Supramolecular assembly articles within Nature Communications

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  • Article
    | Open Access

    Here, the authors use small angle neutron scattering and coarse-grained molecular dynamics simulations to demonstrate that condensates based on the granular components of nucleoli are network fluids.

    • Furqan Dar
    • , Samuel R. Cohen
    •  & Rohit V. Pappu

  • Article
    | Open Access

    Contractile rings are formed from cytoskeletal filaments, specific crosslinkers and motor proteins during cell division. Here, authors form micron-scale contractile DNA rings from DNA nanotubes and synthetic crosslinkers, with both simulations and experiments showing ring contraction without motor proteins, offering a potential first step towards synthetic cell division machinery.

    • Maja Illig
    • , Kevin Jahnke
    •  & Kerstin Göpfrich

  • Article
    | Open Access

    Artificial biomolecular condensates are valuable tools to study the design principles of phase separation. Here, the authors demonstrate and characterize a model system of artificial DNA condensates whose kinetic formation and dissolution depends on DNA inputs that activate or deactivate the phase separating DNA subunits.

    • Siddharth Agarwal
    • , Dino Osmanovic
    •  & Elisa Franco

  • Article
    | Open Access

    Adhesive type-1 pili from Escherichia coli are filamentous protein complexes consisting of a short tip and a long rod formed by up to several thousand copies of a major subunit. Here, Giese et al. reconstitute the entire type-1 pilus rod assembly reaction in vitro, using all constituent protein subunits, and identify a subunit that acts as an irreversible assembly terminator.

    • Christoph Giese
    • , Chasper Puorger
    •  & Rudi Glockshuber

  • Article
    | Open Access

    Dissipative structures are governed by non-equilibrium thermodynamics. Here, the authors describe a size-dependent transition from active droplets to active spherical shells—a dissipative structure that arises from reaction diffusion gradients.

    • Alexander M. Bergmann
    • , Jonathan Bauermann
    •  & Job Boekhoven

  • Article
    | Open Access

    HIV maturation inhibitors such as bevirimat (BVM) interfering with Gag processing are emerging as alternative anti-retroviral drug candidates. Here, the authors report structures of assemblies of HIV-1 Gag fragments spanning the CA C-terminal domain and SP1 region bound to BVM.

    • Sucharita Sarkar
    • , Kaneil K. Zadrozny
    •  & Tatyana Polenova

  • Article
    | Open Access

    In this work, the authors show that metamorphism in the post-translationally modified TDP-43 prion-like domain encodes determinants that command mechanisms with major relevance in disease and stress the relevance of post-translationally modified chains as the targets for disease intervention.

    • Jaime Carrasco
    • , Rosa Antón
    •  & Javier Oroz

  • Article
    | Open Access

    In this work the authors report the structure of nucleotide-free kinesin-1 motor domain (apo-KIF5B) in complex with paclitaxel-stabilized microtubules using magic-angle-spinning (MAS) NMR spectroscopy. The study provides insights into the dynamic changes under which the neck linker goes upon binding to ADP.

    • Chunting Zhang
    • , Changmiao Guo
    •  & Tatyana Polenova

  • Article
    | Open Access

    Amyloid fibrils of β2-microglobulin (β2m) can cause dialysis-related amyloidosis. Here, the authors show that a decrease in serum albumin levels in long-term dialysis deteriorates the inhibitory effects of serum milieux on supersaturation-limited amyloid formation of β2m, suggesting that macromolecular crowding protects the onset of amyloidosis.

    • Kichitaro Nakajima
    • , Keiichi Yamaguchi
    •  & Yuji Goto

  • Article
    | Open Access

    Many autotrophic bacteria rely on Rubisco for carbon dioxide fixation. Here the authors report the position, orientation, and structure of Rubisco within alpha-carboxysomes; showing how it polymerizes and can form a lattice inside this compartment.

    • Lauren Ann Metskas
    • , Davi Ortega
    •  & Grant J. Jensen

  • Article
    | Open Access

    Ayala Mariscal et al have identified and characterized the interface of pathogenic Huntingtin and the molecular chaperone DNAJB1. Histidine-244 of the C-terminal domain of DNAJB1 is a key residues for binding to the poly-proline region of HTT. This binding site is specific for the interaction with Huntingtin.

    • S. M. Ayala Mariscal
    • , M. L. Pigazzini
    •  & J. Kirstein

  • Article
    | Open Access

    Interest in oligonucleotide nanostructures has recently surged in basic and applied research. Here, the authors use native mass spectrometry and ion mobility to elucidate a prototypical hexameric DNA barrel structure as well as intermediates and byproducts of the assembly reaction.

