On June 7, 2011, our Sun erupted, blasting tons of hot plasma into space. Some of that plasma splashed back down onto the Sun’s surface, […]

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The Smithsonian’s National Air and Space Museum announced that it will receive a $6 million donation from the Thomas W. Haas Foundation to establish an […]

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Rooting through the garbage for a late-night snack or stealing food from the cat’s bowl, the suburban raccoon is a nocturnal, intelligent animal. Yet life […]

The post Suburban raccoons more social yet dominance behavior remains that of a solitary animal appeared first on Smithsonian Insider.

As economic expansion and development fragments the forest landscape of central India, the species that rely on that habitat—including endangered tigers and leopards—face dwindling populations […]

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Sometime during the Middle Eocene a prehistoric mosquito slurped down a final blood meal then died and sank to the bottom of a pond in […]

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It is one of the most sensitive noses in the animal kingdom but what its owner seeks is no pungent bed of roses, in fact […]

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Carla Dove is an Ornithologist at the Smithsonian National Museum of Natural History. In this Feb. 12 Webcast join her in analyzing the remains of […]

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The black-headed paradise-flycatcher of western and central Africa is a small colorful forest bird that thrives on the flying insects it chases down by swooping, […]

The post These mites should make birds quiver right down to their quills appeared first on Smithsonian Insider.

Authoritative, intelligent and always accompanied by a young assistant, television’s Mr. Wizard brought science to America’s kids from the 1950s through 1980s with experiments using […]

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Life in the universe might be even rarer than we thought. Recently, astronomers looking for potentially habitable worlds have targeted red dwarf stars because they […]

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Astronomers using the Atacama Large Millimeter/submillimeter Array (ALMA) may have detected the dusty hallmarks of an entire family of Pluto-size objects swarming around an adolescent […]

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Hundreds of thousands of asteroids are known to orbit our Sun at distances ranging from near the Earth to beyond Saturn. The most widely known […]

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Did you know that the blood-sucking parasite known as the tick is actually nearly 900 different species? Or that the tick is not an insect, […]

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Three new species of dragon-esque woodlizards have been discovered in the Andean cloud forests of Peru and Ecuador. The new species differ from their closest […]

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In one of the largest studies of its kind, a volunteer-fueled camera trapping effort showed that where coyotes have moved in, cats are nowhere to […]

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Smithsonian scientists and colleagues have discovered a new genus and species of river dolphin that has long been extinct. They made the discovery after carefully […]

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When astronomers study protoplanetary disks of gas and dust that surround young stars, they sometimes spot a dark gap like the Cassini division in Saturn’s […]

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After decades of attempts, Smithsonian Conservation Biology Institute (SCBI) scientists and researchers at Cornell University have become the first to successfully use in vitro fertilization […]

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Osteoarthritis in dogs is a serious and painful malady that effects many breeds. Recently Janine Brown, a biologist at the Smithsonian Conservation Biology Institute in […]

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The bush dog is one of the most enigmatic of the world’s canid species, seldom seen throughout its range in Central and South America. New […]

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A fossil that has been in the collection of the Smithsonian’s National Museum of Natural History since it was discovered in 1951 is today helping […]

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There’s something exciting and strange about having an idea. It can come suddenly. Unexpectedly. Randomly. Intensely. Ideas can uninvitingly appear full-forced and bright—like the cliché […]

The post Making the Smithsonian’s New “Sidedoor” podcast series a reality appeared first on Smithsonian Insider.

Tool use by sea otters to break open well-armored food is not necessarily a family matter, according to a new study published this week by […]

The post Tool use by sea otters has little to do with genetic ties: Smithsonian study appeared first on Smithsonian Insider.

AUSTIN, Texas — Astronomers at The University of Texas at Austin and Harvard University have put a basic principle of black holes to the test, […]

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Cats are notoriously fickle—purring in your lap one second, then swiping you with an indignant claw the next. One thing is certain however when it […]

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Today’s cutting-edge laboratories rely on ultra-cold refrigeration to keep delicate cells like sperm viable for use in the future. But a new technique using microwaves […]

The post What does candied, microwaved sperm have to do with saving endangered species? appeared first on Smithsonian Insider.

Flitting swiftly through the darkness above the tropical forest canopy in Central and South America, a group of cute little bats with dog-like faces have […]

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Marine mammologist Matthew Leslie aims his crossbow from the bow of a moving boat at the dolphins riding the breaking waves below. A dolphin will […]

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 Extinct species don’t usually get a do-over… but don’t tell that to the scimitar-horned oryx. Erased from the wild for three decades, these desert […]

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When the heat and humidity of the Washington, D.C. summer sends its residents scrambling for air conditioning and iced coffee, the animal care specialists at […]

