Advertisement

October 08, 2010

Volume 285Issue 41p31087-31906, e99972-e99973
Open Access
On The Cover: The image shows a predictive consensus tertiary RNA structure for the human APP IRE based on the two equally probable secondary structures reported. The structure was generated using the Assemble software (an interactive graphical tool to analyze and build RNA architectures at the two-dimensional and three-dimensional levels) by Jossinet et al. (Jossinet, F., Ludwig, T. E., and Westhof, E. (2010) Bioinformatics, doi: 10.1093/bioinformatics/btq321), which referenced established RNA constructs for complex tertiary motifs. An RNA sequence structure from a 70 S ribosome (Protein Data Bank (PDB) entry 1VOR:B 1133–1141) was used as a custom motif model for the AGA apical loop (shown in yellow), accounting for the transient G-C interactions around the 3-nucleotide core. The 1–5 G-bend was predicted using an analogous internal RNA loop from a ribosomal protein L1-mRNA complex (PDB entry 2HW8:B 7–12, 21–30), which also lacked significant internal interactions. The G-C helices were predicted by Assemble (red helices in the image), as were the G-bulges. The image was generated by Sohan Mikkilineni, MIT. For details see the article by Cho et al., pages 31217–31232....
On The Cover: The image shows a predictive consensus tertiary RNA structure for the human APP IRE based on the two equally probable secondary structures reported. The structure was generated using the Assemble software (an interactive graphical tool to analyze and build RNA architectures at the two-dimensional and three-dimensional levels) by Jossinet et al. (Jossinet, F., Ludwig, T. E., and Westhof, E. (2010) Bioinformatics, doi: 10.1093/bioinformatics/btq321), which referenced established RNA constructs for complex tertiary motifs. An RNA sequence structure from a 70 S ribosome (Protein Data Bank (PDB) entry 1VOR:B 1133–1141) was used as a custom motif model for the AGA apical loop (shown in yellow), accounting for the transient G-C interactions around the 3-nucleotide core. The 1–5 G-bend was predicted using an analogous internal RNA loop from a ribosomal protein L1-mRNA complex (PDB entry 2HW8:B 7–12, 21–30), which also lacked significant internal interactions. The G-C helices were predicted by Assemble (red helices in the image), as were the G-bulges. The image was generated by Sohan Mikkilineni, MIT. For details see the article by Cho et al., pages 31217–31232.

Papers of the Week

  • Inflammatory Cooperation♦

    Proinflammatory Cytokines Enhance Estrogen-dependent Expression of the Multidrug Transporter Gene ABCG2 through Estrogen Receptor and NFκB Cooperativity at Adjacent Response Elements

    Published in issue: October 08, 2010
    e99972
    Online Only
  • APP Iron Response SHAPES Up♦

    Selective Translational Control of the Alzheimer Amyloid Precursor Protein Transcript by Iron Regulatory Protein-1

    Published in issue: October 08, 2010
    e99973
    Online Only

Minireviews

Cell Biology

Developmental Biology

DNA and Chromosomes

Enzymology

Gene Regulation

Glycobiology and Extracellular Matrices

Immunology

Membrane Biology

Metabolism

Microbiology

Molecular Bases of Disease

Molecular Biophysics

Neurobiology

Protein Structure and Folding

Protein Synthesis and Degradation

RNA

Signal Transduction

Advertisement