    • Jeroen F. van Dyck
    • , Jonathan R. Burns
    •  & Frank Sobott

  • Article
    | Open Access

    Here the authors report the cryo-EM structure of a triple-mutant of the anti-microbial peptide plectasin, PPI42, assembling in a pH- and concentration dependent manner into helical non-amyloid fibrils. The fibrils formation is reversible, and follows a sigmoidal kinetics. The fibrils adopt a right-handed helical superstructure composed by two protofilaments, stabilized by an outer hydrophobic ring and an inner hydrophobic centre. These findings reveal that α/β proteins can natively assemble into fibrils.

    • Christin Pohl
    • , Gregory Effantin
    •  & Pernille Harris

  • Article
    | Open Access

    Glutamate receptors comprise two obligate subunits and two subunits that confer distinct properties and functions to the specific tetramers, which also localize to distinct synaptic spines. Here, the authors use STimulated Emission Depletion nanoscopy (STED) to provide detailed insights into the spatial organization of glutamate receptor types.

    • Martin Hruska
    • , Rachel E. Cain
    •  & Matthew B. Dalva

  • Article
    | Open Access

    Methods to quantitatively study liquid-liquid phase separation (LLPS) of proteins are lacking. Here the authors report Capillary flow experiments (Capflex) for the quantification of key LLPS parameters; they study Ddx4, the RP3 peptide and the aberrant liquid-to-solid phase transition of α-synuclein.

    • Emil G. P. Stender
    • , Soumik Ray
    •  & Alexander K. Buell

  • Article
    | Open Access

    The centriole exhibits an evolutionarily conserved 9-fold radial symmetry that stems from a cartwheel containing vertically stacked ring polymers that harbor 9 homodimers of the protein SAS-6. Here the authors show how dual properties inherent to surface-guided SAS-6 self-assembly possess spatial information that dictates correct scaffolding of centriole architecture.

    • Niccolò Banterle
    • , Adrian P. Nievergelt
    •  & Pierre Gönczy

  • Article
    | Open Access

    The nucleation mechanisms of biological protein phase separation are poorly understood. Here, the authors perform time-resolved SAXS experiments with the low-complexity domain (LCD) of hnRNPA1 and uncover multiple kinetic regimes on the micro- to millisecond timescale. Initially, individual proteins collapse. Nucleation then occurs via two steps distinguished by their protein cluster size distributions.

    • Erik W. Martin
    • , Tyler S. Harmon
    •  & Tanja Mittag

  • Article
    | Open Access

    Ito and co-workers unravel how bacteria such as Salmonella switch gears with their flagellar driving machinery. External load triggers the dynamic remodeling of the molecular complex sustaining the torque, and the number of stator units is adapted in a non-trivial, cooperative manner.

    • Kenta I. Ito
    • , Shuichi Nakamura
    •  & Shoichi Toyabe

  • Article
    | Open Access

    Adeno-associated viruses (AAVs) have emerged as promising gene therapy vectors.The AAV capsid consists of 60 subunits made up from three distinct viral proteins (VPs). Here authors record high-resolution native mass spectra of intact AAV capsids to assess the VP stoichiometries in a panel of serotypes and reveals an extremely heterogeneous population of capsids of variable composition.

    • Tobias P. Wörner
    • , Antonette Bennett
    •  & Albert J. R. Heck

  • Article
    | Open Access

    Recent advances in computational methods have enabled the predictive design of self-assembling protein nanomaterials with atomic-level accuracy. Here authors investigate the assembly of two computationally designed, 120-subunit icosahedral complexes and find that assembly of each material from its two constituent protein building blocks was highly cooperative.

    • Adam J. Wargacki
    • , Tobias P. Wörner
    •  & Neil P. King

  • Article
    | Open Access

    Liquid ribonucleoprotein condensates typically involve a dense network of multiple proteins and RNAs. Here, the authors employ a minimal system composed of Prion-like polypeptides (PLP), Arg-rich polypeptides (RRP), and RNA to form biphasic condensates with diverse morphologies tunable via mixture stoichiometry and hierarchy of intermolecular interactions.

    • Taranpreet Kaur
    • , Muralikrishna Raju
    •  & Priya R. Banerjee

  • Article
    | Open Access

    Synaptic vesicle clusters were proposed to represent phase separated condensates. Here, the authors show that only two proteins, synapsin and synaptophysin, are sufficient to make vesicle clusters in fibroblasts which are similar to those found at synapses in morphology and liquid-like properties.

    • Daehun Park
    • , Yumei Wu
    •  & Sunghoe Chang

  • Article
    | Open Access

    Female honeybee larvae develop into queens when they are fed exclusively with royal jelly (RJ) and major royal jelly protein 1 (MRJP1) is the main protein component of RJ. Here, the authors present the 3.5 Å cryo-EM structure of native RJ filament, where MRJP1 forms the outer shell surrounding apisimin tetramers with bound lipids at the core of the filament.