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Aldo-keto reductases (AKRs) are NADPH/NADP+-dependent oxidoreductase enzymes that metabolize an aldehyde/ketone to the corresponding alcohol. AKR4C14 from rice exhibits a much higher efficiency in metabolizing malondialdehyde (MDA) than do the Arabidopsis enzymes AKR4C8 and AKR4C9, despite sharing greater than 60% amino-acid sequence identity. This study confirms the role of rice AKR4C14 in the detoxification of methylglyoxal and MDA, and demonstrates that the endogenous contents of both aldehydes in transgenic Arabidopsis ectopically expressing AKR4C14 are significantly lower than their levels in the wild type. The apo structure of indica rice AKR4C14 was also determined in the absence of the cofactor, revealing the stabilized open conformation. This is the first crystal structure in AKR subfamily 4C from rice to be observed in the apo form (without bound NADP+). The refined AKR4C14 structure reveals a stabilized open conformation of loop B, suggesting the initial phase prior to cofactor binding. Based on the X-ray crystal structure, the substrate- and cofactor-binding pockets of AKR4C14 are formed by loops A, B, C and β1α1. Moreover, the residues Ser211 and Asn220 on loop B are proposed as the hinge residues that are responsible for conformational alteration while the cofactor binds. The open conformation of loop B is proposed to involve Phe216 pointing out from the cofactor-binding site and the opening of the safety belt. Structural comparison with other AKRs in subfamily 4C emphasizes the role of the substrate-channel wall, consisting of Trp24, Trp115, Tyr206, Phe216, Leu291 and Phe295, in substrate discrimination. In particular, Leu291 could contribute greatly to substrate selectivity, explaining the preference of AKR4C14 for its straight-chain aldehyde substrate.

The biological processes related to protein homeostasis in Mycobacterium tuberculosis, the etiologic agent of tuberculosis, have recently been established as critical pathways for therapeutic intervention. Proteins of particular interest are ClpC1 and the ClpC1–ClpP1–ClpP2 proteasome complex. The structure of the potent antituberculosis macrocyclic depsipeptide ecumicin complexed with the N-terminal domain of ClpC1 (ClpC1-NTD) is presented here. Crystals of the ClpC1-NTD–ecumicin complex were monoclinic (unit-cell parameters a = 80.0, b = 130.0, c = 112.0 Å, β = 90.07°; space group P21; 12 complexes per asymmetric unit) and diffracted to 2.5 Å resolution. The structure was solved by molecular replacement using the self-rotation function to resolve space-group ambiguities. The new structure of the ecumicin complex showed a unique 1:2 (target:ligand) stoichiometry exploiting the intramolecular dyad in the α-helical fold of the target N-terminal domain. The structure of the ecumicin complex unveiled extensive interactions in the uniquely extended N-terminus, a critical binding site for the known cyclopeptide complexes. This structure, in comparison with the previously reported rufomycin I complex, revealed unique features that could be relevant for understanding the mechanism of action of these potential antituberculosis drug leads. Comparison of the ecumicin complex and the ClpC1-NTD-L92S/L96P double-mutant structure with the available structures of rufomycin I and cyclomarin A complexes revealed a range of conformational changes available to this small N-terminal helical domain and the minor helical alterations involved in the antibiotic-resistance mechanism. The different modes of binding and structural alterations could be related to distinct modes of action.

Pullulanase (EC 3.2.1.41) is a well known starch-debranching enzyme that catalyzes the cleavage of α-1,6-glycosidic linkages in α-glucans such as starch and pullulan. Crystal structures of a type I pullulanase from Paenibacillus barengoltzii (PbPulA) and of PbPulA in complex with maltopentaose (G5), maltohexaose (G6)/α-cyclodextrin (α-CD) and β-cyclodextrin (β-CD) were determined in order to better understand substrate binding to this enzyme. PbPulA belongs to glycoside hydrolase (GH) family 13 subfamily 14 and is composed of three domains (CBM48, A and C). Three carbohydrate-binding sites identified in PbPulA were located in CBM48, near the active site and in domain C, respectively. The binding site in CBM48 was specific for β-CD, while that in domain C has not been reported for other pullulanases. The domain C binding site had higher affinity for α-CD than for G6; a small motif (FGGEH) seemed to be one of the major determinants for carbohydrate binding in this domain. Structure-based mutations of several surface-exposed aromatic residues in CBM48 and domain C had a debilitating effect on the activity of the enzyme. These results suggest that both CBM48 and domain C play a role in binding substrates. The crystal forms described contribute to the understanding of pullulanase domain–carbohydrate interactions.

Mycoplasma hyopneumoniae is a prokaryotic pathogen that colonizes the respiratory ciliated epithelial cells in swine. Infected animals suffer respiratory lesions, causing major economic losses in the porcine industry. Characterization of the immunodominant membrane-associated proteins from M. hyopneumoniae may be instrumental in the development of new therapeutic approaches. Here, the crystal structure of P46, one of the main surface-antigen proteins, from M. hyopneumoniae is presented and shows N- and C-terminal α/β domains connected by a hinge. The structures solved in this work include a ligand-free open form of P46 (3.1 Å resolution) and two ligand-bound structures of P46 with maltose (2.5 Å resolution) and xylose (3.5 Å resolution) in open and closed conformations, respectively. The ligand-binding site is buried in the cleft between the domains at the hinge region. The two domains of P46 can rotate with respect to each other, giving open or closed alternative conformations. In agreement with this structural information, sequence analyses show similarities to substrate-binding members of the ABC transporter superfamily, with P46 facing the extracellular side as a functional subunit. In the structure with xylose, P46 was also bound to a high-affinity (Kd = 29 nM) Fab fragment from a monoclonal antibody, allowing the characterization of a structural epitope in P46 that exclusively involves residues from the C-terminal domain. The Fab structure in the complex with P46 shows only small conformational rearrangements in the six complementarity-determining regions (CDRs) with respect to the unbound Fab (the structure of which is also determined in this work at 1.95 Å resolution). The structural information that is now available should contribute to a better understanding of sugar nutrient intake by M. hyopneumoniae. This information will also allow the design of protocols and strategies for the generation of new vaccines against this important swine pathogen.

Photographs, by virtue of their static nature, not only allow us to look back to a fixed point in time, but also give us a […]

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