2,464 results found
    1. Structural Biology and Molecular Biophysics

    All-atom molecular dynamics of the HBV capsid reveals insights into biological function and cryo-EM resolution limits

    Jodi A Hadden et al.
    All-atom molecular dynamics of the HBV capsid supports a role for structural asymmetry in biological function, reveals the potential for triangular pores to mediate cellular signaling, and indicates that capsid flexibility may limit resolution attainable by cryo-EM.
    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. Structural Biology and Molecular Biophysics

    Changes in the free-energy landscape of p38α MAP kinase through its canonical activation and binding events as studied by enhanced molecular dynamics simulations

    Antonija Kuzmanic et al.
    Extensive molecular dynamics simulations enhanced by advanced sampling techniques give a detailed view of p38α canonical activation mechanism, which reveals novel key electrostatic interactions that are put in context of existing experimental data.
    1. Structural Biology and Molecular Biophysics

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

    Krystel El Hage et al.
    Simulations of the unliganded human hemoglobin tetramer, which for the first time yield a thermodynamically stable system, cast doubts on the use of standard solvent box sizes for molecular dynamics studies of biological macromolecules.
    1. Structural Biology and Molecular Biophysics
    2. Computational and Systems Biology

    The biological function of an insect antifreeze protein simulated by molecular dynamics

    Michael J Kuiper et al.
    Simulations of the biological function of an antifreeze protein reveal its molecular interactions with the ice/water interface.
    1. Structural Biology and Molecular Biophysics
    2. Computational and Systems Biology

    Molecular dynamics-based refinement and validation for sub-5 Å cryo-electron microscopy maps

    Abhishek Singharoy et al.
    New hybrid structure determination methods leveraging the inherent biophysical properties of a macromolecule through molecular dynamics simulations provide accurate and cost-efficient ways of achieving atomic structures from high resolution cryo-electron density maps.
    1. Structural Biology and Molecular Biophysics

    Structure and dynamics underlying elementary ligand binding events in human pacemaking channels

    Marcel P Goldschen-Ohm et al.
    Single-molecule resolution of cAMP binding to the ligand binding domain of pacemaking channels in zero-mode waveguides reveals the dynamics of the distinct steps underlying both binding and isomerization of the binding domain.
    1. Structural Biology and Molecular Biophysics
    2. Computational and Systems Biology

    CryoEM and computer simulations reveal a novel kinase conformational switch in bacterial chemotaxis signaling

    C Keith Cassidy et al.
    An atomic model of the bacterial chemosensory array obtained through the synthesis of cryo-electron tomography and large-scale molecular-dynamics simulations reveals a new kinase conformation during signaling events.
    1. Structural Biology and Molecular Biophysics
    2. Computational and Systems Biology

    Kinesin motility is driven by subdomain dynamics

    Wonmuk Hwang et al.
    The motor protein kinesin utilizes its fuel molecule by active and concerted motions of its subdomains, while it rapidly interacts with the microtubule track by forming a wet and dynamic interface.
    1. Evolutionary Biology
    2. Microbiology and Infectious Disease

    Integrating influenza antigenic dynamics with molecular evolution

    Trevor Bedford et al.
    Combined antigenic and genetic analysis shows that different strains of the human influenza virus display dramatically different rates of antigenic drift, and that these differences have a significant impact on the number of new infections in each flu season.

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