Biopolymers in vivo articles within Nature Communications

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  • Article
    | Open Access

    I-Motifs (iM) are non-canonical DNA structures potentially forming in the accessible, single stranded, cytosine-rich genomic region, but the specific contributions of several factors involved in their formation are unknown. Using in-cell NMR, the authors examined DNA i-motif formation in human cells at body temperature, suggesting i-M occur in a small portion (<1%) of genomic sites predisposed to its formation.

    • Pavlína Víšková
    • , Eva Ištvánková
    •  & Lukáš Trantírek

  • Article
    | Open Access

    It is vital to unveil the effects of extracellular matrix cues on endothelial cell (EC) outgrowth for desirably governing vasculature formation, but the role of matrix plasticity on EC outgrowth is elusive. Here, the authors develop hydrogels with tunable mechanical plasticity independent of stiffness, and elucidate the plasticity-mediated responses of ECs during vasculogenesis and angiogenesis.

    • Zhao Wei
    • , Meng Lei
    •  & Feng Xu

  • Article
    | Open Access

    Bacteria produce several high molecular weight polysaccharides with ill-defined anti-adhesion properties. Here, the authors identified key molecular and biophysical determinants of active antibiofilm polysaccharides, opening new perspectives to identify or engineer new compounds able to control bacterial adhesion and biofilm formation.

    • Joaquín Bernal-Bayard
    • , Jérôme Thiebaud
    •  & Jean-Marc Ghigo

  • Article
    | Open Access

    The cell interior is organized by diverse membrane-less condensates. Here, the authors reveal that the densities of certain condensates are surprisingly low, similar to the surrounding protoplasm and driven by cellular RNA as well as the crowded milieu.

    • Taehyun Kim
    • , Jaeyoon Yoo
    •  & Yongdae Shin

  • Article
    | Open Access

    Enteropathogenic bacteria use extracellular appendages, known as F-pili, to share plasmids carrying antibiotic resistance genes. Here, the authors show that F-pili are highly flexible but robust at the same time, and this is important for plasmid transfer and formation of biofilms that protect against the action of antibiotics.

    • Jonasz B. Patkowski
    • , Tobias Dahlberg
    •  & Tiago R. D. Costa

  • Article
    | Open Access

    To protect from host attack, numerous jumbo bacteriophages establish a micron-scale, protein-based structure to enclose their replicating DNA. Using cryoEM, the authors show that the 2D crystal enclosing this so-called phage nucleus is an assembly of tetramers linked by flexible loops and tails.

    • Eliza S. Nieweglowska
    • , Axel F. Brilot
    •  & David A. Agard

  • Article
    | Open Access

    Nanotherapy has potential utility in cancer, particularly in targeted delivery of therapeutics. Here the authors demonstrate delivery of tranilast loaded micelles to improve the reprogramming of cancer associated fibroblasts and monitor tumour stiffness to predict responses.

    • Myrofora Panagi
    • , Fotios Mpekris
    •  & Triantafyllos Stylianopoulos

  • Article
    | Open Access

    The nuclear pore complex (NPC) barrier is a selective phase assembled from disordered but cohesive FG domains. The authors provide a thermodynamic description of an FG phase that is ultimately simplified and yet closely recapitulates NPC transport selectivity.

    • Sheung Chun Ng
    •  & Dirk Görlich

  • Article
    | Open Access

    The venomous stinging cells of jellyfish, anemones, and corals contain an organelle, the nematocyst, which explosively discharges a venom-laden thread. Here, the authors describe the nematocyst thread and its sub-structures in the sea anemone N. vectensis, revealing a complexity and sophistication underpinning this cellular weapon.

    • Ahmet Karabulut
    • , Melainia McClain
    •  & Matthew C. Gibson

  • Article
    | Open Access

    Bacterial motility relies on the mechanics of the “hook” the 60 nm biopolymer at the base of rotating flagella. Here, authors observe the hook stiffening as it is twisted by the rotation of the flagellum, a mechanical feat evolved for its function.

    • Ashley L. Nord
    • , Anaïs Biquet-Bisquert
    •  & Francesco Pedaci

  • Article
    | Open Access

    Bio-inspired materials are an intense area of study as researchers try to adapt biomaterials for other applications. Here, the authors report on the processing of protein materials derived from the byssal thread of scallops to create high-extensibility materials with self-recovery under wet conditions.

    • Xiaokang Zhang
    • , Mengkui Cui
    •  & Weizhi Liu

  • Article
    | Open Access

    The authors show how tubular surface structures in all cell types, have the ability to twist and perform rotary sweeping motion to explore the extracellular environment. This has implications for migration, sensing and cell communication.

    • Natascha Leijnse
    • , Younes Farhangi Barooji
    •  & Poul Martin Bendix

  • Article
    | Open Access

    The permeability barrier of nuclear pores is formed by disordered and yet self-interacting FG repeat domains, whose sequence heterogeneity is a challenge for mechanistic insights. Here the authors overcome this challenge and characterize the protein’s dynamics by applying NMR techniques to an FG phase system that has been simplified to its essentials.

