Protein folding articles within Nature Communications

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  • Article
    | Open Access

    Genes encoding protein complex subunits are often dispersed in the genome of eukaryotes, raising the question how these protein complexes assemble. Here, the authors provide evidence that mammalian nuclear transcription complexes are formed co-translationally to ensure specific and functional interactions.

    • Ivanka Kamenova
    • , Pooja Mukherjee
    •  & László Tora

  • 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 small heat-shock protein HSP27 occurs predominantly in oligomeric forms, which makes its structural characterisation challenging. Here the authors employ CPMG and high-pressure NMR with native mass spectrometry and biophysical assays to show that the active monomeric form of HSP27 is substantially disordered and highly chaperone-active.

    • T. Reid Alderson
    • , Julien Roche
    •  & Andrew J. Baldwin

  • Article
    | Open Access

    SecB homologs can be associated with stress-responsive type II toxin–antitoxin (TA) systems and form tripartite toxin-antitoxin-chaperone systems (TAC). Here the authors provide structural insights into TACs by presenting the crystal structure of the M. tuberculosis TA-associated SecB chaperone in complex with the C-terminal ChAD (chaperone addiction) extension of the antitoxin HigA1.

    • Valérie Guillet
    • , Patricia Bordes
    •  & Lionel Mourey

  • Article
    | Open Access

    The antitermination factor RfaH adopts two functional states where its C-terminal domain is folded either as an α-helical hairpin or β-barrel. Here the authors employ solution state NMR measurements to show that the C-terminal domain transforms into the β-barrel only upon binding to the elongation complex and refolds back after dissociation.

    • Philipp Konrad Zuber
    • , Kristian Schweimer
    •  & Stefan H. Knauer

  • Article
    | Open Access

    Many 2-Cystein Peroxiredoxins (Prx) can either function as peroxidases or chaperones when exposed to stress. Here the authors present the structures of Leishmania infantum mitochondrial Prx alone and with a bound model client protein, use crosslinking to reveal interaction regions that stabilize the bound client, and provide insights into the mechanism by which Prx’s adopt chaperone activity.

    • Filipa Teixeira
    • , Eric Tse
    •  & Ursula Jakob

  • Article
    | Open Access

    Zinc ions (Zn2+) are imported by Golgi-resident transporters but the function of zinc in the early secretory pathway has remained unknown. Here the authors find that Zn2+ regulates protein quality control in the early secretory pathway by demonstrating that the pH-sensitive chaperone ERp44 binds Zn2+ and solving the Zn2+-bound ERp44 structure.

    • Satoshi Watanabe
    • , Yuta Amagai
    •  & Kenji Inaba

  • Article
    | Open Access

    The role of mesencephalic astrocyte-derived neurotrophic factor (MANF) in maintenance of protein folding homeostasis inside the ER has remained unclear. Here the authors determine the structure of the complex between MANF and the ER-localized chaperone BiP and provide evidence that MANF serves as an anti-nucleotide exchange factor for BiP.

    • Yahui Yan
    • , Claudia Rato
    •  & David Ron

  • Article
    | Open Access

    Designing interfaces that can induce protein-protein interactions is a challenging problem. Here the authors show that a five amino acid sequence known to mediate domain swapping in cystatins can drive oligomerization when grafted onto functionally and structurally unrelated host proteins, providing a simple approach to the design of protein assemblies.

    • Neha Nandwani
    • , Parag Surana
    •  & Shachi Gosavi

  • Article
    | Open Access

    Prion-forming proteins have been found in animals, plants, fungi, and bacteria. Here, Nan et al. report that a baculovirus-encoded protein behaves as prion in a yeast system and forms aggregates at high multiplicity of infection in insect cells that affect baculovirus replication.

    • Hao Nan
    • , Hongying Chen
    •  & Xiaodong Xu

  • Article
    | Open Access

    Imbalanced proteostasis is associated with diverse diseases, including ischemia/reperfusion injury in the heart. Here the authors show that the ATF6 arm of the unfolded protein response can be pharmacologically activated with a small molecule in vivo, providing protection from ischemia/reperfusion injury in the heart, the brain, and the kidney.

    • Erik A. Blackwood
    • , Khalid Azizi
    •  & Christopher C. Glembotski

  • Article
    | Open Access

    Small molecule metabolites like phenylalanine can form amyloid-like structures but so far this has only been demonstrated in vitro. Here the authors generate a yeast in vivo model of adenine self-assembly and characterize the adenine assemblies in cells by indicative amyloid dye and anti-adenine assemblies antibodies.

    • Dana Laor
    • , Dorin Sade
    •  & Ehud Gazit

  • Article
    | Open Access

    BAG3 is a Hsp70 co-chaperone that is highly expressed in muscles. Here the authors show that several myofibrillar myopathy causing BAG3 mutations are not impaired in Hsp70 binding, but rather impair the ADP-ATP exchange step of the Hsp70 cycle, causing the aggregation of BAG3, Hsp70 and Hsp70 clients and leading to a collapse of protein homeostasis.

