Computational biophysics articles within Nature Chemistry

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  • Article
    | Open Access

    The human ATP-hydrolysing enzyme p97 populates a metastable reaction intermediate, the ADP·Pi state, which is poised between hydrolysis and product release. Now, molecular motions at the active site in the temporal window immediately before and after ATP hydrolysis have been elucidated by merging cryo-EM, NMR spectroscopy and molecular dynamics simulations.

    • Mikhail Shein
    • , Manuel Hitzenberger
    •  & Anne K. Schütz

  • News & Views |

    Recent improvements in de novo protein design are likely to support a broad range of applications, but larger complexes will be easier to create if a building block approach is adopted. Now protein filaments with tunable geometry can be made using assemblies that have both cyclic and superhelical symmetries aligned along the same axis.

    • Jeremy R. H. Tame

  • Article |

    Enzymes with identical sequences of amino acids can display varying activities when encoded with mRNA with different properties, but why this is the case has been a mystery. Now, it has been shown that synonymous mutations in mRNA alter the partitioning of proteins into long-lived soluble misfolded states with varying activities.

    • Yang Jiang
    • , Syam Sundar Neti
    •  & Edward P. O’Brien

  • Article |

    The opening mechanism of the SARS-CoV-2 spike protein has been studied by integrating computational and experimental data. Combining weighted ensemble molecular dynamics simulations, biolayer interferometry and ManifoldEM analysis of cryo-EM data revealed that the glycan at N343 plays a gating role in the opening mechanism of the SARS-CoV-2 spike protein.

    • Terra Sztain
    • , Surl-Hee Ahn
    •  & Rommie E. Amaro

  • Article |

    Simulations of the SARS-CoV-2 proteome that include over 0.1 s of aggregate data are reported. Spike opening was observed, revealing cryptic epitopes that differ between variants, explaining differential interactions with antibodies and receptors that determine pathogenicity. The cryptic pockets described provide new targets for antivirals and a wealth of mechanistic insight.

    • Maxwell I. Zimmerman
    • , Justin R. Porter
    •  & Gregory R. Bowman

  • Article |

    That K+ channels conduct K+ ions at near-diffusion limited rates, but block the passage of smaller Na+ ions, creates an apparent contradiction. Now, atomistic simulations and free-energy calculations are used to show that both K+ permeation and ion selectivity are governed by the direct knock-on of completely desolvated ions in the channels’ selectivity filter.

    • Wojciech Kopec
    • , David A. Köpfer
    •  & Ulrich Zachariae

  • Article |

    Molecular dynamics simulations for seven members of the Src kinase family have now revealed a conserved step-wise deactivation process, potentially druggable intermediate states, and quantitatively similar thermodynamics and kinetics across the entire family.

    • Mohammad M. Sultan
    • , Gert Kiss
    •  & Vijay S. Pande

  • Article |

    The rate constant of DNA hybridization varies over several orders of magnitude and is affected by temperature and DNA sequence. A machine-learning algorithm that is capable of accurately predicting hybridization rate constants has now been developed. Tests with this algorithm showed that over 90% of predictions were correct to within a factor of three.

    • Jinny X. Zhang
    • , John Z. Fang
    •  & David Yu Zhang

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