Biochemistry articles within Nature Communications

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  • Article
    | Open Access

    Hyperactivation of Akt promotes tumorigenesis. Here, the authors show that SAV1, a member of Hippo signalling, interacts with Akt to suppress Akt activity and MERTK-mediated Akt phosphorylation relieves this suppression to facilitate Akt oncogenic activity in clear cell renal carcinomas.

    • Yao Jiang
    • , Yanqiong Zhang
    •  & Pengda Liu

  • Article
    | Open Access

    RNA sensors—Riboswitches—respond to the binding of small molecules ligands through structure modification. Here the authors identify synthetic small molecules that bind and regulate the activity of PreQ1 Riboswitches despite having no obvious chemical similarity to the cognate ligand.

    • Colleen M. Connelly
    • , Tomoyuki Numata
    •  & John S. Schneekloth Jr.

  • Article
    | Open Access

    D-lactic acidosis typically occurs in the context of short bowel syndrome; excess D-lactate is produced by intestinal bacteria. Here, the authors identify two point mutations in the human lactate dehydrogenase D (LDHD) gene that cause enzymatic loss of function and are associated with elevated plasma D-lactate.

    • Glen R. Monroe
    • , Albertien M. van Eerde
    •  & Judith J. Jans

  • Article
    | Open Access

    Accurate monitoring of chronic kidney disease (CKD) progression is essential for efficient disease management. Here Chen et al. identify five serum metabolites in patients with stage 1–5 CKD whose levels associate with disease progression, and find that 5-methoxytryptophan and its regulatory enzyme TPH-1 exert anti-fibrotic effects in mouse models of kidney injury.

    • Dan-Qian Chen
    • , Gang Cao
    •  & Ying-Yong Zhao

  • Article
    | Open Access

    Spider silk is widely studied for its structural properties; however, other creatures produce silk that could be of interest. Here, the authors study the properties and structure of Bagworm silk and report it as being extraordinarily strong and tough compared to other known silks.

    • Taiyo Yoshioka
    • , Takuya Tsubota
    •  & Tsunenori Kameda

  • Article
    | Open Access

    Phosphatidylethanolamine (PE) is synthesized by four separate pathways, although surprisingly, perturbing mitochondrial PE synthesis compromises mitochondrial function. Here, the authors show that mitochondrial PE synthesis is required for Complex III function and challenge PE trafficking dogma.

    • Elizabeth Calzada
    • , Erica Avery
    •  & Steven M. Claypool

  • Article
    | Open Access

    The cell wall of Gram-positive bacteria consists of peptidoglycan modified with other polymers, such as the capsular polysaccharide. Here, the authors reconstitute the biosynthesis of capsular polysaccharide and elucidate its interplay with the cell wall biosynthetic machinery.

    • Marvin Rausch
    • , Julia P. Deisinger
    •  & Tanja Schneider

  • Article
    | Open Access

    Protein kinase A (PKA) is typically activated by cAMP. Here, Bachmaier et al. show that PKA of Trypanosoma is activated by nucleoside-related ligands, explain the ligand selectivity swap by a co-crystal structure of trypanosome PKAR, and identify potential downstream targets by phosphoproteomics.

    • Sabine Bachmaier
    • , Yuri Volpato Santos
    •  & Michael Boshart

  • Article
    | Open Access

    Nitrogen pollution is influenced by many stressors, and their combined effects are poorly constrained. Here the authors used a global land biosphere model to analyse the past two and a half centuries of land N pollution budgets and fluxes to the ocean and atmosphere and found that land sequesters 11% of global annual reactive N inputs.

    • Minjin Lee
    • , Elena Shevliakova
    •  & P. C. D. Milly

  • Article
    | Open Access

    Copper (Cu) is an essential trace element for growth and development and the Cu+ transporter Ctr1 is crucial for both dietary Cu uptake and peripheral distribution. Here authors solve Cu+ -free and Cu+ -bound Ctr1 structures which adopt a homo-trimeric Cu+ -selective ion channel-like architecture

    • Feifei Ren
    • , Brandon L. Logeman
    •  & Peng Yuan

  • Article
    | Open Access

    G-protein-gated inward rectifying potassium channels (GIRKs) require Gβγ subunits and phosphorylated phosphatidylinositides (PIPs) for gating. Here authors use native ion mobility mass spectrometry to monitor small molecule binding events to GIRK2 and shed light on the selectivity of GIRK2 towards PIPs.

    • Yang Liu
    • , Catherine E. LoCaste
    •  & Arthur Laganowsky

  • Article
    | Open Access

    The mechanisms that control the presynaptic abundance of GABAB receptors (GBRs) remains unclear. This study shows that sequence-related epitopes in APP, AJAP-1 and PIANP bind with nanomolar affinities to the N-terminal sushi-domain of presynaptic GBRs, and that selective loss of APP impaired GBR-mediated presynaptic inhibition and axonal GBR expression

    • Margarita C. Dinamarca
    • , Adi Raveh
    •  & Bernhard Bettler

  • Article
    | Open Access

    Tight regulation of retrotransposons such as endogenous retroviruses (ERVs) is essential for genome and transcriptome integrity. Here, the authors show that the ATPase function of the chromatin remodeler SMARCAD1 facilitates the binding of KAP1 to ERVs and is required for their repression in embryonic stem cells.

