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Table of Contents for this page:

  • Current Issue
  • Advanced Online Publications Articles

  • Current Issue of Nature Structural and Molecular Biology

    Nature Structural aamp; Molecular Biology - Issue - science feeds

  • The noncoding explosion

  • The long-held view that the primary role of RNA is to code for proteins has been severely undermined. This Focus explores the remarkable functional diversity of RNA in light of recent breakthroughs in noncoding-RNA biology.

  • Roles for noncoding RNAs in cell-fate determination and regeneration

  • Cellular fate is determined by transcriptional networks and epigenetic states. In addition to protein factors, noncoding RNAs (ncRNAs), particularly microRNAs and long ncRNAs, are able to remodel transcriptional circuits and reshape epigenetic landscapes. This Commentary highlights the emerging roles of these ncRNAs in cellular reprogramming, transdifferentiation and organ regeneration.

  • Discovery and annotation of long noncoding RNAs

  • Recent advances in RNA-sequencing technologies have led to the discovery of thousands of previously unannotated noncoding transcripts, including many long noncoding RNAs (lncRNAs) whose functions remain largely unknown. Here, the authors discuss considerations and best practices when identifying and annotating lncRNAs that should aid their functional and mechanistic exploration.

  • Using synthetic RNAs as scaffolds and regulators

  • The natural versatility of RNA makes it an ideal substrate for bioengineering. Its structural properties and predictable base-pairing permit its use as molecular scaffold, and its ability to interact with nucleic acids, proteins and small molecules confers a regulatory potential that can be harvested to design RNA regulators in diverse contexts.

  • Noncoding RNAs in eukaryotic ribosome biogenesis and function

  • The ribosome is a complex molecular machine that is central to protein synthesis. This Review highlights the various roles of noncoding RNAs during the different steps of ribosome biogenesis and discusses the consequences for ribosome function.

  • From guide to target: molecular insights into eukaryotic RNA-interference machinery

  • RNA interference (RNAi) is a process by which small noncoding RNAs direct molecular machinery to silence gene expression. In this Review, Ipsaro and Joshua-Tor discuss the mechanisms and structures that govern RNAi in higher organisms.

  • Technologies to probe functions and mechanisms of long noncoding RNAs

  • In this Perspective, Spitale, Chang and Chu discuss recent technological advances that will aid in the functional characterization of long noncoding RNAs, which up to now has posed a substantial challenge.

  • Ribozyme crosses chirality borders

  • Lnc-ing BCAR4 to metastasis

  • A CRISPR cut to bacteria

  • Crystal structure of a BRAF kinase domain monomer explains basis for allosteric regulation

  • All RAF kinase domain structures reported to date have adopted a dimer configuration. Marc Therrien, Frank Sicheri and colleagues now report a crystal structure of the BRAF monomeric 'off' state, providing insight into its catalytic activation.

  • 5-Formylcytosine alters the structure of the DNA double helix

  • 5-Formylcytosine (5fC) is implicated in active DNA demethylation and has been proposed to act as an epigenetic signal. Balasubramanian and colleagues now report that this base modification imparts a unique, previously undescribed conformation to DNA.

  • A coiled-coil domain acts as a molecular ruler to regulate O-antigen chain length in lipopolysaccharide

  • Bacterial LPS O-antigen is synthesized with a narrow size range by polymerase WbdA and terminating protein WbdD. An extended coiled-coil domain in WbdD determines the length of the synthesized O-chain, acting as a molecular ruler.

  • Conformational dynamics in substrate-binding domains influences transport in the ABC importer GlnPQ

  • Bacterial ABC importer GlnPQ has two fused substrate-binding domains (SBDs). Single-molecule FRET is now used to probe the conformational dynamics of the SBDs, which are shown to directly influence transport rates.

  • Visualizing phosphodiester-bond hydrolysis by an endonuclease

  • Different catalytic steps of endonuclease I-DmoI are captured crystallographically to allow direct observation of the generation of a DNA double-strand break. A third metal ion enters the active site and has a key role in hydrolysis.

