Protein folding articles within Nature Communications

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  • Article
    | Open Access

    Detection of amyloid beta deposits is often performed with fluorescent compounds that bind plaques. Here the authors develop turn-on chemiluminescent probes that bind amyloid beta plaques in vivo, and amplify the signal via chemiluminescence resonance energy transfer to the plaque-binding fluorescent molecule CRANAD-3.

    • Jing Yang
    • , Wei Yin
    •  & Chongzhao Ran

  • Article
    | Open Access

    ALS is a neurodegenerative disease characterized by loss of motor neurons. Here, the authors showed that reduced levels of the VSP35 subunit in the retromer complex is a conserved ALS feature and identified a new lead compound increasing retromer stability ameliorating the disease phenotype.

    • Luca Muzio
    • , Riccardo Sirtori
    •  & Gianvito Martino

  • Article
    | Open Access

    The ATPase SecA drives Sec-dependent protein translocation across the bacterial plasma membrane. Here, the authors combine kinetic translocation measurements with single-molecule force spectroscopy and demonstrate that the SecA motor generates mechanical force to unfold and translocate preproteins.

    • Riti Gupta
    • , Dmitri Toptygin
    •  & Christian M. Kaiser

  • Article
    | Open Access

    As assembling 60S subunits transit from the nucleolus to the nucleoplasm, they undergo significant changes in protein composition and structure. Here, the authors provide a structural view of interconnected events during the middle steps of assembly that include the maturation of the central protuberance, the peptidyltransferase center and the nascent polypeptide exit tunnel.

    • Jelena Micic
    • , Yu Li
    •  & John L. Woolford Jr.

  • Article
    | Open Access

    Three-colour FRET is a powerful tool to study macromolecular conformational dynamics, but is temporally limited due to the experimental complexity. Here the authors develop experimental and analytical methods for probing submillisecond-time scale dynamics using single continuous-wave excitation.

    • Janghyun Yoo
    • , Jae-Yeol Kim
    •  & Hoi Sung Chung

  • Article
    | Open Access

    The Sorting and Assembly Machinery (SAM) complex folds beta-barrel proteins and inserts them into the mitochondrial outer membrane. Here authors report cryoEM structures of the SAM complex from Myceliophthora thermophila, which reveals a GST-like fold for Sam35 and Sam37 and sheds light on how the Sam50 beta-barrel opens a lateral gate to accommodate its substrates.

    • Kathryn A. Diederichs
    • , Xiaodan Ni
    •  & Susan K. Buchanan

  • Article
    | Open Access

    Rift Valley fever virus (RVFV) can cause severe diseases in humans, including encephalitis. Here the authors show that NSs, the major virulence factor of RVFV, is an amyloidogenic protein forming fibrils in infected mouse brains and causing increased mortality in mice.

    • Psylvia Léger
    • , Eliana Nachman
    •  & Pierre-Yves Lozach

  • Article
    | Open Access

    Phosphorylation of eIF4E binding proteins (4E-BPs) controls their folding and regulates cap-dependent translation. Here, the authors show that phosphorylation of the C-terminal disordered region stabilizes the non-cooperatively folded 4E-BP domain to an eIF4E binding-incompatible state to control translation.

    • Jennifer E. Dawson
    • , Alaji Bah
    •  & Julie D. Forman-Kay

  • Article
    | Open Access

    Nonsense-mediated mRNA decay (NMD) is a translation-coupled process that eliminates mRNAs containing premature translation-termination codons. Here the authors identify a role for the NMD factor UPF1 in protein quality control, whereby truncated misfolded polypeptides are cleared through autophagy.

    • Yeonkyoung Park
    • , Joori Park
    •  & Yoon Ki Kim

  • Article
    | Open Access

    Changes in osmotic homeostasis alter metabolites and therefore chemical milieu of the cells. Here, the authors show that altering metabolites in E. coli also change the cellular capacity for buffering mutations that impair protein folding and influences proteostasis irrespective of molecular chaperones

    • Kanika Verma
    • , Kanika Saxena
    •  & Kausik Chakraborty

  • Article
    | Open Access

    The unfolded protein response (UPR) is a stress response pathway implicated in numerous diseases and chemotherapy resistance. Here, the authors define the UPR regulon with a multi-omics strategy, uncovering changes to mitochondrial one-carbon metabolism and concomitant resistance to folate-based therapeutics.

    • Stefan Reich
    • , Chi D. L. Nguyen
    •  & Jan Medenbach

  • Article
    | Open Access

    Tau plays an important role in tauopathies and undergoes liquid-liquid phase separation (LLPS). The authors show that disease-related P301L mutant and phosphomimic (S199E/S202E/T205E) tau enhance LLPS in vitro at physiological levels, and using specific antibodies, that tau LLPS leads to pathological conformations such as N-terminal exposure and oligomeric species.