    • Eszter E. Najbauer
    • , Sheung Chun Ng
    •  & Loren B. Andreas

  • Article
    | Open Access

    Phase-separated biomolecular condensates are implicated in a myriad of biological processes. Here the authors apply optical tweezers to characterize the viscoelasticity and interfacial tension of a range of condensates, finding that condensates can deviate from simple fluids in opposite directions; and identify shear relaxation as a governing measure of condensate dynamics.

    • Archishman Ghosh
    • , Divya Kota
    •  & Huan-Xiang Zhou

  • Article
    | Open Access

    Mechanical strength of in situ assembled nuclear lamin filaments arranged in a 3D meshwork is unclear. Here, using mechanical, structural and simulation tools, the authors report the hierarchical organization of the lamin meshwork that imparts strength and toughness to lamin filaments at par with silk and Kevlar®

    • K. Tanuj Sapra
    • , Zhao Qin
    •  & Ohad Medalia

  • Article
    | Open Access

    In vivo experiments and optical tweezers force-spectroscopy measurements assessing the co-translational folding of the G-domain from bacterial elongation factor G reveal a sequential folding pathway initiating from the C-terminus. These results suggest that protein folding and synthesis proceed in opposite directions.

    • Xiuqi Chen
    • , Nandakumar Rajasekaran
    •  & Christian M. Kaiser

  • Article
    | Open Access

    The design principles underlying biomolecular phase separation of membrane-less organelles remain poorly understood. Using model homopolymers, Fisher et al. show that the formation kinetics of coexisting liquid phases can be tuned by exploiting differences between arginine and lysine residues.

    • Rachel S. Fisher
    •  & Shana Elbaum-Garfinkle

  • Article
    | Open Access

    The existence, nature and biological relevance of mechanoradicals in proteins are unknown. Here authors show that mechanical stress on collagen produces radicals and subsequently reactive oxygen species and suggest that collagen I evolved as a radical sponge against mechano-oxidative damage.

    • Christopher Zapp
    • , Agnieszka Obarska-Kosinska
    •  & Frauke Gräter

  • Article
    | Open Access

    The phase separation of two species of associating polymers is suppressed by a magic-number effect for certain combinations of the numbers of binding sites. Here the authors use lattice simulations and analytical calculations to show that this magic-number effect can be greatly enhanced if one component has a rigid shape.

    • Bin Xu
    • , Guanhua He
    •  & Ned S. Wingreen

  • Article
    | Open Access

    The actin homolog MreB directs cell-wall insertion and maintains cell shape in many rod-shaped bacteria. Here, Shi et al. perform molecular dynamics simulations for MreB to extract mechanical parameters for inputs into a coarse-grained biophysical polymer model that predicts MreB filament properties.

    • Handuo Shi
    • , David A. Quint
    •  & Kerwyn Casey Huang

  • Article
    | Open Access

    Fluorogenic RNA aptamers have been used for RNA imaging, but folding and fluorescence stability often limited their use in high resolution applications. Here the authors present an array of stably folding Mango II aptamers for imaging of coding and non-coding RNAs at single-molecule resolution, in both live and fixed cells.

    • Adam D. Cawte
    • , Peter J. Unrau
    •  & David S. Rueda

  • Article
    | Open Access

    The mussel byssus cuticle is a wear-resistant and extensible metalloprotein composite. Here, the authors probed the cuticle nanostructure and composition before, during and after fabrication revealing a crucial role of metal-binding proteins that self-organize via liquid-liquid phase separation.

    • Franziska Jehle
    • , Elena Macías-Sánchez
    •  & Matthew J. Harrington

  • Article
    | Open Access

    Glass transition in soft materials can be affected by the topology of constituent particles, but the detail remains elusive. Here, Smrek et al. show that the interplay between circular topology of ring polymers and their active segments generates a new state of matter, namely active topological glass.

    • Jan Smrek
    • , Iurii Chubak
    •  & Kurt Kremer

  • Article
    | Open Access

    The ability to encapsulate living cells could lead to many applications. Here, the authors present a flexible method to graft DNA polymers onto bacteria, yeast and mammalian cells, polymerize them into DNA cocoons and use these to manipulate and select cells based on the encoded polymer sequences on DNA cocoons.

    • Tao Gao
    • , Tianshu Chen
    •  & Genxi Li

  • Article
    | Open Access

    Antibodies are generated through remote genomic interactions involving immunoglobulin variable (VH), diversity (DH) and joining (JH) gene segments. Here the authors develop a strategy to track VH-DHJH motion in B-lymphocytes and provide evidence that chromosome organisation near the sol-gel phase transition dictates the timing of genomic interactions to orchestrate gene expression and somatic recombination.

    • Nimish Khanna
    • , Yaojun Zhang
    •  & Cornelis Murre

  • Article
    | Open Access

    Bacteria assemble the surface layer (S-layer), a crystalline protein coat surrounding the curved surface, using protein self-assembly. Here authors image native and purified RsaA, the S-layer protein from C. crescentus, and show that protein crystallization alone is sufficient to assemble and maintain the S-layer in vivo.