  • The AAA3 domain of cytoplasmic dynein acts as a switch to facilitate microtubule release

  • Cytoplasmic dynein has multiple ATPase subunits, with AAA1 as the primary ATPase. Single-molecule and biochemical approaches reveal that AAA3 ATPase has a role in switching dynein between cargo-transport and microtubule-anchoring modes.

  • Structure of myosin-1c tail bound to calmodulin provides insights into calcium-mediated conformational coupling

  • Myo1c is a monomeric, unconventional myosin that can sense mechanical force in the cell. The structure of Myo1c's entire tail and neck domains in complex with apocalmodulin reveals a new mode of calmodulin interaction.

  • Human cells contain natural double-stranded RNAs with potential regulatory functions

  • Gronemeyer and colleagues identify naturally occurring double-stranded RNAs arising from sense-antisense transcript pairs and demonstrate that one of these RNAs, nds-2a, interacts with mitotic protein complexes and is required for cellular mitosis.

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    Nature -Advance Online Publications

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    Nature Structural aamp; Molecular Biology - AOP - science feeds

  • Tracking replication enzymology in vivo by genome-wide mapping of ribonucleotide incorporation

  • HydEn-seq, a new sequencing method that maps the distribution of ribonucleotides misincorporated by low-fidelity DNA polymerases in budding yeast, reveals unexpected strand-specific replication patterns in both nuclear and mitochondrial genomes.

  • K63 polyubiquitination is a new modulator of the oxidative stress response

  • Oxidative stress induces a number of cellular responses. Silva et al. uncover a peroxide-mediated K63-linked polyubiquitination pathway, and identify its targets and regulators.

  • The RNA helicase Aquarius exhibits structural adaptations mediating its recruitment to spliceosomes

  • Aquarius is an RNA helicase associated with spliceosomes. Lührmann, Pena and colleagues now provide structural insights into how Aquarius is recruited to the spliceosome, revealing a new spliceosomal building block that aids in Aquarius positioning.

  • Ring closure activates yeastγTuRC for species-specific microtubule nucleation

  • Theγ-tubulin ring complex (γTuRC) nucleates microtubules in the cell. The functional, closed state of yeast γTuRC is now visualized, and its microtubule-nucleating activity is found to be species specific.

  • Toll-like receptor 8 senses degradation products of single-stranded RNA

  • Toll-like receptors (TLRs) have key roles in innate immunity. Here, Shimizu and colleagues report crystal structures of TLR8 in complex with single-stranded RNA that reveal the molecular basis for recognition of a natural ligand.

  • Tetrameric Ctp1 coordinates DNA binding and DNA bridging in DNA double-strand-break repair

  • Structural, biophysical and genetic analyses reveal that Schizosaccharomyces pombe Ctp1 forms a flexible tetramer with multivalent DNA-binding and bridging activities that contribute to Ctp1's role in repair of DNA double-strand breaks.

  • The energy landscape of adenylate kinase during catalysis

  • Structural, computation and kinetics approaches reveal the energy landscape of catalysis by adenylate kinase and show that the cofactor Mg2+ activates two distinct molecular events in the reaction cycle: phosphoryl transfer and lid opening.

  • Control of repeat-protein curvature by computational protein design

  • Leucine-rich repeats (LRRs) can form horseshoe-like structures with different curvatures in nature. A computational approach now allows the design of 12 new LRR proteins with precise curvatures, using defined building blocks and junction modules.

  • CtIP tetramer assembly is required for DNA-end resection and repair

  • CtIP helps maintain genomic stability by promoting DNA double-strand-break repair. Structural and biophysical analyses now show that the N terminus of human CtIP forms a tetrameric structure that is required for resection of broken DNA ends to permit their repair by homologous recombination.

  • Charge-driven dynamics of nascent-chain movement through the SecYEG translocon

  • Proteins with charged amino acid residues encounter an electric force as they transit through membranes holding membrane potential. Von Heijne and colleagues measure this force to assess how membrane electrostatics contributes to translocation dynamics.
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