2,829 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. 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

    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. Computational and Systems Biology
    2. Structural Biology and Molecular Biophysics

    Response to comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'

    Krystel El Hage et al.
    We are writing to respond to the comment by Gapsys and de Groot, 2019 on our article about molecular dynamics simulations of human hemoglobin (El Hage et al., 2018).
    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

    Structure and dynamics of a nanodisc by integrating NMR, SAXS and SANS experiments with molecular dynamics simulations

    Tone Bengtsen et al.
    Molecular simulations, small-angle X-ray and neutron scattering experiments and previously measured NMR experiments were combined to study the structure and dynamics of the proteins and lipids in a nanodisc.
    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

    Breakage of the oligomeric CaMKII hub by the regulatory segment of the kinase

    Deepti Karandur et al.
    Activation and autophosphorylation of CaMKII releases the regulatory segment, which can then bind to and destabilize the hub assembly by trapping large fluctuations in the hub architecture.
    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. Structural Biology and Molecular Biophysics
    2. Computational and Systems Biology

    The selectivity of the Na+/K+-pump is controlled by binding site protonation and self-correcting occlusion

    Huan Rui et al.
    Computations based on detailed atomic models explain how the ATP-driven sodium-potassium pump avoids transporting the wrong type of ions in order to maintain the physiological concentration of sodium and potassium ions across the cell membrane.

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