8,159 results found
    1. Evolutionary Biology

    Contingency and chance erase necessity in the experimental evolution of ancestral proteins

    Victoria Cochran Xie et al.
    Replicating experimental evolution from ancestral proteins shows that historical contingency steadily overwhelms chance and necessity as the primary cause of evolutionary variation in molecular sequences on long phylogenetic timescales.
    1. Evolutionary Biology
    2. Microbiology and Infectious Disease

    Stability-mediated epistasis constrains the evolution of an influenza protein

    Lizhi Ian Gong et al.
    Some of the mutations that occur during influenza evolution can only be tolerated in conjunction with other mutations that increase the stability of a viral protein.
    1. Evolutionary Biology

    Molecular function limits divergent protein evolution on planetary timescales

    Mariam M Konaté et al.
    Orthologous proteins that continuously maintain the same molecular function do not usually diverge beyond a certain level of sequence and structural similarity.
    1. Structural Biology and Molecular Biophysics

    Sequence co-evolution gives 3D contacts and structures of protein complexes

    Thomas A Hopf et al.
    Interactions in protein complexes can be predicted from evolutionary information from genomic sequences.
    1. Chromosomes and Gene Expression

    A simple method for generating high-resolution maps of genome-wide protein binding

    Peter J Skene, Steven Henikoff
    Building on previous work (Skene et al., 2014), we show that a new ChIP-seq protocol provides superior resolution and ease of use at low sequence depth of coverage for generating genome-wide maps of protein binding.
    1. Cell Biology
    2. Evolutionary Biology

    Evolution of an ancient protein function involved in organized multicellularity in animals

    Douglas P Anderson et al.
    Experimentally reconstructing the evolution of the molecular complex that animals use to orient the mitotic spindle establishes a simple genetic and physical mechanism for the emergence of a function essential for multicellularity.
    1. Structural Biology and Molecular Biophysics
    2. Computational and Systems Biology

    Emergence and evolution of an interaction between intrinsically disordered proteins

    Greta Hultqvist et al.
    The resurrection of ancient ancestral intrinsically disordered proteins reveals the evolution of a protein-protein interaction in molecular detail.
    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 et al.
    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. Computational and Systems Biology

    Origin of a folded repeat protein from an intrinsically disordered ancestor

    Hongbo Zhu et al.
    Minimal changes allow an ancestral, unfolded peptide to adopt a known fold by repetition, illuminating a possible path for the emergence of folded proteins at the origin of life.
    1. Biochemistry and Chemical Biology
    2. Evolutionary Biology

    Evolution of multifunctionality through a pleiotropic substitution in the innate immune protein S100A9

    Joseph L Harman et al.
    In the ancestor of mammals, a multifunctional innate immune protein evolved when a mutation enhanced the protein’s pro-inflammatory activity and proteolytic regulation without disrupting the protein’s antimicrobial activity.

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