    • Simone Mattei
    • , Arvid Ban
    •  & Daniel Boehringer

  • Article
    | Open Access

    Immune cells express immunoproteasomes (i20S), which bind to specialized regulators, contain different catalytic subunits and generate immunogenic peptides. HDX-MS—based assessment of the differences between the conformational dynamics of standard and i20s reveals specific, allosteric changes in i20S and upon regulator binding.

    • Jean Lesne
    • , Marie Locard-Paulet
    •  & Julien Marcoux

  • Article
    | Open Access

    For almost forty years, N-(1-pyrene) iodoacetamide has been used to label actin at C374, but the mechanisms of the fluorescence changes are still unknown due to the lack of structural information. Here authors provide cryo-EM structures of actin filaments with N-1-pyrene conjugated to cysteine 374 and either ADP or ADP-phosphate in the active site.

    • Steven Z. Chou
    •  & Thomas D. Pollard

  • Article
    | Open Access

    The low-complexity (LC) domain mediates liquid-liquid phase separation and fibril formation of the RNA-binding protein FUS (FUsed in Sarcoma). Here, the authors combine cryo-EM, solid-state NMR measurements and MD simulations to structurally characterise the fibrils formed by the C-terminal half of the FUS LC domain and discuss stabilizing interactions within the fibril core.

    • Myungwoon Lee
    • , Ujjayini Ghosh
    •  & Robert Tycko

  • Article
    | Open Access

    Microtubules are dynamic tubulin polymers which elongate by addition of bent guanosine triphosphate tubulin to the tips of curving protofilaments. Here authors use Brownian dynamics modeling and electron cryotomography to show that the lateral activation energy barrier in tubulin-tubulin interactions is a key parameter for this process, controlling the development of high pulling forces.

    • Nikita B. Gudimchuk
    • , Evgeni V. Ulyanov
    •  & J. Richard McIntosh

  • Article
    | Open Access

    Archaeal type IV pili (T4P) mediate adhesion to surfaces and are receptors for hyperthermophilic archaeal viruses. Here, the authors present the cryo-EM structures of two archaeal T4P from Pyrobaculum arsenaticum and Saccharolobus solfataricus and discuss evolutionary relationships between bacterial T4P, archaeal T4P and archaeal flagellar filaments.

    • Fengbin Wang
    • , Diana P. Baquero
    •  & Edward H. Egelman

  • Article
    | Open Access

    Multi-subunit Cullin (CUL)-RING ligases (CRL) form the largest family of E3 ligases and are composed of a substrate receptor, a CUL, and a RING-box (RBX) protein. Here, the authors use cryo-EM and HDX-MS to characterise the ASB9 CUL-RING E3 ligase and present the structure of ASB9-ELOB/C bound to the substrate creatine kinase and the full-length CUL5 structure in complex with RBX2, and they propose a revised allosteric mechanism for CUL-E3 ligase function.

    • Ryan J. Lumpkin
    • , Richard W. Baker
    •  & Elizabeth A. Komives

  • Article
    | Open Access

    The contraction of cardiac and skeletal muscles is regulated by Ca2+ released from the sarcoplasmic reticulum in muscle cells. Here the authors provide molecular insights into Ca2+ regulation of muscle contraction by determining the cryo-EM structures of the human cardiac muscle thin filament in the absence and presence of Ca2+.

    • Yurika Yamada
    • , Keiichi Namba
    •  & Takashi Fujii

  • Article
    | Open Access

    The bacterial flagellar hook is a molecular universal joint that connects the rotary motor and long helical propeller of the bacterial flagellum. Here the authors present the 3.6 Å resolution cryo-EM structure of the native supercoiled Salmonella hook that provides insights into the dynamic changes of subunit conformations and intermolecular interactions of the hook protein FlgE.

    • Takayuki Kato
    • , Fumiaki Makino
    •  & Keiichi Namba

  • Article
    | Open Access

    Studying the condensation of proteins into membraneless organelles in live cells is highly challenging. Here the authors develop a fluorescence lifetime imaging approach to monitor the condensation of proteins in nuclear organelles and report coordinated and cyclic changes in several nuclear organelles.

    • Artem Pliss
    • , Svitlana M. Levchenko
    •  & Paras N. Prasad

  • Article
    | Open Access

    The interactions of lignin with polysaccharides in plant secondary cell walls are not well understood. Here the authors employ solid-state NMR measurements to analyse intact stems of maize, Arabidopsis, switchgrass and rice and observe that lignin self-aggregates and forms highly hydrophobic microdomains that make extensive surface contacts to xylan.

    • Xue Kang
    • , Alex Kirui
    •  & Tuo Wang

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