5,924 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

    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. Neuroscience

    Filopodial dynamics and growth cone stabilization in Drosophila visual circuit development

    Mehmet Neset Özel et al.
    Long-term live imaging in intact developing Drosophila brains reveals a role for N-Cadherin-mediated fast filopodial dynamics and growth cone stabilization during neural circuit assembly.
    1. Structural Biology and Molecular Biophysics

    Modelling dynamics in protein crystal structures by ensemble refinement

    B Tom Burnley et al.
    A combination of molecular dynamics simulations and X-ray diffraction data has been used to construct more realistic models of proteins and to provide new insights into their interactions with other proteins and biomolecules.
    1. Structural Biology and Molecular Biophysics

    Comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'

    Vytautas Gapsys, Bert L de Groot
    We are writing to comment on the article by El Hage et al., 2018 about molecular dynamics simulations of human hemoglobin.
    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics

    A Ras-like domain in the light intermediate chain bridges the dynein motor to a cargo-binding region

    Courtney M Schroeder et al.
    The dynein light intermediate chain is a member of the G protein superfamily and links the motor to several intracellular cargo adaptors.
    1. Structural Biology and Molecular Biophysics

    Binding mechanism of the matrix domain of HIV-1 gag on lipid membranes

    Viviana Monje-Galvan, Gregory A Voth
    Unbiased molecular dynamics simulations reveal the insertion mechanism of the lipidated tail of the matrix domain of HIV-1 Gag into realistic membrane models and show its effect on lipid sorting.
    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics

    Fusion surface structure, function, and dynamics of gamete fusogen HAP2

    Juan Feng et al.
    Structure, dynamics, and mutation of a gamete fusion protein and comparisons to viral homologues suggest that after trimerization the domain bearing the membrane-inserting fusion loops can pivot with respect to the trimer 3-fold axis.
    1. Structural Biology and Molecular Biophysics

    Kinesin and dynein use distinct mechanisms to bypass obstacles

    Luke S Ferro et al.
    Dynein bypasses obstacles on microtubules more efficiently than single kinesin, and kinesins overcome this limitation when transporting intracellular cargos in teams.
    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics

    A dynamic charge-charge interaction modulates PP2A:B56 substrate recruitment

    Xinru Wang et al.
    A novel dynamic charge-charge interaction between B56 and a subset of PP2A-B56 substrates is essential for substrate specificity, dephosphorylation and, for KIF4A, binding condensin I.

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