    • Nicholas M. Kanaan
    • , Chelsey Hamel
    •  & Benjamin Combs

  • Article
    | Open Access

    Small molecule polyamines participate in diverse aspects of cell growth and differentiation and are known to regulate ion channel gating. Here authors reveal that cellular polyamines control nicotinic acetylcholine receptor (nAChR) biogenesis, and either catabolic degradation or inhibition of polyamine production augments nAChR assembly.

    • Madhurima Dhara
    • , Jose A. Matta
    •  & David S. Bredt

  • Article
    | Open Access

    The Na+-pumping KR2 rhodopsin from Krokinobacter eikastus is a light-driven non-proton cation pump whose mechanism of pumping remains to be understood. Here authors solved crystal structures of the O-intermediate state of the pentameric form of KR2 and its D116N and H30A mutants, which sheds light on the mechanism of non-proton cation light-driven pumping.

    • Kirill Kovalev
    • , Roman Astashkin
    •  & Valentin Gordeliy

  • Article
    | Open Access

    The chaperone SurA is involved in outer membrane protein (OMP) biogenesis in Gram-negative bacteria, but its mechanism of action is not fully understood. Combining mass spectrometric, biophysical and computational approaches, the authors here show how the conformational dynamics of SurA facilitate OMP binding.

    • Antonio N. Calabrese
    • , Bob Schiffrin
    •  & Sheena E. Radford

  • Article
    | Open Access

    Protein aggregation remains a significant challenge for manufacturing of protein biopharmaceuticals. Here, the authors demonstrate the use of directed evolution and an assay for in vivo innate protein aggregation-propensity to generate aggregation-resistant scFv fragments.

    • Jessica S. Ebo
    • , Janet C. Saunders
    •  & David J. Brockwell

  • Article
    | Open Access

    The ribosome-associated complex (RAC), which contains the Hsp40 protein Zuo1 and the non-canonical Hsp70 protein Ssz1 forms a chaperone triad with the fungal-specific Hsp70 protein Ssb. Here the authors combine X-ray crystallography, crosslinking and biochemical experiments and present the structure of the Zuo1 N-terminus bound to Ssz1 and demonstrate that Ssz1 is an active chaperone for nascent chains.

    • Ying Zhang
    • , Genís Valentín Gesé
    •  & Irmgard Sinning

  • Article
    | Open Access

    Inhibition of PERK, an endoplasmic reticulum (ER) unfolded protein response (UPR) protein, is a potential pharmacological target for cancer treatment. Here, the authors show that inhibition of PERK under ER stress affects trafficking from the ER to the surface of several key receptor tyrosine kinases, suggesting a selective ER retention.

    • Mohamed Mahameed
    • , Shatha Boukeileh
    •  & Boaz Tirosh

  • Article
    | Open Access

    Galectin-3 consists of an unstructured N-terminal domain (NTD) and a structured carbohydrate-recognition domain and agglutinates neutrophils and glycosylated molecules in the extracellular milieu. Here the authors combine biophysical and biochemical experiments with NMR measurements and show that the galectin-3 NTD undergoes liquid-liquid phase separation (LLPS) and agglutinates other molecules through this process.

    • Yi-Ping Chiu
    • , Yung-Chen Sun
    •  & Jie-rong Huang

  • Article
    | Open Access

    Methylation of a lysine residue in Hsp90 is a recently discovered post-translational modification but the mechanistic effects of this modification have remained unknown so far. Here the authors combine biochemical and biophysical approaches, molecular dynamics (MD) simulations and functional experiments with yeast and show that this lysine is a switch point, which specifically modulates conserved Hsp90 functions including co-chaperone regulation and client activation.

    • Alexandra Rehn
    • , Jannis Lawatscheck
    •  & Johannes Buchner

  • Article
    | Open Access

    It is not yet clear how ubiquitously-expressed proteins can cause the selective degeneration of particular populations of neurons, such as in spinocerebellar ataxia type 17, SCA17, which results from a CAG trinucleotide repeat expansion in the ubiquitously expressed transcription factor TBP. Here, the authors show that mutant TBP suppresses the cerebellum-enriched transcription of Inpp5a and link altered levels of INPP5A to the selective degeneration of cerebellar neurons.

    • Qiong Liu
    • , Shanshan Huang
    •  & Shihua Li

  • Article
    | Open Access

    Saccharomyces cerevisiae is a model organism to study proteins involved in neurodegeneration. Here, the authors performed a yeast genome-wide synthetic genetic interaction array (SGA) to screen for toxicity modifiers of Aβ42 and identify riboflavin kinase and its metabolic product flavin mononucleotide as modulators that alleviate cellular Aβ42 toxicity, which is supported by further experimental analyses.