    • Parysatis Sachs
    • , Dong Ding
    •  & Jacqueline E. Mermoud

  • Article
    | Open Access

    Mass spectrometry facilitates large-scale glycosylation profiling but in-depth analysis of intact glycopeptides is still challenging. Here, the authors show that activated ion electron transfer dissociation is suitable for glycopeptide fragmentation and improves glycoproteome coverage.

    • Nicholas M. Riley
    • , Alexander S. Hebert
    •  & Joshua J. Coon

  • Article
    | Open Access

    Attachment of human noroviruses to histo blood group antigens (HBGAs) is essential for infection. Here the authors report that an asparagine residue located near the HBGA-attachment site can convert into an iso-aspartate residue through spontaneous deamidation and influence HBGA recognition.

    • Alvaro Mallagaray
    • , Robert Creutznacher
    •  & Thomas Peters

  • Article
    | Open Access

    Proteins continuously undergo non-enzymatic modifications such as glycation, which accumulate under physiological conditions but can be enhanced in disease. Here the authors characterise histone glycation, provide evidence that it affects chromatin, particularly in breast cancer, and identify DJ-1 as a deglycase.

    • Qingfei Zheng
    • , Nathaniel D. Omans
    •  & Yael David

  • Article
    | Open Access

    Halogenase enzymes are of interest as halogenating tools for organic synthesis. Here the authors show that the bacterial FAD-dependent phenolic halogenase PltM chlorinates, brominates and iodinates a variety of substrates and reveal the structural basis for its substrate versatility and provide insights into the FAD recycling mechanism of PltM.

    • Shogo Mori
    • , Allan H. Pang
    •  & Oleg V. Tsodikov

  • Article
    | Open Access

    The cellular functions of arrestins are determined in part by the pattern of phosphorylation on the G protein-coupled receptors (GPCRs) to which arrestins bind. Here, authors use a library of synthetic phosphopeptide analogues of the GPCR rhodopsin C-terminus and determine the ability of these peptides to bind and activate arrestins using a variety of biochemical and biophysical methods.

    • Daniel Mayer
    • , Fred F. Damberger
    •  & Dmitry B. Veprintsev

  • Article
    | Open Access

    Ufmylation is a ubiquitylation-like protein modification but only a few ufmylation substrates and functions have been discovered so far. Here, the authors demonstrate ufmylation of histone H4 upon DNA damage and show that this modification is involved in the amplification of ATM activation.

    • Bo Qin
    • , Jia Yu
    •  & Zhenkun Lou

  • Article
    | Open Access

    Piezo channels are mechanosensitive and rely on membrane composition to transduce physical stimuli into electrical signals. Here authors analyse the membrane components that modulate Piezo1 function using lipid profiling which shows that fatty acid metabolism can modulate ion channel activity.

    • Luis O. Romero
    • , Andrew E. Massey
    •  & Valeria Vásquez

  • Review Article
    | Open Access

    ADP-ribose erasing enzymes are increasingly recognized as critical regulators of protein ADP-ribosylation dynamics in living systems. Here, the authors review recent advances in the discovery and characterization of ADP-ribose erasers and discuss their role within the cellular ADP-ribosylation machinery.

    • Julia O’Sullivan
    • , Maria Tedim Ferreira
    •  & Guy G. Poirier

  • 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

    Human adenoviruses (HAd) cause respiratory, gastrointestinal and ocular infections. Here, the authors provide insights into the early stages of adenovirus infection by determining the cryo-EM structure of the trimeric HAd type 3 fibre knob bound to its cellular receptor human desmoglein 2, which reveals residues critical for HAd-receptor interactions.

    • Emilie Vassal-Stermann
    • , Gregory Effantin
    •  & Pascal Fender

  • Article
    | Open Access

    The centrosome is a membraneless organelle composed of two centrioles and an amorphous pericentriolar material but the overall centrosome organizations remains unknown. Here authors show that two scaffold proteins, Cep63 and Cep152, self-assemble into a higher-order cylindrical architecture capable of recruiting downstream components, including Plk4.

    • Tae-Sung Kim
    • , Liang Zhang
    •  & Kyung S. Lee

  • Article
    | Open Access

    Extra-cytoplasmic function (ECF) σ factors allow bacteria to rapidly respond to stress conditions. Here the authors provide insights into the mechanism of bacterial stress-induced transcription by determining the crystal structures of the M. tuberculosis ECF σ factor bound RNA Polymerase (RNAP) holoenzyme and the ECF σ factor-RNAP transcription initiation complex.

    • Lingting Li
    • , Chengli Fang
    •  & Yu Zhang

  • Article
    | Open Access

    The mode of miRNA transfer between tumour-immune cells is usually via exosomes. Here, the authors show that an alternative mode of transfer whereby miR-375 from apoptotic tumour cells can be transferred to tumour-associated macrophages via CD36 receptor, which induces macrophage migration and infiltration to the tumours.

