Chemical biology

  • Article
    | Open Access

    So far most of the de novo designed proteins are for single states only. Here, the authors present the de novo design and crystal structure determination of a coiled-coil peptide that assembles into multiple, distinct conformational states under the same conditions and further characterise its properties with biophysical experiments, NMR and MD simulations.

    • William M. Dawson
    • , Eric J. M. Lang
    •  & Derek N. Woolfson
  • Article
    | Open Access

    Survivin’s dual function as apoptosis inhibitor and regulator of cell proliferation is mediated via its interaction with the export receptor CRM1. Here authors report a strategy addressing its dimer interface overlapping with the nuclear export signal, the binding site of CRM1, with advanced supramolecular tweezers for lysine and arginine.

    • Annika Meiners
    • , Sandra Bäcker
    •  & Shirley K. Knauer
  • Article
    | Open Access

    The ability to dynamically control protein-protein interactions and localization of proteins is critical in synthetic biological systems. Here the authors develop a peptide-based molecular switch that regulates dimer formation and lipid membrane targeting via reversible phosphorylation.

    • Leon Harrington
    • , Jordan M. Fletcher
    •  & Petra Schwille
  • Article
    | Open Access

    Monitoring the activity of the processive motor protein kinesin-1 in live cells is currently difficult. Here the authors report the fluorogenic small molecule QPD-OTf, a kinesin-1 substrate that causes activity-dependent dye precipitation.

    • Simona Angerani
    • , Eric Lindberg
    •  & Nicolas Winssinger
  • Article
    | Open Access

    Rubromycin family of natural products belongs to aromatic polyketides with diverse bioactivities, but details of their biosynthesis are limited. Here, the authors report the complete in vitro reconstitution of enzymatic formation of the spiroketal moiety of rubromycin polyketides, driven by flavin-dependent enzymes, and characterize reaction intermediates.

    • Britta Frensch
    • , Thorsten Lechtenberg
    •  & Robin Teufel
  • Article
    | Open Access

    Trans-acyltransferase polyketide synthases are multimodular enzymes that synthesise diverse polyketides. Here, the authors present an algorithm for the global study of their diversity, showing exchange of conserved consecutive modules as a driver of diversification, and guiding the discovery of polyketides.

    • Eric J. N. Helfrich
    • , Reiko Ueoka
    •  & Marnix H. Medema
  • Article
    | Open Access

    Furanocembranoid-like natural products with the alkene-substituted furan scaffold display a range of biological activities, but are difficult to access. Here, the authors report a modular biomimetic strategy to synthesise diverse alkene-substituted furan-containing macrolactams via palladium-catalysed unactivated Csp3-H olefination.

    • Jiping Hao
    • , Xueying Guo
    •  & Weibo Yang
  • Article
    | Open Access

    2,5-Dihydroxypyridine dioxygenase NicX uses a mononuclear non-heme Fe(II) to catalyze the oxidative pyridine ring cleavage of the pollutant 2,5-hydroxypyridine. Here, the authors report crystal structures of NicX, identify residues involved in substrate stabilization and Fe(II) coordination, and propose the catalytic mechanism of NicX.

    • Gongquan Liu
    • , Yi-Lei Zhao
    •  & Ping Xu
  • Article
    | Open Access

    Glycolipids are glycoconjugates with important biological functions, but techniques for their analysis are deficient. Here, the authors report the use of cryogenic gas-phase infrared spectroscopy to investigate isomerism in a set of immunologically relevant glycolipids, and show that their structural features can be accurately resolved based on a narrow spectral fingerprint region.

    • Carla Kirschbaum
    • , Kim Greis
    •  & Kevin Pagel
  • Article
    | Open Access

    The connection between metal binding to proteins and availabilities of different metals in cells has been unclear. Here, the authors report a metalation-calculator that takes into account competition between metals and their variable accessibility, and thereby elucidate in vivo metal occupancies of three different proteins, CobW, YeiR and YjiA.

    • Tessa R. Young
    • , Maria Alessandra Martini
    •  & Nigel J. Robinson
  • Article
    | Open Access

    Direct cloning of biosynthetic gene clusters is difficult due to their size and repetitive nature. Here, the authors present CAPTURE, which uses Cas12a and in vivo Cre-lox recombination for efficient cloning of gene clusters up to 113 kb, and demonstrate how this method can be used for large-scale discovery of novel natural products.

    • Behnam Enghiad
    • , Chunshuai Huang
    •  & Huimin Zhao
  • Article
    | Open Access

    The BCL-2 family protein BAX functions to regulate mitochondria-driven cell death. Here the authors show that the drug Eltrombopag inhibits BAX and prevents apoptosis induced by cytotoxic stimuli.

