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7,377 results found
    1. Computational and Systems Biology
    2. Structural Biology and Molecular Biophysics

    Linking time-series of single-molecule experiments with molecular dynamics simulations by machine learning

    Yasuhiro Matsunaga, Yuji Sugita
    A general machine learning scheme for integrating time-series data from single-molecule experiments and molecular dynamics simulations is proposed and successfully demonstrated for the folding dynamics of the WW domain.
    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics

    Homology sensing via non-linear amplification of sequence-dependent pausing by RecQ helicase

    Yeonee Seol et al.
    The rate of DNA unwinding by RecQ helicases is dramatically modulated by the DNA duplex stability in a geometry-dependent manner, providing an intrinsic mechanism for suppressing illegitimate recombination.
    1. Chromosomes and Gene Expression
    2. Physics of Living Systems

    Chromosome organization by one-sided and two-sided loop extrusion

    Edward J Banigan et al.
    Seemingly contradictory findings of single-molecule and in vivo experiments on a major mechanism of chromosome organization are reconciled by computationally investigating mechanisms of loop extrusion that are consistent with both.
    1. Structural Biology and Molecular Biophysics
    2. Computational and Systems Biology

    Robust model-based analysis of single-particle tracking experiments with Spot-On

    Anders S Hansen et al.
    Spot-On is an easy-to-use website that makes a rigorous and bias-corrected modeling framework for analysis of single-molecule tracking experiments available to all.
    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics

    Lis1 regulates dynein by sterically blocking its mechanochemical cycle

    Katerina Toropova et al.
    Structural and functional studies reveal how a ubiquitous regulator of dynein keeps the microtubule-based motor in a persistent track-bound state.
    1. Structural Biology and Molecular Biophysics
    2. Chromosomes and Gene Expression

    Single-molecule tracking of the transcription cycle by sub-second RNA detection

    Zhengjian Zhang et al.
    A new technique called fastFISH enables nearly real-time and stoichiometric detection of nascent RNA and the tracking of individual stages of transcription at the level of single-molecules.
    1. Chromosomes and Gene Expression
    2. Physics of Living Systems

    DNA sequence encodes the position of DNA supercoils

    Sung Hyun Kim et al.
    Single-molecule experiments reveal that plectonemic supercoils occupy specific positions on DNA and a physical model relates this to the intrinsic curvature, providing an insight into how supercoiling organizes the genome.
    1. Structural Biology and Molecular Biophysics

    Structural dynamics of E. coli single-stranded DNA binding protein reveal DNA wrapping and unwrapping pathways

    Sukrit Suksombat et al.
    Single-molecule force and fluorescence spectroscopy reveal the structural states and dynamics of E. coli single-stranded DNA binding proteins and the energy landscape of the nucleo–protein complex.
    1. Computational and Systems Biology
    2. Structural Biology and Molecular Biophysics

    tRNA sequences can assemble into a replicator

    Alexandra Kühnlein et al.
    Rudimentary cross-catalytic replication can be established by double-hairpins of tRNA-like sequences, implying that replication and translation could have emerged along a common evolutionary trajectory.
    1. Neuroscience
    2. Structural Biology and Molecular Biophysics

    Conformational dynamics between transmembrane domains and allosteric modulation of a metabotropic glutamate receptor

    Vanessa A Gutzeit et al.
    Single molecule subunit counting, FRET and electrophysiology experiments reveal that metabotropic glutamate receptor subunits interact and rearrange at the level of the transmembrane domains in response to allosteric modulators.

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