    • Ann-Christin Frank
    • , Stefanie Ebersberger
    •  & Bernhard Brüne

  • Article
    | Open Access

    In many AMPylating FIC proteins a structurally conserved glutamate represses AMPylation. Here, the authors show that this glutamate supports deAMPylation in Enterococcus faecalis FIC (EfFIC), and that EfFIC switches from AMPylation to deAMPylation by binding Ca2+ at distinct sites.

    • Simon Veyron
    • , Giulia Oliva
    •  & Jacqueline Cherfils

  • Article
    | Open Access

    The human transferrin receptor 1 (CD71) is a transmembrane protein responsible for iron uptake. Here the authors present the 3.9 Å resolution cryo-EM structure of the CD71 ectodomain-human ferritin (H-Ft) complex and find that H-Ft binds a CD71 region different from the transferrin one that overlaps with the surface recognized by select pathogens.

    • Linda Celeste Montemiglio
    • , Claudia Testi
    •  & Beatrice Vallone

  • Article
    | Open Access

    The Ups/PRELI family mediates intramitochondrial lipid distribution and synthesis by shuttling phospholipids between both mitochondrial membranes. Here the authors combine X-ray crystallography, MD simulations and yeast genetic screens and identify residues that are important for Ups/PRELI lipid specificity and reveal a dual lipid recognition mechanism in Ups/PRELI family members.

    • Xeni Miliara
    • , Takashi Tatsuta
    •  & Thomas Langer

  • Article
    | Open Access

    Microtubules in cilia are sufficiently stable to withstand the beating motion, but how they are stabilized while serving as tracks for intraflagellar transport and axonemal dyneins remains unknown. Here authors identify two microtubule inner proteins, FAP45 and FAP52, which stabilize the ciliary axonemes in Chlamydomonas.

    • Mikito Owa
    • , Takayuki Uchihashi
    •  & Masahide Kikkawa

  • Article
    | Open Access

    The diheme enzyme MauG forms a bis-Fe(IV) state. Here the authors identify and determine the structure of BthA, a diheme peroxidase conserved in all Burkholderia and show that BthA also forms a bis-Fe(IV) species but mechanistically differs from MauG by combining magnetic resonance, near-IR and Mössbauer spectroscopies and electrochemical methods.

    • Kimberly Rizzolo
    • , Steven E. Cohen
    •  & Sean J. Elliott

  • 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

    Many human proteins are regulated by lysine acetylation, but the degree of acetylation at individual sites is poorly characterized. Here, the authors measure acetylation stoichiometry in the HeLa cell proteome, providing a resource to assess mechanistic constraints on acetylation-mediated protein regulation.

    • Bogi Karbech Hansen
    • , Rajat Gupta
    •  & Brian T. Weinert

  • Article
    | Open Access

    Amphihelical antimicrobial peptides (AMPs) are bactericidal host defense factors, but their function as immunomodulators is emerging. Here the authors show that several AMPs organize DNA into periodic nanocrystals by self-assembling into superhelical protofibril scaffolds, which potentiates DNA sensing by TLR9.

    • Ernest Y. Lee
    • , Changsheng Zhang
    •  & Gerard C. L. Wong

  • Article
    | Open Access

    Despite many recent advances in cryo-EM, imaging smaller macromolecules (below 100 kDa) has remained a challenge. Here the authors show that biological specimens amassing <100 kDa can be resolved to better than 3 Å resolution using conventional defocus-based single-particle analysis methods.

    • Mark A. Herzik Jr.
    • , Mengyu Wu
    •  & Gabriel C. Lander

  • Article
    | Open Access

    AMP-activated protein kinase AMPK senses and regulates cellular energy state. Here the authors engineer a synthetic sensor, AMPfret, that allows direct, real-time readout of the AMPK conformational state by fluorescence resonance energy transfer (FRET).

    • Martin Pelosse
    • , Cécile Cottet-Rousselle
    •  & Uwe Schlattner

  • Article
    | Open Access

    RNA binding proteins are important regulators of RNA function. Here the authors describe a method for isolation of RNA-protein complexes that does not rely on a specific RNA sequence or motif, and demonstrate the approach by providing the global RNA-bound proteomes of human HEK293 cells and Salmonella Typhimurium.

    • Erika C. Urdaneta
    • , Carlos H. Vieira-Vieira
    •  & Benedikt M. Beckmann

  • Article
    | Open Access

    Chromatophores in cephalopod skin are known for fast changes in coloration due to light-scattering pigment granules. Here, authors demonstrate structural coloration facilitated by reflectin in sheath cells and offer insights into the interplay between structural and pigmentary coloration elements.

    • Thomas L. Williams
    • , Stephen L. Senft
    •  & Leila F. Deravi

  • Article
    | Open Access

    The biological functions of lipids critically depend on their highly diverse molecular structures. Here, the authors determine the mass-resolved collision cross sections of 456 sphingolipid and glycerophospholipid species, providing a reference for future structural lipidomics studies.

    • Katrina L. Leaptrot
    • , Jody C. May
    •  & John A. McLean

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