Nature Structural & Molecular Biology - Issue - nature.com science feeds

Raising standards

2013-05-06

Nature Structural & Molecular Biology 20, 533 (2013). doi:10.1038/nsmb.2590

Nature journals' updated editorial policies aim to improve transparency and reproducibility.

The design principle of paddle motifs in voltage sensors

Jeet Kalia — 2013-05-06

Nature Structural & Molecular Biology 20, 534 (2013). doi:10.1038/nsmb.2578

Authors: Jeet Kalia & Kenton J. Swartz

Voltage-activated ion channels contain S1–S4 domains that endow them with exquisite voltage sensitivity. X-ray crystal structures provided a major breakthrough in elucidating the mechanistic basis of voltage sensing, revealing a helix-turn-helix motif termed the voltage-sensor paddle. A study in this issue demonstrates that this motif exists in the open state of Kv channels when embedded in native biological membranes and puts forward new ideas about its functional role in the mechanism of voltage sensing.

Direct BAKtivation

Loren D. Walensky — 2013-05-06

Nature Structural & Molecular Biology 20, 536 (2013). doi:10.1038/nsmb.2579

Author: Loren D. Walensky

BAK is a proapoptotic BCL-2–family protein that resides in the mitochondrial outer membrane and transforms into a toxic oligomeric pore in response to overwhelming cellular stress. Biochemical and structural analyses of hydrocarbon-stapled signaling peptides in complex with BAK establish a direct mechanism for BAK activation.

Unraveling the structural basis of GPCR activation and inactivation

Michel Bouvier — 2013-05-06

Nature Structural & Molecular Biology 20, 539 (2013). doi:10.1038/nsmb.2584

Author: Michel Bouvier

By comparing ligand-free G protein–coupled receptor (GPCR) structures with those of receptors bound to inverse agonists, agonists and signaling effectors, two recent papers refine the understanding of GPCR activation. One group also reported the oligomeric assembly of the β1 adrenergic receptor in its ligand-free form, raising the question of the role of oligomers in receptor activation.

From pseudo-ceRNAs to circ-ceRNAs: a tale of cross-talk and competition

Riccardo Taulli — 2013-05-06

Nature Structural & Molecular Biology 20, 541 (2013). doi:10.1038/nsmb.2580

Authors: Riccardo Taulli, Cristian Loretelli & Pier Paolo Pandolfi

RNA is believed to have been the first reservoir of genetic information, but despite its ancient history, RNA continues to fascinate and is only now beginning to be understood in its entire variety and communication modality. New discoveries include the pseudogene RNA network regulating PTEN transcription and translation and the identification of circular RNAs as a new class of competing endogenous RNA molecules that sequester microRNAs to suppress their function.

A role for eIF4AII in microRNA–mediated mRNA silencing

Elisa Izaurralde — 2013-05-06

Nature Structural & Molecular Biology 20, 543 (2013). doi:10.1038/nsmb.2582

Author: Elisa Izaurralde

A recent study on the mechanism of microRNA–mediated gene silencing suggests that microRNA–induced silencing complexes inhibit ribosome scanning by recruiting the DEAD-box RNA helicase eIF4AII through an interaction with the NOT1 subunit of the CCR4–NOT deadenylase complex.

Dengue likes it hot

Inês Chen — 2013-05-06

Nature Structural & Molecular Biology 20, 546 (2013). doi:10.1038/nsmb.2587

Author: Inês Chen

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A histone mutation in cancer

Arianne Heinrichs — 2013-05-06

Nature Structural & Molecular Biology 20, 546 (2013). doi:10.1038/nsmb.2589

Author: Arianne Heinrichs

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Helicase disc breaks

Beth Moorefield — 2013-05-06

Nature Structural & Molecular Biology 20, 546 (2013). doi:10.1038/nsmb.2588

Author: Beth Moorefield

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HDAC-mediated suppression of histone turnover promotes epigenetic stability of heterochromatin

Ozan Aygün — 2013-04-21

The mechanisms underlying gene silencing and epigenetic stability of heterochromatin are not fully understood. New studies in fission yeast now show that heterochromatin differs from euchromatin in the turnover of histones, and they identify the histone deacetylase Clr3 as a factor that inhibits histone turnover across heterochromatin domains and is crucial for the stable inheritance of heterochromatin in cis.

Assembly, analysis and architecture of atypical ubiquitin chains

Manuela K Hospenthal — 2013-04-07

Nature Structural & Molecular Biology 20, 555 (2013). doi:10.1038/nsmb.2547

Authors: Manuela K Hospenthal, Stefan M V Freund & David Komander

Human inactive X chromosome is compacted through a PRC2-independent SMCHD1-HBiX1 pathway

Ryu-Suke Nozawa — 2013-03-31

Nature Structural & Molecular Biology 20, 566 (2013). doi:10.1038/nsmb.2532

Authors: Ryu-Suke Nozawa, Koji Nagao, Ken-Taro Igami, Sachiko Shibata, Natsuko Shirai, Naohito Nozaki, Takashi Sado, Hiroshi Kimura & Chikashi Obuse

Energetic role of the paddle motif in voltage gating of Shaker K+ channels

Yanping Xu — 2013-03-31

In voltage-gated ion channels, transmembrane segments S3 and S4 are involved in voltage sensing and adopt a helix-turn-helix conformation, called the paddle motif, in crystal structures. Now extensive mutagenesis and electrophysiology analyses of the Shaker K+ channel demonstrate the physiological relevance of the paddle motif and dissect the roles of each segment in voltage sensing.

