2,697 results found
    1. Structural Biology and Molecular Biophysics

    Modelling dynamics in protein crystal structures by ensemble refinement

    B Tom Burnley, Pavel V Afonine ... Piet Gros
    A combination of molecular dynamics simulations and X-ray diffraction data has been used to construct more realistic models of proteins and to provide new insights into their interactions with other proteins and biomolecules.
    1. Computational and Systems Biology

    Dynamics of co-substrate pools can constrain and regulate metabolic fluxes

    Robert West, Hadrien Delattre ... Orkun S Soyer
    Mathematical analyses explore the impact of co-substrate cycling on the dynamics of cellular metabolism, and demonstrate that these dynamics can limit cellular fluxes and that co-substrate pool dynamics can be regulated to regulate fluxes.
    1. Evolutionary Biology

    Evolution of diversity in metabolic strategies

    Rodrigo Caetano, Yaroslav Ispolatov, Michael Doebeli
    Analytical and numerical analyses reveal that the number of coexisting species exceeds the number of resource only for the structurally unstable case of linear tradeoff.
    1. Microbiology and Infectious Disease
    2. Physics of Living Systems

    The transpeptidase PBP2 governs initial localization and activity of the major cell-wall synthesis machinery in E. coli

    Gizem Özbaykal, Eva Wollrab ... Sven van Teeffelen
    For initiation of cell-wall insertion, the cross-linking enzyme PBP2 stably binds to a component of the cell envelope that is different from MreB filaments.
    1. Biochemistry and Chemical Biology
    2. Physics of Living Systems

    A coarse-grained NADH redox model enables inference of subcellular metabolic fluxes from fluorescence lifetime imaging

    Xingbo Yang, Gloria Ha, Daniel J Needleman
    Mitochondrial metabolic fluxes display a subcellular spatial gradient within a single mouse oocyte, and the fluxes are not controlled by nutrient supply or energy demand of the cell, but by the intrinsic rates of mitochondrial respiration.
    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.
    1. Physics of Living Systems

    Symmetry breaking meets multisite modification

    Vaidhiswaran Ramesh, J Krishnan
    Network symmetry represents a new vantage point for dissecting complex information processing characteristics in multisite modification, and the breaking of symmetry can confer ordering of modification and absolute concentration robustness.
    1. Neuroscience
    2. Computational and Systems Biology

    A stochastic model of hippocampal synaptic plasticity with geometrical readout of enzyme dynamics

    Yuri Elias Rodrigues, Cezar M Tigaret ... Romain Veltz
    A computational model of glutamatergic synapse uncovers a new plasticity rule which takes into account the various experimental conditions.
    1. Ecology
    2. Microbiology and Infectious Disease

    Noisy metabolism can promote microbial cross-feeding

    Jaime G Lopez, Ned S Wingreen
    Noise-averaging cooperation (NAC) is a novel theory for the emergence of microbial cross-feeding by which noisy intracellular metabolism can promote cooperation and cross-feeding among cells.
    1. Chromosomes and Gene Expression

    The Smc5/6 complex counteracts R-loop formation at highly transcribed genes in cooperation with RNase H2

    Shamayita Roy, Hemanta Adhikary ... Damien D'Amours
    Genetic analyses in budding yeast coupled with biochemical assays have revealed an unexpected role for the Smc5/6 complex in cellular pathways responsible for the prevention of RNA formation in genomic DNA.

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