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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 - nature.com science feeds

  • Synergistic activation of Toll-like receptor 8 by two RNA degradation products

  • Recognition of nucleic acids is a key strategy of the innate immune system to detect infectious organisms and tissue damage. Toll-like receptor (TLR) 8 was long assumed to be a receptor for single-stranded (ss) RNA. Unexpected findings now suggest that TLR8 recognizes RNA degradation products rather than ssRNA and that synergistic binding of two uridine-containing agonists at distinct sites of the receptor leads to activation of the innate immune response.

  • An enzyme cofactor with a split personality

  • Little is currently known about the molecular determinants of energy barriers along enzyme catalytic pathways. Kern and co-workers have studied this question in adenylate kinase (Adk) and now reveal that a single Mg2+ ion can accelerate two distinct steps, thus uncovering an unexpected dual role for this ubiquitous cofactor.

  • Designs on a curve

  • The structural rules governing the curving folds of solenoid proteins, as distilled down to the level of the underlying sequence repeats, provide designers with the tools to reliably fashion new variants with tunable geometries. Bespoke leucine-rich repeat (LRR) scaffolds, as recognition proteins, can now be tailored to better fit their targets.

  • Muscling in on the ryanodine receptor

  • The ryanodine receptor (RyR), an ion channel regulating intracellular calcium release in excitable cells, has been challenging for structural analysis because of its colossal proportions compared to most other ion channels. Three independent groups have now used recent technological advancements in single-particle cryo-EM to make giant strides in solving the structure of this elusive protein complex.

  • Bringing phosphorylation into the fold

  • Histone acetylome mapped

  • Resolving stalled ribosomes

  • 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.

  • 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 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.

  • 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.

  • 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.

  • 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.

  • 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.

  • 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.

  • 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.

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    Nature -Advance Online Publications

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    Nature Structural aamp; Molecular Biology - AOP - nature.com science feeds

  • A molecular chaperone breaks the catalytic cycle that generates toxic Aβ oligomers

  • Aβ peptide aggregation is associated with Alzheimer's disease, and Aβ fibrils can catalyze formation of toxic oligomers. Molecular chaperone Brichos binds to the fibril surface, inhibiting the catalytic cycle in vitro, and limits Aβ toxicity.

  • Crystal structure of a phosphorylation-coupled vitamin C transporter

  • Crystal structures of the bacterial vitamin C transporter UlaA, a member of the AG family of the phosphoenolpyruvate-dependent phosphotransferase system, provide insights on binding to ascorbate and its transport across the cell membrane.

  • Structures of CYLD USP with Met1- or Lys63-linked diubiquitin reveal mechanisms for dual specificity

  • Tumor-suppressor protein CYLD cleaves linear and Lys63-linked ubiquitin chains. Structures of CYLD USP domain with Met1- and Lys63-linked diubiquitins and biochemical analyses reveal the mechanism for dual specificity and provide insight into tumor-associated mutations.

  • A global profile of replicative polymerase usage

  • Genome-wide DNA polymerase usage maps determined in fission yeast, using a new sequencing strategy based on ribonucleotide misincorporation, track the division of labor between replicative polymerases and reveal locations and efficiencies of replication origins.

  • Yersinia effector YopO uses actin as bait to phosphorylate proteins that regulate actin polymerization

  • The crystal structure of Yersinia enterocolitica kinase YopO in complex with monomeric actin, together with biochemical analyses, reveals that YopO uses actin as bait to disrupt host cytoskeleton function and prevent phagocytosis.

  • Exon-intron circular RNAs regulate transcription in the nucleus

  • The identification of a new subclass of circular RNAs that are predominantly nuclear and promote transcription of their parental genes reveals a new regulatory function for these noncoding RNAs.

  • Sequence composition of disordered regions fine-tunes protein half-life

  • The proteasome initiates protein degradation at disordered regions within substrates. The proteasomal sequence preferences for the amino acid composition of these regions identified here affect protein half-life and explain unusual stability trends.

  • Mechanism of microhomology-mediated end-joining promoted by human DNA polymeraseθ

  • Human DNA Polθ can mediate microhomology-mediated end-joining (MMEJ) of DNA molecules in cells and in vitro. Biochemistry work shows that Polθ promotes formation of DNA synapses and strand annealing, activities that require insertion loop 2.

  • Structural basis for amyloidogenic peptide recognition by sorLA

  • The neuronal sorting receptor SorLA protects against Alzheimer's disease by binding Aβ peptides. Three new structures of the Vps10p Aβ-binding domain in ligand-free and ligand-bound forms explain the basis of SorLA peptide recognition.

  • DNA interstrand cross-link repair requires replication-fork convergence

  • New biochemical analyses in Xenopus cell-free extracts show that two replication forks must converge on a DNA interstrand cross-link (ICL) to permit translesion synthesis and repair.

  • 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.

  • Structural basis for bifunctional peptide recognition at humanδ-opioid receptor

  • Serial femtosecond crystallography of the humanδ-opioid receptor in complex with an endomorphin-derived peptide reveals interactions that are important for understanding the pharmacology of opioid peptides and developing analgesics with reduced side effects.

  • Structure of a Yeast 40S–eIF1–eIF1A–eIF3–eIF3j initiation complex

  • A high-resolution cryo-EM structure of yeast eIF3-bound 40S ribosomal subunits reveals the network of interactions between eIF3 subunits.
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