3,263 results found
    1. Computational and Systems Biology
    2. Chromosomes and Gene Expression

    Combinatorial bZIP dimers display complex DNA-binding specificity landscapes

    José A Rodríguez-Martínez et al.
    Cognate site identification uncovers the impact of combinatorial dimerization in specifying new DNA binding sites for human bZIP transcription factors and comprehensive specificity landscapes predict the impact of SNPs on bZIP binding at previously unannotated regulatory loci.
    1. Computational and Systems Biology

    Building accurate sequence-to-affinity models from high-throughput in vitro protein-DNA binding data using FeatureREDUCE

    Todd R Riley et al.
    A biophysically principled algorithm can build quantitative models of protein-DNA binding specificity of unprecedented accuracy from a leading type of high-throughput in vitro binding data.
    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics

    Molecular insights into RNA and DNA helicase evolution from the determinants of specificity for a DEAD-box RNA helicase

    Anna L Mallam et al.
    The core domains of an RNA helicase interact with a wide variety of NTPs and nucleic acids suggesting how related enzymes may have evolved to have diverse functions.
    1. Biochemistry and Chemical Biology

    Conserved RNA-binding specificity of polycomb repressive complex 2 is achieved by dispersed amino acid patches in EZH2

    Yicheng Long et al.
    Biochemical and mutagenesis analysis reveal the long-anticipated RNA-binding elements of Polycomb Repressive Complex 2 (PRC2), an important chromatin modifier, allowing construction of separation-of-function mutants of PRC2 defective in RNA binding but retaining histone-modifying activity.
    1. Chromosomes and Gene Expression
    2. Evolutionary Biology

    Conservation of transcription factor binding specificities across 600 million years of bilateria evolution

    Kazuhiro R Nitta et al.
    Drosophila has almost all transcription factor binding specificities available to humans; and human transcription factors with divergent specificities operate in cell types that are not found in fruit flies.
    1. Genetics and Genomics
    2. Microbiology and Infectious Disease

    An atlas of the binding specificities of transcription factors in Pseudomonas aeruginosa directs prediction of novel regulators in virulence

    Tingting Wang et al.
    The transcription factor (TF)-binding specificities of Pseudomonas aeruginosa allow us to predict virulence-associated TFs and their target genes, which will facilitate to find effective treatment and prevention for its associated diseases.
    1. Developmental Biology
    2. Structural Biology and Molecular Biophysics

    A crystal structure of a collaborative RNA regulatory complex reveals mechanisms to refine target specificity

    Chen Qiu et al.
    A Caenorhabitis elegans RNA-binding protein, FBF-2, modulates RNA sequence motif recognition through conformational change and partner protein interaction.
    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics

    BRCT domains of the DNA damage checkpoint proteins TOPBP1/Rad4 display distinct specificities for phosphopeptide ligands

    Matthew Day et al.
    Structural and biochemical analyses of BRCT domain interactions defines TOPBP1/Rad4 selectivity for phosphorylated motifs, allowing identification of new interactions, and providing insights into assembly of different TOPBP1-scaffolded DNA repair complexes.
    1. Structural Biology and Molecular Biophysics

    Casposase structure and the mechanistic link between DNA transposition and spacer acquisition by CRISPR-Cas

    Alison B Hickman et al.
    The tetrameric structure of a casposase bound to DNA and its biochemical properties show how a transposase could have evolved to perform CRISPR-Cas spacer acquisition.
    1. Biochemistry and Chemical Biology
    2. Microbiology and Infectious Disease

    Structure and mechanism of a Hypr GGDEF enzyme that activates cGAMP signaling to control extracellular metal respiration

    Zachary F Hallberg et al.
    A newfound signaling enzyme that diverged from a protein family ubiquitous in bacteria provides mechanistic insights into how new signaling activity emerges to control distinct cellular function and physiology.

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