Dynamics of translation by single ribosomes through mRNA secondary structures

Chunlai Chen — 2013-03-31

Nature Structural & Molecular Biology 20, 582 (2013). doi:10.1038/nsmb.2544

Authors: Chunlai Chen, Haibo Zhang, Steven L Broitman, Michael Reiche, Ian Farrell, Barry S Cooperman & Yale E Goldman

BID-induced structural changes in BAK promote apoptosis

Tudor Moldoveanu — 2013-04-21

Nature Structural & Molecular Biology 20, 589 (2013). doi:10.1038/nsmb.2563

Authors: Tudor Moldoveanu, Christy R Grace, Fabien Llambi, Amanda Nourse, Patrick Fitzgerald, Kalle Gehring, Richard W Kriwacki & Douglas R Green

Regulation of Mus81–Eme1 Holliday junction resolvase in response to DNA damage

Pierre-Marie Dehé — 2013-04-14

Nature Structural & Molecular Biology 20, 598 (2013). doi:10.1038/nsmb.2550

Authors: Pierre-Marie Dehé, Stéphane Coulon, Sarah Scaglione, Paul Shanahan, Arato Takedachi, James A Wohlschlegel, John R Yates, Bertrand Llorente, Paul Russell & Pierre-Henri L Gaillard

Structural basis of signal sequence surveillance and selection by the SRP–FtsY complex

Ottilie von Loeffelholz — 2013-04-07

The signal recognition particle (SRP) targets nascent proteins with hydrophobic signal sequences to translocation machineries at the target membrane. Structural, thermodynamic and kinetic studies of a 'false' early complex, formed by SRP and its receptor with ribosomes translating an incorrect cargo, suggest an unstable complex that rearranges inefficiently into subsequent conformational states, resulting in receptor dissociation rather than successful targeting.

A conserved Mediator–CDK8 kinase module association regulates Mediator–RNA polymerase II interaction

Kuang-Lei Tsai — 2013-04-07

The CDK8 kinase module (CKM) is a subcomplex that interacts with Mediator and represses transcription. Structural and biochemical analyses now show that interaction of the CKM with Mediator interferes with C-terminal domain–dependent binding of RNA polymerase II to a previously unknown Mediator binding site and with holoenzyme formation, which forms the basis for CKM's repressive effect on transcription.

Interaction with Shc prevents aberrant Erk activation in the absence of extracellular stimuli

Kin Man Suen — 2013-04-14

Nature Structural & Molecular Biology 20, 620 (2013). doi:10.1038/nsmb.2557

Authors: Kin Man Suen, Chi-Chuan Lin, Roger George, Fernando A Melo, Eleanor R Biggs, Zamal Ahmed, Melanie N Drake, Swathi Arur, Stefan T Arold & John E Ladbury

Conformational selection of translation initiation factor 3 signals proper substrate selection

Margaret M Elvekrog — 2013-04-14

Translation initiation factor 3 (IF3) regulates the fidelity with which the initiator tRNA and mRNA start codon substrates are selected into the 30S ribosomal subunit initiator complex (30S IC). Single-molecule FRET analyses now suggest the existence of a conformational selection mechanism by which a single conformation of IF3 is stabilized through proper substrate selection.

Binding thermodynamics of a glutamate transporter homolog

Nicolas Reyes — 2013-04-07

Glutamate transporters translocate their substrate-binding site across the membrane, in a cycle fueled by the energy of the sodium gradient. Now GltPh is trapped by cross-linking, with its substrate-binding site facing inward or outward, to reveal that the Na+ potential is coupled to substrate binding and release, not to substrate translocation.

The structural basis for specific decoding of AUA by isoleucine tRNA on the ribosome

Rebecca M Voorhees — 2013-03-31

Nature Structural & Molecular Biology 20, 641 (2013). doi:10.1038/nsmb.2545

Authors: Rebecca M Voorhees, Debabrata Mandal, Cajetan Neubauer, Caroline Köhrer, Uttam L RajBhandary & V Ramakrishnan

Decoding of the AUA isoleucine codon in bacteria and archaea requires modification of a C in the anticodon wobble position of the isoleucine tRNA. Here, we report the crystal structure of the archaeal tRNA2Ile, which contains the modification agmatidine in its anticodon, in complex with the AUA codon on the 70S ribosome. The structure illustrates how agmatidine confers codon specificity for AUA over AUG.