    • Melanie Meister-Broekema
    • , Rebecca Freilich
    •  & Harm H. Kampinga

  • Article
    | Open Access

    Integral membrane proteins are assembled into the ER membrane via the ribosome-translocon channel. Here authors use in vitro translation assays and MD simulations to show that folding in the ribosome is favorable for TM helices, but unfavorable for soluble helices.

    • Manuel Bañó-Polo
    • , Carlos Baeza-Delgado
    •  & Ismael Mingarro

  • Article
    | Open Access

    Staphylococcal pathogens adhere to their human targets using adhesins, which can withstand extremely high forces. Here, authors use single-molecule force spectroscopy to determine the similarly high unfolding forces of B domains that link the adhesin to the bacterium.

    • Lukas F. Milles
    • , Eduard M. Unterauer
    •  & Hermann E. Gaub

  • Article
    | Open Access

    The chaperone Hsp90 plays a key role in maintaining cellular homeostasis. Here the authors provide structural insights into substrate recognition and the pro-folding mechanism of Hsp90/co-chaperone complexes by studying the complex of Hsp90 with its co-chaperone FKBP51 and the substrate Tau bound Hsp90/FKBP51 ternary complex using a NMR based integrative approach.

    • Javier Oroz
    • , Bliss J. Chang
    •  & Markus Zweckstetter

  • Article
    | Open Access

    Impaired kidney function can lead to an increase of β2-microglobulin (β2m) serum levels, which can cause β2m aggregation and amyloid fibril formation. Here the authors combine cryo-EM and magic angle spinning NMR measurements to determine the structure of a β2m fibril and they also present the low resolution model of a β2m fibril with a different morphology.

    • Matthew G. Iadanza
    • , Robert Silvers
    •  & Sheena E. Radford

  • Article
    | Open Access

    Collagen proteins assemble into trimers from distinct monomers with high specificity, yet the molecular basis for this specificity remains unclear. Here the authors demonstrate the crucial role of conserved C-terminal domain cysteine residues and calcium in homotrimeric procollagen assembly.

    • Andrew S. DiChiara
    • , Rasia C. Li
    •  & Matthew D. Shoulders

  • Article
    | Open Access

    Manual sample deposition on a substrate can introduce artifacts in quantitative AFM measurements. Here the authors present a microfluidic spray device for reliable deposition of subpicoliter droplets which dry out in milliseconds after landing on the surface, thereby avoiding protein self-assembly.

    • Francesco Simone Ruggeri
    • , Jerome Charmet
    •  & Tuomas P. J. Knowles

  • Article
    | Open Access

    Artemisinin (ART) is a widely used antimalarial drug, but its mechanism of action is poorly understood. Here, Bridgford et al. show that ART kills parasites by a two-pronged mechanism, causing protein damage and compromising proteasome function, and that accumulation of proteasome substrates activates the ER stress response.

    • Jessica L. Bridgford
    • , Stanley C. Xie
    •  & Leann Tilley

  • Article
    | Open Access

    The phenol-soluble modulin PSMα3 secreted by Staphylococcus aureus forms cross-α amyloid-like fibrils. Here the authors reveal the amyloid polymorphism of PSMs by presenting the cross-β amyloid fibril structures of the biofilm-associated PSMα1 and PSMα4 and showing that truncated PSMα3 antibacterial peptides form distinct out-of-register β-sheets and a polymorph with a hexameric architecture of β-sheets.

    • Nir Salinas
    • , Jacques-Philippe Colletier
    •  & Meytal Landau

  • Article
    | Open Access

    Mutations in LRRK2 kinase are associated with Parkinson’s disease. Here the authors show that LRRK2 modulates propagation of α-synuclein, using rodent and C. elegans models, and show that this is dependent on phosphorylation of one of its substrates, RAB35.

    • Eun-Jin Bae
    • , Dong-Kyu Kim
    •  & Seung-Jae Lee

  • Article
    | Open Access

    The pilus type 1 of uropathogenic E. coli must resist mechanical forces to remain attached to the epithelium. Here the authors use single-molecule force spectroscopy to demonstrate a hierarchy of mechanical stability among the pilus domains and show that the oxidoreductase DsbA also acts as a folding chaperone on the domains.

    • Alvaro Alonso-Caballero
    • , Jörg Schönfelder
    •  & Raul Perez-Jimenez

  • Article
    | Open Access

    Many bacterial proteins exhibit spatially defined localization important for function. Here the authors show that the polar localization of Shigella IpaC type III secretion substrate is mediated by its interaction with the DnaK chaperone and occlusion by the bacterial nucleoid.

    • Clémence Collet
    • , Jenny-Lee Thomassin
    •  & Guy Tran Van Nhieu

  • Article
    | Open Access

    The structures of amyloid fibres are currently primarily studied through solid state NMR and cryo-EM. Here the authors present a free-standing graphene support device that allows diffraction imaging of non-crystalline amyloid fibrils with single X-ray pulses from an X-ray free-electron laser.

    • Carolin Seuring
    • , Kartik Ayyer
    •  & Henry N. Chapman

  • Article
    | Open Access

    The aggregation prone D76N beta-2 microglobulin mutant causes systemic amyloidosis. Here the authors combine crystallography, solid-state NMR, and computational studies and show that the D76N mutation increases protein dynamics and destabilizes the outer strands, which leads to an exposure of amyloidogenic parts explaining its aggregation propensity.