    • Adam Z. Spitz
    • , Emmanouil Zacharioudakis
    •  & Evripidis Gavathiotis
  • Article
    | Open Access

    Active-site loops are important for catalytic properties of enzymes, but challenging to engineer due to their high flexibility and diversity. Here, the authors identify and engineer hot-spots in the loops of cumene dioxygenase, obtain variants with changed activity, regio- and enantioselectivity, and present a Linker In Loop Insertion approach for loop modification.

    • Peter M. Heinemann
    • , Daniel Armbruster
    •  & Bernhard Hauer
  • Article
    | Open Access

    Coiled-coil protein origami (CCPO) is a strategy for the design of polyhedral cage-shaped protein folds based on coiled-coil (CC) dimer-forming peptides. Here, the authors show that CCPO proteins fold in a multistep process governed by the spatial distance between CC modules in the primary sequence and subsequent folding intermediates, which enables the use of identical CC modules for the CCPO tetrahedron design.

    • Jana Aupič
    • , Žiga Strmšek
    •  & Roman Jerala
  • Article
    | Open Access

    Coiled-coil protein origami is a strategy for the de novo design of polypeptide nanostructures based on coiled-coil dimer forming peptides, where a single chain protein folds into a polyhedral cage. Here, the authors design a single-chain triangular bipyramid and also demonstrate that the bipyramid can be self-assembled as a heterodimeric complex, comprising pre-defined subunits.

    • Fabio Lapenta
    • , Jana Aupič
    •  & Roman Jerala
  • Article
    | Open Access

    Accurately predicting the secondary structure of non-coding RNAs can help unravel their function. Here the authors propose a method integrating thermodynamic information and deep learning to improve the robustness of RNA secondary structure prediction compared to several existing algorithms.

    • Kengo Sato
    • , Manato Akiyama
    •  & Yasubumi Sakakibara
  • Article
    | Open Access

    Hundreds of BRAF mutations have been identified in patients with cancer but currently approved drugs only target BRAF V600 mutants. Here, the authors develop a vemurafenib-based PROTAC that induces degradation of all classes of BRAF mutants without affecting wild-type RAF proteins.

    • Shanique Alabi
    • , Saul Jaime-Figueroa
    •  & Craig M. Crews
  • Article
    | Open Access

    Biosynthesis of the statin precursor lovastatin depends on the LovB–LovC megasynthase complex. Here, the authors present cryoEM structures of LovB–LovC and core LovB, providing structural insights into the catalytic cycle underlying lovastatin production.

    • Jialiang Wang
    • , Jingdan Liang
    •  & Zhijun Wang
  • Article
    | Open Access

    Synthetic gene circuits may not function as expected due to the resource competition between modules. Here the authors build cascading bistable switches to achieve two successive cell fate transitions but found a ‘winner-takes-all’ behaviour, which is overcome by a division of labour strategy.

    • Rong Zhang
    • , Hanah Goetz
    •  & Xiao-Jun Tian
  • Article
    | Open Access

    Fluorescent protein reporters based on GFP exist, but have intrinsic disadvantages. Here the authors incorporate pH, Ca2+ and protein–protein interaction sensing modalities into de novo designed mini-fluorescence-activating proteins (mFAPs), with increased photostability and smaller size, which bind a range of DFHBI chromophore variants.

    • Jason C. Klima
    • , Lindsey A. Doyle
    •  & David Baker
  • Article
    | Open Access

    The analysis of AMPA-type glutamate receptor (AMPAR) trafficking is essential for understanding molecular mechanisms of learning and memory, but the analytical tools are currently limited. Here, the authors report a method that combines affinity-based receptor labeling and bioorthogonal click chemistry to quantify AMPAR distribution and trafficking under physiological conditions.

    • Kento Ojima
    • , Kazuki Shiraiwa
    •  & Shigeki Kiyonaka
  • Article
    | Open Access

    Carbon dots have attracted much attention for biomedical applications but potential degradation and associated toxicity are still poorly understood. Here, the authors report on a study into the photo-degradation of carbon dots, the products produced and associated cytotoxicity.

    • Yue-Yue Liu
    • , Nan-Yang Yu
    •  & Ai-Jun Miao
  • Article
    | Open Access

    A world preceding the prebiotic RNA-world may have been based on xeno nucleic acids (XNAs), but their replication likely did not require enzymes. Here, the authors demonstrate template-directed non-enzymatic synthesis of an XNA, acyclic l-threoninol nucleic acid, via chemical ligation mediated by N-cyanoimidazole, and achieve a pseudo-primer extension of this XNA with all four nucleobases.

    • Keiji Murayama
    • , Hikari Okita
    •  & Hiroyuki Asanuma
  • Article
    | Open Access

    PARP1 is the target of clinically approved anti-cancer drugs whose in vivo efficacy has been hard to predict. Here the authors show how an altered active site formed between PARP1 and Histone PARylation Factor 1 (HPF1) changes the efficacy of some of these inhibitors.

