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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

  • Announcement: double-blind peer review

  • Nature and Nature Research Journals start offering anonymity to authors during the peer-review process.

  • Ribonucleotides in DNA: hidden in plain sight

  • Mapping of ribonucleotides to single-nucleotide resolution in yeast genomes provides new insight into the enzymology of DNA replication.

  • Subversive bacteria reveal new tricks in their cytoskeleton-hijacking arsenal

  • During infection, pathogenic Yersinia species secrete the antiphagocytic factor YopO (or YpkA), which contains a kinase domain and a Rho GTPase guanine nucleotide–dissociation inhibitor (GDI) domain. The structure of YopO in complex with actin, along with biochemical analyses, reveals the mechanism by which YopO uses actin to activate its kinase domain and recruit, phosphorylate and deactivate actin-assembly factors implicated in phagocytic clearance of the bacterium.

  • Secondary nucleation wears the BRICHOS in this family

  • A chaperone segment provides powerful evidence for the molecular mechanism underlying Alzheimer's disease.

  • The proteasome gets a grip on protein complexity

  • Amyloids escape elimination by the proteasome, and their accumulation and subsequent aggregation contribute to various neurodegenerative conditions. A signature feature of amyloidogenic proteins is extended sequences rich in single amino acids. In this issue, Matouschek and colleagues now show that, to initiate degradation, the proteasome prefers substrates that have disordered regions with complex amino acid composition, thus indicating why it fails to rid the cell of most amyloids.

  • Released from the chains of death

  • m6A drives structural changes in RNA

  • TSPO through the crystal looking glass

  • 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.

  • 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.

  • 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.

  • 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.

  • 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.

  • 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.

  • 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.

  • 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.

  • 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.

  • 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.

  • 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.

  • Corrigendum: Structure of EF-G–ribosome complex in a pretranslocation state

  • Corrigendum: Cross-talking noncoding RNAs contribute to cell-specific neurodegeneration in SCA7

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    Nature -Advance Online Publications

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    Nature Structural aamp; Molecular Biology - AOP - science feeds

  • How a homolog of high-fidelity replicases conducts mutagenic DNA synthesis

  • Though related to high-fidelity replicases, DNA Polν performs mutagenic DNA synthesis. These properties are now explained by structural and biochemistry analyses of human DNA Pol ν revealing conformational changes involving the finger and thumb domains.

  • High-resolution structure of the Escherichia coli ribosome

  • High-resolution structure of the E. coli ribosome highlights rRNA and protein modifications and provides details on solvation characteristics and the structural impacts of ribosome modifications.

  • Human DNA polymeraseθ grasps the primer terminus to mediate DNA repair

  • DNA polymeraseθ is involved in alternative end-joining repair of DNA double-strand breaks. Structural and biochemical analyses shed light on pol θ's ability to prime DNA synthesis from nonoptimal base-pairing.

  • NAD+-SIRT1 control of H3K4 trimethylation through circadian deacetylation of MLL1

  • MLL1 regulates circadian promoters by depositing H3K4 trimethyl marks, whose levels are also modulated by the NAD+-dependent deacetylase SIRT1. SIRT1 is now shown to promote circadian deacetylation of MLL1, thus affecting MLL1's methyltransferase activity.

  • Evidence that processing of ribonucleotides in DNA by topoisomerase 1 is leading-strand specific

  • In the absence of RNase H2, ribonucleotides incorporated during DNA replication can be processed by Top1. This activity is directed to the nascent leading strand, because gaps in the lagging strand would limit torsional tension.

  • Microprocessor mediates transcriptional termination of long noncoding RNA transcripts hosting microRNAs

  • The finding that miRNA transcripts originating from long-noncoding-RNA loci use Microprocessor, rather than canonical cleavage and polyadenylation, to terminate transcription establishes a new RNase III–mediated transcriptional-termination pathway.

  • Small-RNA loading licenses Argonaute for assembly into a transcriptional silencing complex

  • New biochemical and genetic analyses in S. pombe show that Argonaute must be loaded with small RNAs to promote association of the GW-protein components required to assemble a functional transcriptional silencing complex.

  • A specialized molecular motion opens the Hv1 voltage-gated proton channel

  • Voltage- and patch-clamp fluorometry reveal structural rearrangements of the S1 helix and its surroundings that are important for gating of the Hv1 voltage-gated proton channel.

  • Structural insights into the role of rRNA modifications in protein synthesis and ribosome assembly

  • High-resolution crystal structures of Thermus thermophilus ribosomes reveal previously unseen modifications of rRNA and their contacts with mRNA and tRNAs or the protein pY.

  • Structural organization of the dynein–dynactin complex bound to microtubules

  • EM analyses reveal the architecture of cytoplasmic dynein in complex with dynactin and the BicD2 cargo adaptor on microtubules, showing the quaternary complex positioned for unidirectional movement and cargo recruitment.
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