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672 results found
    1. Structural Biology and Molecular Biophysics

    Identification of ligand-specific G protein-coupled receptor states and prediction of downstream efficacy via data-driven modeling

    Oliver Fleetwood et al.
    Ligands with different efficacy profiles shift the free energy landscape of the beta2 adrenergic receptor activation and stabilize diverse active-like states via the switch of microswitches lining an allosteric pathway.
    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics

    Mapping transiently formed and sparsely populated conformations on a complex energy landscape

    Yong Wang et al.
    Molecular simulations can capture key aspects of the conformational exchange in a protein.
    1. Computational and Systems Biology
    2. Structural Biology and Molecular Biophysics

    Investigating the trade-off between folding and function in a multidomain Y-family DNA polymerase

    Xiakun Chu et al.
    The physical interaction network encoded in the multi-domain protein native structure handles the trade-off between the fast, stable folding and the efficient, reliable function.
    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 et al.
    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

    Promiscuous binding by Hsp70 results in conformational heterogeneity and fuzzy chaperone-substrate ensembles

    Rina Rosenzweig et al.
    Multiple chaperone binding sites on substrates suggest a mechanism by which the Hsp70 chaperone can circumvent kinetic traps in protein folding.
    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics

    Single-molecule FRET unveils induced-fit mechanism for substrate selectivity in flap endonuclease 1

    Fahad Rashid et al.
    Structure specific nucleases that act in DNA replication, repair and recombination actively mold their DNA while transforming their own structure to achieve precise cleavage of their cognate DNA and avoid the deleterious cleavage of noncognate DNA.
    1. Computational and Systems Biology
    2. Chromosomes and Gene Expression

    Combinatorial bZIP dimers display complex DNA-binding specificity landscapes

    José A Rodríguez-Martínez et al.
    Cognate site identification uncovers the impact of combinatorial dimerization in specifying new DNA binding sites for human bZIP transcription factors and comprehensive specificity landscapes predict the impact of SNPs on bZIP binding at previously unannotated regulatory loci.
    1. Structural Biology and Molecular Biophysics

    Structural dynamics of E. coli single-stranded DNA binding protein reveal DNA wrapping and unwrapping pathways

    Sukrit Suksombat et al.
    Single-molecule force and fluorescence spectroscopy reveal the structural states and dynamics of E. coli single-stranded DNA binding proteins and the energy landscape of the nucleo–protein complex.
    1. Plant Biology
    2. Structural Biology and Molecular Biophysics

    Identification of distinct pH- and zeaxanthin-dependent quenching in LHCSR3 from Chlamydomonas reinhardtii

    Julianne M Troiano et al.
    Light-harvesting complex stress-related is a protein from photosynthetic green algae that prevents damage from sunlight via two distinct conformational processes, which protect against different timescales of solar fluctuations.
    1. Computational and Systems Biology
    2. Neuroscience

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

    Mason Klein et al.
    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.

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