1,175 results found
    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics

    An improved fluorescent noncanonical amino acid for measuring conformational distributions using time-resolved transition metal ion FRET

    William N Zagotta, Brandon S Sim ... Sharona E Gordon
    Time-resolved transition metal ion fluorescence resonance energy transfer using a fluorescent, noncanonical amino acid donor and metal ion acceptor measures distances and distance distributions in proteins, allowing the equilibrium distributions among conformational states to be accurately determined.
    1. Cell Biology

    Nucleotide binding is the critical regulator of ABCG2 conformational transitions

    Zsuzsanna Gyöngy, Gábor Mocsár ... Katalin Goda
    The conformational switch of ABCG2 from the high substrate affinity inward-facing to a low substrate affinity outward-facing state is induced by nucleotide binding and accelerated by transported substrates.
    1. Structural Biology and Molecular Biophysics

    Structural dynamics determine voltage and pH gating in human voltage-gated proton channel

    Shuo Han, Sophia Peng ... Shizhen Wang
    Visualization of the real-time conformational transitions of the human voltage-gated proton channel hHv1 provided novel insights into how voltage and pH gradients modify the dynamic behaviors of channel structures to control proton flow across membrane.
    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics

    The inherent flexibility of receptor binding domains in SARS-CoV-2 spike protein

    Hisham M Dokainish, Suyong Re ... Yuji Sugita
    Computer simulations explore the experimentally unknown S-protein structures, revealing novel drug binding sites.
    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, Pablo Artigas, Benoît Roux
    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.
    1. Computational and Systems Biology
    2. Structural Biology and Molecular Biophysics

    Free-energy simulations reveal molecular mechanism for functional switch of a DNA helicase

    Wen Ma, Kevin D Whitley ... Klaus Schulten
    Integration of structural bioinformatics and free-energy simulations reveals how a helicase switches its function from unwinding to rezipping DNA, during which a key metastable conformation is predicted and verified by single-molecule measurements.
    1. Structural Biology and Molecular Biophysics

    Single molecule compression reveals intra-protein forces drive cytotoxin pore formation

    Daniel M Czajkowsky, Jielin Sun ... Zhifeng Shao
    Compressive force spectroscopy of single molecules reveals that intra-protein forces underlie the long-distance coordination of structural changes within a cytotoxin during pore formation.
    1. Computational and Systems Biology
    2. Structural Biology and Molecular Biophysics

    Evolutionary divergence in the conformational landscapes of tyrosine vs serine/threonine kinases

    Joan Gizzio, Abhishek Thakur ... Ronald M Levy
    Computational methods based on both sequence and structure show evidence that tyrosine kinases are energetically biased to populate the 'DFG-out' type-II inhibitor binding conformation relative to serine/threonine kinases.
    1. Neuroscience

    Tracking multiple conformations occurring on angstrom-and-millisecond scales in single amino-acid-transporter molecules

    Yufeng Zhou, John H Lewis, Zhe Lu
    The present fluorescence polarization microscopy method enables the determination of the spatial orientations and lifetimes of a transporter protein in individual conformational states required for understanding the complex conformational mechanism underlying its function, applicable to investigation of other membrane proteins.
    1. Structural Biology and Molecular Biophysics

    Mapping the conformational landscape of a dynamic enzyme by multitemperature and XFEL crystallography

    Daniel A Keedy, Lillian R Kenner ... James S Fraser
    The conformations of the enzyme cyclophilin A that are essential for its catalytic activity are temperature dependent and exhibit diverse responses, which is consistent with a complex energy landscape.

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