    • Xin Chen
    • , Boyang Ji
    •  & Dina Petranovic

  • Article
    | Open Access

    Tau fibril formation is a hallmark of Alzheimer’s disease. Here the authors reveal an aggregation-dependent protein interaction pattern of Tau and further show that π-stacking of the arginine side-chains drives aberrant protein binding to Tau fibrils.

    • Luca Ferrari
    • , Riccardo Stucchi
    •  & Stefan G. D. Rüdiger

  • Article
    | Open Access

    Native mass spectrometry allows monitoring the folding and interactions of multiple coexisting species but its temporal resolution is traditionally limited. Here, the authors develop a temperature-jump electrospray source for mass spectrometry that enables fast kinetics experiments at different temperatures.

    • Adrien Marchand
    • , Martin F. Czar
    •  & Renato Zenobi

  • Article
    | Open Access

    The Hsp70 system prevents protein aggregation and increases folding yields, but it is unknown whether it also enhances the rate of folding. Here the authors combine refolding assays, FRET and hydrogen/deuterium exchange-mass spectrometry measurements to study the folding of firefly luciferase and find that the bacterial Hsp70 actively promotes the folding of this multi-domain protein.

    • Rahmi Imamoglu
    • , David Balchin
    •  & F. Ulrich Hartl

  • Article
    | Open Access

    Metastatic cells can mimic many of the phenotypic behaviors of embryonic cells. Here, the authors generate a melanoblast-specific transcriptome using a genetically engineered mouse model and identify KDELR3 as a pro-metastasis gene in melanoma.

    • Kerrie L. Marie
    • , Antonella Sassano
    •  & Pravin J. Mishra

  • Article
    | Open Access

    The design of protein assemblies is a major thrust for biomolecular engineering and nanobiotechnology. Here the authors demonstrate a general mechanism for designing allosteric macromolecular assemblies and showcase a proof of concept for engineered allosteric protein assembly.

    • Luis A. Campos
    • , Rajendra Sharma
    •  & Victor Muñoz

  • Article
    | Open Access

    Single-molecule in vitro assays require dedicated confocal microscopes equipped with fluorescence correlation spectroscopy (FCS) modules. Here the authors present a compact, cheap and open-source 3D-printed confocal microscope for single photon counting and FCS measurements, and use it to detect α-synuclein aggregation.

    • James W. P. Brown
    • , Arnaud Bauer
    •  & Yann Gambin

  • Article
    | Open Access

    While the cellular recycling process autophagy has been linked to aging, the impact of selective autophagy on lifespan remains unclear. Here Kumsta et al. show that the autophagy receptor p62/SQSTM1 is required for hormetic benefits and p62/SQSTM1 overexpression is sufficient to extend C. elegans lifespan and improve proteostasis.

    • Caroline Kumsta
    • , Jessica T. Chang
    •  & Malene Hansen

  • Article
    | Open Access

    Chiral inversion of amino acids is thought to modulate the structure and function of amyloid beta (Aβ) but these processes are poorly understood. Here, the authors develop an ion mobility-mass spectrometry based approach to study chirality-regulated structural features of Aβ fragments and their influence on receptor recognition.

    • Gongyu Li
    • , Kellen DeLaney
    •  & Lingjun Li

  • Article
    | Open Access

    Systemic amyloidosis of the ATTR is one of the most abundant forms of systemic amyloidosis and caused by misfolding of the circulating blood protein transthyretin (TTR). Here the authors present the cryo-EM structure of patient-derived Val30Met ATTR amyloid fibrils which reveals that the protofilament consists of an N-terminal and a C-terminal TTR fragment and discuss implications for the mechanism of misfolding.

    • Matthias Schmidt
    • , Sebastian Wiese
    •  & Marcus Fändrich

  • Article
    | Open Access

    Deposition of tau protein aggregates occurs during aging and Alzheimer disease. Here, the authors show that tau burden in the anterior-temporal memory network is associated with disrupted fMRI connectivity and functional isolation of the hippocampus from other memory network components.

    • Theresa M. Harrison
    • , Anne Maass
    •  & William J. Jagust

  • Article
    | Open Access

    The sequestration of misfolded proteins into large assemblies by sequestrases is now considered as the third pillar in protein quality control besides chaperones and proteases. Here the authors characterise the functions of the sequestrases Hsp42 and Btn2 in the proteostasis network of S. cerevisiae and find that they protect cells from too exhaustive depletion of the Hsp70 system.

    • Chi-ting Ho
    • , Tomas Grousl
    •  & Axel Mogk

  • Article
    | Open Access

    Spy is an ATP independent chaperone that allows folding of its client protein Im7 while continuously bound to Spy. Here the authors employ kinetics measurements to study the folding of another Spy client protein SH3 and find that Spy’s ability to allow a client to fold while bound is inversely related to how strongly it interacts with that client.

