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Showing 1–13 of 13 results
Advanced filters: Author: Gregory A. Voth Clear advanced filters

  • It is desirable for scientists to be able to predict the structures, spectra and phase diagrams of molecular crystals using ab initio computation. Li et al. demonstrate such an approach, which is able to determine the phase behaviour of solid carbon dioxide at a range of pressures and temperatures.

    • Jinjin Li
    • Olaseni Sode
    • So Hirata
    Research
    Nature Communications
    Volume: 4, P: 1-8

  • BAR domain proteins are known to reshape cell membranes. Using coarse-grained molecular dynamics simulations, Simunovic and Voth demonstrate that membrane tension strongly affects the association of BAR proteins, in turn controlling their recruitment to membrane-remodelling sites.

    • Mijo Simunovic
    • Gregory A. Voth
    ResearchOpen Access
    Nature Communications
    Volume: 6, P: 1-8

  • Tripartite-motif containing (TRIM) proteins modulate cellular responses to viral infection. Here the authors use molecular dynamics simulations to demonstrate that TRIM5α uses a two-dimensional lattice hopping mechanism to aggregate on the HIV capsid surface and initiate lattice growth.

    • Alvin Yu
    • Katarzyna A. Skorupka
    • Gregory A. Voth
    ResearchOpen Access
    Nature Communications
    Volume: 11, P: 1-10

  • Host proteins CPSF6, NUP153, and SEC24C are vital for HIV-1 infection. They bind to the viral capsid protein and contribute to shuttling of virions through the cytoplasm (SEC24C), import into the nucleus (NUP153 and CPSF6) and subsequent trafficking to preferred integration sites (CPSF6). Here, Wei et al. combine structural, biochemical and virological assays to emphasize the importance of prion-like low complexity domains surrounding short phenylalanine-glycine regions in binding and increasing the avidity when interacting with viral capsid.

    • Guochao Wei
    • Naseer Iqbal
    • Mamuka Kvaratskhelia
    ResearchOpen Access
    Nature Communications
    Volume: 13, P: 1-19

  • Incorporating polar residues into hydrophobic protein channel pores facilitates selective proton transport. Now, classical and multiscale reactive molecular dynamics simulations of designed channels reveal dynamic water wires within the channel lumen that are proton conductive according to structural and functional validation. These results provide some guiding principles for biological and engineered proton conduction.

    • Huong T. Kratochvil
    • Laura C. Watkins
    • William F. DeGrado
    Research
    Nature Chemistry
    Volume: 15, P: 1012-1021

  • 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

  • A crystal structure of human ESCRT-I headpiece reveals a helical assembly that is required for autophagosome closure and HIV-1 release in cells. The work suggests that ESCRT-I assembly templates ESCRT-III assembly for membrane scission.

    • Thomas G. Flower
    • Yoshinori Takahashi
    • James H. Hurley
    Research
    Nature Structural & Molecular Biology
    Volume: 27, P: 570-580

  • Significant morphological changes occur during the conversion of the immature HIV virion into a mature infectious form. Here the authors use coarse-grained molecular dynamics simulations to model HIV-1 capsid self-assembly and disassembly events that suggests several metastable capsid intermediates sensitive to local conditions.

    • John M. A. Grime
    • James F. Dama
    • Gregory A. Voth
    ResearchOpen Access
    Nature Communications
    Volume: 7, P: 1-11

  • The fission yeast cytokinetic ring assembles by Search-Capture-Pull-Release from precursor nodes that include formin Cdc12 and myosin Myo2. The authors reconstitute Search-Capture-Pull in vitro and find that Myo2 pulling on Cdc12-associated actin filaments mechano-inhibits Cdc12-mediated assembly, which enables proper ring assembly in vivo.

    • Dennis Zimmermann
    • Kaitlin E. Homa
    • David R. Kovar
    ResearchOpen Access
    Nature Communications
    Volume: 8, P: 1-13

  • The PLUMED consortium unifies developers and contributors to PLUMED, an open-source library for enhanced-sampling, free-energy calculations and the analysis of molecular dynamics simulations. Here, we outline our efforts to promote transparency and reproducibility by disseminating protocols for enhanced-sampling molecular simulations.

    • Massimiliano Bonomi
    • Giovanni Bussi
    • Andrew White
    Comments & Opinion
    Nature Methods
    Volume: 16, P: 670-673