Molecular biophysics articles within Nature Chemistry

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  • Article |

    Key molecular features that drive protein liquid–liquid phase separation (LLPS) for biomolecular condensate have been reported. A spectrum of additional interactions that influence protein LLPS and material properties have now been characterized. These interactions extend beyond a limited set of residue types and can be modulated by environmental factors such as temperature and salt concentration.

    • Shiv Rekhi
    • , Cristobal Garcia Garcia
    •  & Jeetain Mittal

  • Research Briefing |

    Ribonucleoprotein granules are ubiquitous in living organisms with the protein and RNA components having distinct roles. In the absence of proteins, RNAs are shown to undergo phase separation upon heating. This transition is driven by desolvation entropy and ion-mediated crosslinking and is tuned by the chemical specificity of the RNA nucleobases.

  • Article |

    The physicochemical driving forces of protein-free, RNA-driven phase transitions were previously unclear, but it is now shown that RNAs undergo entropically driven liquid–liquid phase separation upon heating in the presence of magnesium ions. In the condensed phase, RNAs can undergo an enthalpically favourable percolation transition that leads to arrested condensates.

    • Gable M. Wadsworth
    • , Walter J. Zahurancik
    •  & Priya R. Banerjee

  • Article
    | Open Access

    Understanding of the molecular mechanisms underlying the maturation of protein condensates into amyloid fibrils associated with neurodegenerative diseases has so far remained elusive. Now it has been shown that in condensates formed by the low-complexity domain of the amyotrophic lateral sclerosis-associated protein hnRNPA1, fibril formation is promoted at the interface, which provides a potential therapeutic target for counteracting aberrant protein aggregation.

    • Miriam Linsenmeier
    • , Lenka Faltova
    •  & Paolo Arosio

  • Research Briefing |

    An infrared laser-induced temperature jump provides a rapid and broadly applicable perturbation to protein dynamics. Temperature-jump crystallography was paired with time-resolved X-ray crystallography to study the dynamic enzyme lysozyme. Measurements with and without a functional inhibitor revealed different patterns in the propagation of motion throughout the enzyme.

  • Article
    | Open Access

    Shifts in temperature alter the structure and dynamics of macromolecules. Now, infra-red laser-induced temperature jump is combined with X-ray crystallography to observe protein structural dynamics in real time. Using this method, motions related to the catalytic cycle of lysozyme, a model enzyme, are visualized at atomic resolution and across broad timescales.

    • Alexander M. Wolff
    • , Eriko Nango
    •  & Michael C. Thompson

  • Article
    | Open Access

    Biological membranes are asymmetric bilayers, but little is known about how this asymmetry modulates membrane protein folding or stability. Now, folding and stability assays with bacterial outer membrane proteins reveal an exquisite sensitivity to asymmetric membrane charge distribution and a required matching of protein charge for efficient folding.

    • Jonathan M. Machin
    • , Antreas C. Kalli
    •  & Sheena E. Radford

  • News & Views |

    Complexity is a hallmark of biological systems, but scientific experiments are typically conducted in simplified conditions. Now, diverse polymers that mimic the local environments of complex biological mixtures have been shown to improve protein folding, stability and function.

    • Alana P. Gudinas
    •  & Danielle J. Mai

  • Article |

    The complex link between protein sequence and phase behaviour for a family of prion-like low-complexity domains (PLCDs) has now been revealed. The results have uncovered a set of rules—which are interpreted using a stickers-and-spacers model—that govern the sequence-encoded phase behaviour of such PLCDs and enable physicochemical rationalizations that are connected to the underlying sequence composition.

    • Anne Bremer
    • , Mina Farag
    •  & Tanja Mittag

  • Article |

    The correct function of ribozymes in a prebiotic world would be dependent on the presence of optimal salt compositions and concentrations. Now, local heat fluxes have been shown to create an ideal salt habitat for ribozyme activity based on geologically plausible salt-leaching processes.

    • T. Matreux
    • , K. Le Vay
    •  & C. B. Mast

  • News & Views |

    Although critically important for protein function, post-translational modifications are complex and notoriously difficult to study. Now, the effects of O-GlcNAcylation on chaperone activity and the accompanying inhibition of amyloid fibril formation have been revealed, potentially yielding new routes to combat neurodegeneration.

    • Sheena E. Radford
    •  & Theodoros K. Karamanos

  • Article |

    The mechanism of nucleation for α-synuclein (α-Syn) aggregation and amyloid formation in Parkinson’s disease is unclear. Now, α-Syn has been shown to undergo liquid–liquid phase separation and a liquid-to-solid-like transition leading to amyloid fibril formation. This raises the possibility that liquid–liquid phase separation is a key pathogenic mechanism behind α-Syn aggregation in Parkinson’s disease.

    • Soumik Ray
    • , Nitu Singh
    •  & Samir K. Maji

  • Article |

    Aβ42 oligomers are key toxic species associated with protein aggregation; however, the molecular pathways determining the dynamics of oligomer populations have remained unknown. Now, direct measurements of oligomer populations, coupled to theory and computer simulations, define and quantify the dynamics of Aβ42 oligomers formed during amyloid aggregation.

    • Thomas C. T. Michaels
    • , Andela Šarić
    •  & Tuomas P. J. Knowles

  • Article |

    Understanding how structural dynamics contribute to protein function is a longstanding challenge in structural biology. Now, time-resolved X-ray solution scattering following an infrared laser-induced temperature jump has been used to probe functional, intramolecular motions in the dynamic enzyme cyclophilin A.

    • Michael C. Thompson
    • , Benjamin A. Barad
    •  & James S. Fraser

  • Article |

    Understanding the mechanism of photoconversion in fluorescent proteins is essential to optimizing applications in imaging and optogenetics. It has now been demonstrated that photoconversion in the photoswitchable protein dronpa follows a multi-step mechanism, with both chromophore and protein structural dynamics occurring on multiple timescales from picoseconds to hundreds of microseconds.

    • Sergey P. Laptenok
    • , Agnieszka A. Gil
    •  & Stephen R. Meech

  • Article |

    Molecules that bind to DNA for extended periods can modulate its transcription or other biological processes. Kinetic studies on the non-covalent complex formed by a threading tetra-intercalator and a DNA double-helix have now revealed a multi-step association, and a particularly slow dissociation leading to sequence specificity and a 16-day half-life.

    • Garen G. Holman
    • , Maha Zewail-Foote
    •  & Brent L. Iverson

  • News & Views |

    The aggregation of proteins into fibrils plays a crucial role in neurological conditions such as Parkinson's disease. Further insight into fibril formation has now been gained that reveals the effect of hydrophobic surfaces, including air.

    • Ian W. Hamley

  • Article |

    Whereas synthetic DNA nanostructures are widely studied, the use of RNA as a structural building block is much less common. Now, it has been shown that tRNA molecules can be designed to assemble into a rigid and thermally stable square antiprism structure that may prove useful for delivery applications inside cells.

    • Isil Severcan
    • , Cody Geary
    •  & Luc Jaeger

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