Browse the search results

Page 2 of 766
    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, Juan R Perilla ... Klaus Schulten
    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. 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

    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, Ludovico Sutto ... Modesto Orozco
    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. Ecology

    Synthetic eco-evolutionary dynamics in simple molecular environment

    Luca Casiraghi, Francesco Mambretti ... Tommaso Bellini
    A variant of SELEX introduced here to induce abiotic evolution in a molecular system enables to observe and study speciation, the nature of fitness, and the interplay between use of resources and interactions between individuals.
    1. Structural Biology and Molecular Biophysics

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

    Krystel El Hage, Florent Hédin ... Martin Karplus
    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, Craig J Morton ... Angus Gray-Weale
    Simulations of the biological function of an antifreeze protein reveal its molecular interactions with the ice/water interface.
    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, Viktor L Holm ... Kresten Lindorff-Larsen
    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
    2. Computational and Systems Biology

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

    Abhishek Singharoy, Ivan Teo ... Klaus Schulten
    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

    The liquid structure of elastin

    Sarah Rauscher, Régis Pomès
    Molecular simulations show how hydrophobicity and conformational disorder underlie the phase separation of elastin-like peptides and the elasticity of human tissues.
    1. Neuroscience
    2. Structural Biology and Molecular Biophysics

    Fuzzy supertertiary interactions within PSD-95 enable ligand binding

    George L Hamilton, Nabanita Saikia ... Mark E Bowen
    A combination of single molecule fluorescence with DMD simulations and disulfide mapping resolved the multistate structural landscape of the PSG supramodule from PSD-95, which explains how interdomain interactions within PSD-95 enable PDZ3 binding of the critical synaptic adhesion protein neuroligin.