Arabidopsis
Astrid Agorio, Jérôme Giraudat, Michele Wolfe Bianchi, Jessica Marion, Christelle Espagne, Loren Castaings, Françoise Lelièvre, Catherine Curie, Sébastien Thomine, and Sylvain Merlot
Metal homeostasis is essential for living organisms. Metal transporters play key roles in metal uptake and compartmentalization. The tight regulation of metal homeostasis thus depends on accurate targeting of these metal transporters. Although the main metal transporters in plants have been identified, the mechanisms involved in their trafficking are still poorly understood. This study reveals that AtPH1, a pleckstrin homology (PH) domain containing protein binding to phosphatidylinositol 3-phosphate (PI3P), controls the subcellular localization of the iron and manganese transporter AtNRAMP1. Our results further indicate that, in addition to proteins containing the FYVE and PHOX domains, proteins containing the PH domain can decode the PI3P signal in endosomal function. (See pp. E3354–E3363.)