587 results found
    1. Physics of Living Systems

    Quantitative dissection of transcription in development yields evidence for transcription-factor-driven chromatin accessibility

    Elizabeth Eck et al.
    Confronting different models of chromatin accessibility with temporally resolved transcription profiles favors a scenario where transcription factors actively, rather than passively, drive chromatin from the inaccessible to the accessible state.
    1. Computational and Systems Biology

    The genetic landscape of a physical interaction

    Guillaume Diss, Ben Lehner
    First comprehensive analysis of how many different mutations combine within and between two genes to alter a molecular phenotype.
    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics

    Conformational distributions of isolated myosin motor domains encode their mechanochemical properties

    Justin R Porter et al.
    Shifts in the balance between nucleotide-favorable and nucleotide-unfavorable conformations of myosin motors encode duty ratios and ADP release rates, demonstrating the power of an ensemble perspective for uncovering sequence-function relationships.
    1. Physics of Living Systems

    Negative reciprocity, not ordered assembly, underlies the interaction of Sox2 and Oct4 on DNA

    John W Biddle et al.
    Rigorous reanalysis of single-molecule data yields evidence for energy expenditure in the interaction of transcription factors on DNA.
    1. Genetics and Genomics

    On the mechanistic nature of epistasis in a canonical cis-regulatory element

    Mato Lagator et al.
    Thermodynamic framework accurately predicts the sign of epistasis and its environment dependence for a canonical cis-regulatory element.
    1. Structural Biology and Molecular Biophysics

    Viral genome structures are optimal for capsid assembly

    Jason D Perlmutter et al.
    Computer simulations reveal that viral nucleic acids have an ideal structure for being packaged into outer protein shells called capsids.
    1. Computational and Systems Biology
    2. Medicine

    An integrative model of cardiometabolic traits identifies two types of metabolic syndrome

    Amit Frishberg et al.
    A novel type of metabolic syndrome, derived from computational modeling of phenotypic diversity in normal physiological settings, increases the risk of certain complex diseases.
    1. Structural Biology and Molecular Biophysics

    Automated cryo-EM structure refinement using correlation-driven molecular dynamics

    Maxim Igaev et al.
    Correlation-driven molecular dynamics provides a fully automated and human-bias-free framework for quantitative interpretation of modern cryo-electron microscopy data.
    1. Physics of Living Systems
    2. Structural Biology and Molecular Biophysics

    Efficient conversion of chemical energy into mechanical work by Hsp70 chaperones

    Salvatore Assenza et al.
    A multiscale modeling approach reveals how the energy from ATP hydrolysis is used by Hsp70 chaperones to remodel the conformation of their substrates through a novel force-generating mechanism.
    1. Computational and Systems Biology
    2. Structural Biology and Molecular Biophysics

    Investigating the trade-off between folding and function in a multidomain Y-family DNA polymerase

    Xiakun Chu et al.
    The physical interaction network encoded in the multi-domain protein native structure handles the trade-off between the fast, stable folding and the efficient, reliable function.

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