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Showing 1–11 of 11 results
Advanced filters: Author: Rosana Collepardo-Guevara Clear advanced filters

  • Biomolecular condensates can transition from liquid-like to more solid-like states, a process termed “ageing” that is often pathological. Here, the authors present a computational framework to simulate the impact of designed small peptides on condensate ageing.

    • Ignacio Sanchez-Burgos
    • Andres R. Tejedor
    • Jorge R. Espinosa
    ResearchOpen Access
    Nature Communications
    Volume: 16, P: 1-14

  • Internucleosomal linker length alters the stability and dynamics of chromatin condensates by shifting the balance between inter- and intramolecular interactions. Further, by changing the linker lengths, a remodeler can induce or suppress chromatin phase separation.

    • Lifeng Chen
    • M. Julia Maristany
    • Michael K. Rosen
    ResearchOpen Access
    Nature Communications
    Volume: 16, P: 1-18

  • Montez et al. show that cold induces local nucleosome dynamics mediated by a non-sequence-specific DNA-binding protein important for controlling flowering time in plants. This has helped understand how plants adjust gene expression to the environment.

    • Miguel Montez
    • Danling Zhu
    • Caroline Dean
    ResearchOpen Access
    Nature Communications
    Volume: 16, P: 1-15

  • The realization that the cell is abundantly compartmentalized into biomolecular condensates has opened new opportunities for understanding the physics and chemistry underlying many cellular processes1, fundamentally changing the study of biology2. The term biomolecular condensate refers to non-stoichiometric assemblies that are composed of multiple types of macromolecules in cells, occur through phase transitions, and can be investigated by using concepts from soft matter physics3. As such, they are intimately related to aqueous two-phase systems4 and water-in-water emulsions5. Condensates possess tunable emergent properties such as interfaces, interfacial tension, viscoelasticity, network structure, dielectric permittivity, and sometimes interphase pH gradients and electric potentials6–14. They can form spontaneously in response to specific cellular conditions or to active processes, and cells appear to have mechanisms to control their size and location15–17. Importantly, in contrast to membrane-enclosed organelles such as mitochondria or peroxisomes, condensates do not require the presence of a surrounding membrane.

    • Simon Alberti
    • Paolo Arosio
    • Tanja Mittag
    Comments & OpinionOpen Access
    Nature Communications
    Volume: 16, P: 1-14

  • In this work the authors propose a multiscale computational approach, integrating atomistic and coarse-grained models simulations, to study the thermodynamic and kinetic factors playing a major role in the liquid-to-solid transition of biomolecular condensates. It is revealed how the gradual accumulation of inter-protein β-sheets increases the viscosity of functional liquid-like condensates, transforming them into gel-like pathological aggregates, and it is also shown how high concentrations of RNA can decelerate such transition.

    • Andres R. Tejedor
    • Ignacio Sanchez-Burgos
    • Jorge R. Espinosa
    ResearchOpen Access
    Nature Communications
    Volume: 13, P: 1-15

  • Resolving nucleosomes with chemical accuracy inside sub-Mb chromatin provides molecular insight into the modulation of chromatin structure and its liquid–liquid phase separation (LLPS). By developing a multiscale chromatin model, the authors find that DNA breathing enhances the valency, heterogeneity, and dynamics of nucleosomes, promoting disordered folding and LLPS.

    • Stephen E. Farr
    • Esmae J. Woods
    • Rosana Collepardo-Guevara
    ResearchOpen Access
    Nature Communications
    Volume: 12, P: 1-17

  • Combining bioinformatics data and atomistic simulations, this study develops a sequence-dependent coarse-grained model for biomolecular phase separation. This model achieves a quantitative agreement with experimental observations. Extensive benchmarks exemplify its performance.

    • Jerelle A. Joseph
    • Aleks Reinhardt
    • Rosana Collepardo-Guevara
    Research
    Nature Computational Science
    Volume: 1, P: 732-743

  • Elucidating the molecular driving forces underlying liquid–liquid phase separation is a key objective for understanding biological function and malfunction. Here the authors show that a wide range of cellular proteins, including FUS, TDP-43, Brd4, Sox2, and Annexin A11, which form condensates at low salt concentrations, can reenter a phase-separated regime at high salt concentrations.

    • Georg Krainer
    • Timothy J. Welsh
    • Tuomas P. J. Knowles
    ResearchOpen Access
    Nature Communications
    Volume: 12, P: 1-14

  • In the Big Data era, a change of paradigm in the use of molecular dynamics is required. Trajectories should be stored under FAIR (findable, accessible, interoperable and reusable) requirements to favor its reuse by the community under an open science paradigm.

    • Rommie E. Amaro
    • Johan Åqvist
    • Modesto Orozco
    Comments & Opinion
    Nature Methods
    Volume: 22, P: 641-645