703 results found
    1. Computational and Systems Biology
    2. Structural Biology and Molecular Biophysics

    Markov state models of proton- and pore-dependent activation in a pentameric ligand-gated ion channel

    Cathrine Bergh, Stephanie A Heusser ... Erik Lindahl
    Computational models of gating processes in an ion channel show how stability shifts upon ligand-binding and mutations are reproduced, which highlights mechanistic details and proposes a new role for symmetry in gating.
    1. Structural Biology and Molecular Biophysics

    Discovery of lipid binding sites in a ligand-gated ion channel by integrating simulations and cryo-EM

    Cathrine Bergh, Urška Rovšnik ... Erik Lindahl
    A combination of molecular dynamics simulations and electron cryomicroscopy characterizes interactions of a pentameric ligand-gated ion channel with 25 lipid molecules, specifically in a functional state in which they were not previously observed.
    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. Neuroscience

    A unifying mechanism governing inter-brain neural relationship during social interactions

    Wujie Zhang, Maimon C Rose, Michael M Yartsev
    Experiments and modeling suggest that a mechanism involving positive and negative feedback can explain the relationship between the neural activity of socially interacting bats.
    1. Computational and Systems Biology
    2. Structural Biology and Molecular Biophysics

    Simulation of spontaneous G protein activation reveals a new intermediate driving GDP unbinding

    Xianqiang Sun, Sukrit Singh ... Gregory R Bowman
    Combining powerful simulation methods uncovers the structural and dynamical changes driving G protein activation in atomic detail, revealing the allosteric network that triggers GDP release and reconciling diverse experimental data.
    1. Neuroscience

    Statistical structure of locomotion and its modulation by odors

    Liangyu Tao, Siddhi Ozarkar ... Vikas Bhandawat
    A fly's locomotion can be decomposed into a small number of locomotor features which can be modulated by odors and other sensory information.
    1. Biochemistry and Chemical Biology

    The dynamic conformational landscape of the protein methyltransferase SETD8

    Shi Chen, Rafal P Wiewiora ... Minkui Luo
    Integrated experimental-computational approaches were implemented to reveal the dynamic conformational landscape of a biologically relevant protein methyltransferase SETD8 for functional annotation.
    1. Neuroscience

    Intrinsic mechanisms in the gating of resurgent Na+ currents

    Joseph L Ransdell, Jonathan D Moreno ... Jeanne M Nerbonne
    Experimental and modeling results reveal that the activation of resurgent sodium currents relies on the recovery of inactivated channels into a conducting state, and that the decay of resurgent currents reflects the accumulation of these channels into a slow-inactivated state.
    1. Computational and Systems Biology
    2. Neuroscience

    Exploratory search during directed navigation in C. elegans and Drosophila larva

    Mason Klein, Sergei V Krivov ... Martin Karplus
    Crawling Drosophila larvae and C. elegans exhibit diffusive behavior alongside directed motion, and the dynamics of this navigation can be analyzed with techniques developed in understanding protein folding, using a Markov state model.
    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics

    Conformational distributions of isolated myosin motor domains encode their mechanochemical properties

    Justin R Porter, Artur Meller ... Gregory R Bowman
    Shifts in the balance between nucleotide-favorable and nucleotide-unfavorable conformations of myosin motors encode duty ratios and ADP release rates, demonstrating the power of an ensemble perspective for uncovering sequence-function relationships.

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