    • Kevin Wu
    • , Frederick Stull
    •  & James C. A. Bardwell

  • Article
    | Open Access

    Myosin, a motor protein essential for intracellular transport to muscle contraction, requires a chaperone UNC-45 for folding and assembly. Here authors use in vitro reconstitution and structural biology to characterize the interplay between UNC-45 and muscle myosin MHC-B.

    • Doris Hellerschmied
    • , Anita Lehner
    •  & Tim Clausen

  • Article
    | Open Access

    Processing bodies are membrane less organelles that contain enzymes involved in mRNA turnover, among them enhancer of decapping 3 (Edc3). Here the authors use solid- and solution-state NMR spectroscopy to characterize the structural organization and dynamics of Edc3 and find that its interactions with RNA and between the different Edc3 domains are largely preserved in the phase-separated state.

    • Reinier Damman
    • , Stefan Schütz
    •  & Marc Baldus

  • Article
    | Open Access

    Accumulation of abnormal tau protein drives neurodegeneration in Alzheimer’s disease and related dementia disorders. Here, the authors demonstrate the endoplasmic reticulum unfolded protein response mediator XBP-1 controls pathological tau accumulation and the resultant neurodegeneration in a transgenic C. elegans model.

    • Sarah M. Waldherr
    • , Timothy J. Strovas
    •  & Brian C. Kraemer

  • Article
    | Open Access

    It is unclear how unassembled secretory pathway proteins are discriminated from misfolded ones. Here the authors combine biophysical and cellular experiments to study the folding of heterodimeric interleukin 23 and describe how ER chaperones recognize unassembled proteins and aid their assembly into protein complexes while preventing the premature degradation of unassembled units.

    • Susanne Meier
    • , Sina Bohnacker
    •  & Matthias J. Feige

  • Article
    | Open Access

    Studying the unfolding of membrane proteins in a native-like lipid environment is challenging. Here the authors describe a method combining hydrogen-deuterium exchange and solid-state NMR measurements that allows the characterization of unfolding events in lipid-embedded membrane proteins and use the photoreceptor Anabaena Sensory Rhodopsin as a test case.

    • Peng Xiao
    • , David Bolton
    •  & Vladimir Ladizhansky

  • Article
    | Open Access

    The Src-homology 3 domain of phosphatidyl-inositol-3-kinase (PI3K-SH3) is a model system for studying amyloid fibril formation. Here the authors present the 3.4 Å cryo-EM structure of the PI3K-SH3 amyloid fibril, which allows them to rationalize the effects of mutations on the kinetics of fibril formation.

    • Christine Röder
    • , Nicola Vettore
    •  & Gunnar F. Schröder

  • Article
    | Open Access

    S. cerevisiae encodes two Hsp90 isoforms, the constitutively expressed Hsc82 and stress-inducible Hsp82 that are 97% identical. Here, the authors combine a range of biophysical methods and show that they differ in their enzymatic properties, resilience to stress and client range, which suggests that they evolved to provide fine-tuned chaperone assistance under physiological and stress conditions.

    • Hannah Girstmair
    • , Franziska Tippel
    •  & Johannes Buchner

  • Article
    | Open Access

    Hsp chaperones stabilize the inactive conformation of androgen receptor (AR) and are released upon hormone-induced AR activation. Here, the authors locate the Hsp binding region on AR, and show that Hsp70 reduces AR aggregation and promotes AR degradation in cellular and mouse models of a neuromuscular disorder.

    • Bahareh Eftekharzadeh
    • , Varuna C. Banduseela
    •  & Xavier Salvatella

  • Article
    | Open Access

    Proteins have been used in the synthesis of magnetic nanoparticles but issues with aggregation limit this application. Here, the authors report on the synthesis of coiled proteins that display the active loop of the natural proteins to avoid aggregation and investigate the application in nanoparticle synthesis.

    • Andrea E. Rawlings
    • , Lori A. Somner
    •  & Sarah S. Staniland

  • Article
    | Open Access

    β-propeller domains are an important class of folding substrates for the eukaryotic cytosolic chaperonin CTT. Here the authors find that CTT contributes to the folding and assembly of two β-propeller proteins from mTOR complexes, mLST8 and Raptor, and determine the 4.0 Å cryoEM structure of a human mLST8-CCT intermediate that shows mLST8 in a near-native state.

    • Jorge Cuéllar
    • , W. Grant Ludlam
    •  & José M. Valpuesta

  • Article
    | Open Access

    Bacterial ClpB is a disaggregase that solubilizes protein aggregates. Here the authors present the 2.9 Å cryo-EM structure of a hyperactive variant of ClpB bound to the substrate casein in active translocation states and discuss its polypeptide translocation mechanism.

    • Alexandrea N. Rizo
    • , JiaBei Lin
    •  & Daniel R. Southworth

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