    • Tanguy Le Marchand
    • , Matteo de Rosa
    •  & Stefano Ricagno

  • Article
    | Open Access

    The heat shock protein 90 (Hsp90) chaperone undergoes large conformational changes during its functional cycle. Here the authors combine in vivo, biochemical, biophysical and computational approaches and provide insights into the allosteric regulation of Hsp90 by identifying and characterizing a switch point in the Hsp90 middle domain.

    • Daniel Andreas Rutz
    • , Qi Luo
    •  & Johannes Buchner

  • Article
    | Open Access

    Disruption of the ubiquitin proteasome system (UPS) is often associated with neurodegenerative diseases. Here the authors demonstrate the existence of a general mechanism of proteasomal impairment triggered by a specific protein oligomer structure, irrespective of its protein constituent.

    • Tiffany A. Thibaudeau
    • , Raymond T. Anderson
    •  & David M. Smith

  • Article
    | Open Access

    An integrated network of chaperones and protein degradation machineries called the proteostasis network (PN) is required to maintain protein homeostasis. Here the authors show that one of the components of the PN, the chaperonin TRiC, interacts with the core transcription-coupled nucleotide excision repair protein CSA to ensure its assembly into the CRLCSA complex.

    • Alex Pines
    • , Madelon Dijk
    •  & Haico van Attikum

  • Article
    | Open Access

    Aggregation is sequence-specific and nucleated by short aggregating protein segments (APR). Here authors use a multidisciplinary approach to show that in E.coli some frequently occurring APRs lead to protein aggregation and ultimately bacterial cell death, which could serve as antibacterial strategy.

    • Ladan Khodaparast
    • , Laleh Khodaparast
    •  & Joost Schymkowitz

  • Article
    | Open Access

    Amyloid fibril structures can display polymorphism. Here the authors reveal the cryo-EM structures of several different fibril morphologies of a peptide derived from an amyloidogenic immunoglobulin light chain and present a mathematical analysis of physical factors that influence fibril polymorphism.

    • William Close
    • , Matthias Neumann
    •  & Marcus Fändrich

  • Article
    | Open Access

    The U-box ubiquitin ligase UFD-2 is one of the most abundant components of the ubiquitin proteasome system in muscle cells. Here the authors perform in vitro and in vivo experiments and show that UFD-2 has E3 ligase activity and that it ubiquitinates unfolded myosin using the C. elegans myosin chaperone UNC-45 as an adaptor protein.

    • Doris Hellerschmied
    • , Max Roessler
    •  & Tim Clausen

  • Article
    | Open Access

    A pool of quality control proteins (QC) maintains the protein-folding homeostasis in the cell, but its quantitative analysis is challenging. Here the authors develop a FRET sensor based on the protein barnase, able to quantify QC holdase activity and its ability to suppress protein aggregation.

    • Rebecca J. Wood
    • , Angelique R. Ormsby
    •  & Danny M. Hatters

  • Article
    | Open Access

    The Hsp90 chaperone cycle is influenced by multiple phosphorylation events but their regulatory functions are poorly understood. Here, the authors show that phosphorylation and unfolding of cochaperone Cdc37 tailors the Hsp90 chaperone cycle by recruiting kinases that promote distinct phosphorylation patterns.

    • Ashleigh B. Bachman
    • , Dimitra Keramisanou
    •  & Ioannis Gelis

  • Article
    | Open Access

    Protein phosphatase 2A (PP2A) forms different holoenzymes but little is known about the disassembly of these important signalling complexes. Here the authors present the crystal structure of PP2A bound to TOR signaling pathway regulator (TIPRL) and give insights into the methylation-dependent disassembly of PP2A holenzymes.

    • Cheng-Guo Wu
    • , Aiping Zheng
    •  & Yongna Xing

  • Article
    | Open Access

    Porins, like OmpG, are embedded in the outer membrane of bacteria and facilitate uptake and secretion of nutrients and ions. Here the authors present a protocol for solid state NMR structure determination of proteins larger than 25 kDa and use it to structurally characterize membrane embedded OmpG.

    • Joren S. Retel
    • , Andrew J. Nieuwkoop
    •  & Hartmut Oschkinat

  • Article
    | Open Access

    The BRICHOS domain is a chaperone that can act against amyloid-β peptide fibril formation and non-fibrillar protein aggregation. Here the authors use a multidisciplinary approach and show that the Bri2 BRICHOS domain has qualitatively different chaperone activities depending on its quaternary structure.

    • Gefei Chen
    • , Axel Abelein
    •  & Jan Johansson

  • Article
    | Open Access

    The bacterial chaperone Trigger Factor (TF) is a dynamic protein and its dimer structure is unknown. Here the authors present a protocol combining NMR, computational and biophysical methods for the structural characterization of large dynamic protein complexes and show that TF forms a symmetric head-to-tail dimer.

    • Leonor Morgado
    • , Björn M. Burmann
    •  & Sebastian Hiller

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