    • Colin J. Comerci
    • , Jonathan Herrmann
    •  & W. E. Moerner

  • Article
    | Open Access

    During mitosis, tension at the centromere occurs from the spindle but the role of centromere mechanics in controlling metaphase tension is poorly understood. Here, the authors report that mechanical stiffnness of the centromere matures during mitotic progression and is amplified specifically at metaphase.

    • Lauren A. Harasymiw
    • , Damien Tank
    •  & Melissa K. Gardner

  • Article
    | Open Access

    Studying protein kinetics and stability in living organisms is challenging and most studies are performed in cell culture. Here the authors combine meganuclease-mediated transformation and fluorescence-detected temperature-jump microscopy to quantify protein stability in different tissues of living zebrafish.

    • Ruopei Feng
    • , Martin Gruebele
    •  & Caitlin M. Davis

  • Article
    | Open Access

    The promoter variant rs35705950 confers a gain of function to the MUC5B gene and is the dominant risk factor for idiopathic pulmonary fibrosis. Here the authors show that mice overexpressing Muc5b in distal airspaces show impaired mucociliary clearance and increased susceptibility to bleomycin-induced lung fibrosis, and that both characteristics are reduced by treatment with a mucolytic agent.

    • Laura A. Hancock
    • , Corinne E. Hennessy
    •  & David A. Schwartz

  • Article
    | Open Access

    The nucleolus is a membrane-less organelle and both Nucleophosmin (NPM1) and Surfeit locus protein 6 (SURF6) are abundant proteins within the nucleolus. Here the authors employ biophysical methods to study the properties of NPM1-S6N droplets and provide insights into the role of SURF6 in maintaining and modulating the liquid-like structure of the nucleolus.

    • Mylene C. Ferrolino
    • , Diana M. Mitrea
    •  & Richard W. Kriwacki

  • Article
    | Open Access

    Despite their importance in plant development and defence the properties of (1,3)-β-glucan remain largely unknown. Here, the authors find that addition of (1,3)-β-glucans increases the flexibility of cellulose and its resilience to high strain, an effect originating in molecular level interactions.

    • Radwa H. Abou-Saleh
    • , Mercedes C. Hernandez-Gomez
    •  & Yoselin Benitez-Alfonso

  • Article
    | Open Access

    How transcription factors find their targets in vivo is still poorly understood. Here the authors use molecular dynamics simulations to investigate how transcription factors diffuse on chromatin, providing a theoretical framework for understanding the key role of genome conformation in this process.

    • Ruggero Cortini
    •  & Guillaume J. Filion

  • Article
    | Open Access

    Cellular contractility is regulated by the GTPase RhoA, but how local signals are translated to a cell-level response is not known. Here the authors show that targeted RhoA activation results in propagation of force along stress fibres and actin flow, and identify zyxin as a regulator of stress fibre mechanics and homeostasis.

    • Patrick W. Oakes
    • , Elizabeth Wagner
    •  & Margaret L. Gardel

  • Article
    | Open Access

    In vitro models of actin organization show the formation of vortices, asters and stars. Here Fritzsche et al. show that such actin structures form in living cells in a manner dependent on the Arp2/3 complex but not myosin, and such structures influence membrane architecture but not cortex elasticity.

    • M. Fritzsche
    • , D. Li
    •  & C. Eggeling

  • Article
    | Open Access

    The interaction between myosin motors and F-actin is well described, but the impact of actin organization on contractility is not well described. Here the authors use a 2D biomimetic system and computational modelling to show that contractility of isotropic actomyosin is cooperative, and contraction velocity scales with myosin activation area.

    • Ian Linsmeier
    • , Shiladitya Banerjee
    •  & Michael P. Murrell

  • Article |

    The degradation of chitin and cellulose is dependent on the processivity of degrading enzymes. Here, Igarashi et al. use high-speed atomic force microscopy to visualize the movement of two chitinases (ChiA and ChiB) and show them to move in opposite directions, allowing a molecular mechanism to be proposed.

    • Kiyohiko Igarashi
    • , Takayuki Uchihashi
    •  & Masahiro Samejima

  • Article |

    Hagfish slime contains fibres that are produced in gland cells, but how these threads are assembled within the cell is unclear. Here, using electron microscopy and three-dimensional modelling, the authors show that during gland cell maturation the shape of the nucleus changes, permitting the coiling of the threads around it.

    • Timothy Winegard
    • , Julia Herr
    •  & Douglas Fudge

  • Article |

    Encapsulating molecules within supramolecular frameworks for potential biological application is challenging. Bhatiaet al. incorporate a fluorescent polymer within an icosahedral DNA nanocapsule, and show that it can be used to target specific cells in vivoand map pH spatially and temporally.

    • Dhiraj Bhatia
    • , Sunaina Surana
    •  & Yamuna Krishnan

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