    • Johannes Rudolph
    • , Genevieve Roberts
    •  & Karolin Luger
  • Article
    | Open Access

    [FeFe]-hydrogenases catalyze the conversion of protons and electrons to molecular hydrogen, but upon exposure to oxygen, their catalytic cofactor is irreversibly inactivated. Here, the authors determine the crystal structure of hydrogenase CbA5H and identify a cysteine residue, which acts as a safety cap that shields the active site from oxygen.

    • Martin Winkler
    • , Jifu Duan
    •  & Thomas Happe
  • Article
    | Open Access

    The human neuropeptide Y receptor Y2 (Y2R) is a drug target for the treatment of obesity and anxiety. Crystal structure of Y2R bound to a selective antagonist and accompanying mutagenesis provide insights into ligand recognition and subtype specificity of NPY receptors.

    • Tingting Tang
    • , Christin Hartig
    •  & Beili Wu
  • Article
    | Open Access

    Covalent conjugation of endogenous protein complexes offers many opportunities for fundamental and clinical research. Based on a bacterial protein domain that forms a reactive anhydride in the presence of Ca2+, the authors here develop a system that enables the covalent capture of endogenous binding partners.

    • Arne H. A. Scheu
    • , Sheryl Y. T. Lim
    •  & Mark Howarth
  • Article
    | Open Access

    Synthetic biologists often co-opt heterologous parts to affect new functions in living cells, yet such an approach has rarely been extended to structural components of the ribosome. Here, the authors describe generalizable methods to express ribosomes from divergent microbes in E. coli and maximize their function.

    • Natalie S. Kolber
    • , Ranan Fattal
    •  & Ahmed H. Badran
  • Article
    | Open Access

    TNF can be inhibited by small molecules that stabilize the TNF trimer in an asymmetric conformation. Here, the authors develop a monoclonal antibody that selectively binds this inactive form of TNF, enabling both target engagement assessment and structural characterization of TNF binding to TNF receptor 1.

    • Daniel J. Lightwood
    • , Rebecca J. Munro
    •  & Alastair D. G. Lawson
  • Article
    | Open Access

    The Legionella effector DrrA AMPylates the host protein Rab1 during infection, but the mechanism is still under debate. Here, the authors provide structural insights into the low-affinity DrrA:Rab1 interaction, showing that Rab1 allosterically activates DrrA through a non-conventional binding mechanism.

    • Jiqing Du
    • , Marie-Kristin von Wrisberg
    •  & Aymelt Itzen
  • Article
    | Open Access

    Post transcriptional modification of RNAs represents an important layer of gene regulation. Here the authors describe NAIL-MS—a method for monoisotopic RNA labeling in cell culture—demonstrating its capabilities by analyzing the modification kinetics of total tRNA, 18S rRNA and tRNAPhe as models.

    • Matthias Heiss
    • , Felix Hagelskamp
    •  & Stefanie Kellner
  • Article
    | Open Access

    Nonribosomal lipopeptides contain an acyl chain important for bioactivity, but its incorporation into the peptidyl backbone, mediated by the starter condensation (Cs) domain of nonribosomal peptide synthases, is not fully understood. Here, the authors show that acyl chains of different lengths can be obtained by engineering Cs domains and identify residues that determine the selectivity for acyl chains.

    • Lin Zhong
    • , Xiaotong Diao
    •  & Xiaoying Bian
  • Article
    | Open Access

    Remdesivir is a nucleoside analog that inhibits the SARS-CoV-2 RNA dependent RNA polymerase (RdRp) and is used as a drug to treat COVID19 patients. Here, the authors provide insights into the mechanism of remdesivir-induced RdRp stalling by determining the cryo-EM structures of SARS-CoV-2 RdRp with bound RNA molecules that contain remdesivir at defined positions and observe that addition of the fourth nucleotide following remdesivir incorporation into the RNA product is impaired by a barrier to further RNA translocation.

    • Goran Kokic
    • , Hauke S. Hillen
    •  & Patrick Cramer
  • Article
    | Open Access

    Multistep enzymatic reactions (cascades) can be achieved by confining enzymes in synthetic materials, but ways to simultaneously energize, control and observe the reactions in real time are lacking. Here, bidirectional interconversion between aspartate and pyruvate by a five enzyme cascade trapped in electrode nanopores, addressable by laptop commands, is demonstrated.

    • Giorgio Morello
    • , Clare F. Megarity
    •  & Fraser A. Armstrong
  • Article
    | Open Access

    Existing optogenetic methods to induce calcium mobilisation lack selectivity and specificity. Here, the authors design and engineer a single-component light-operated calcium channel to provide optical control over calcium signals and calcium-dependent physiological responses: LOCa.

    • Lian He
    • , Liuqing Wang
    •  & Yubin Zhou
  • Article
    | Open Access

    FR900359 (FR) is a Gq protein inhibitor depsipeptide isolated from an uncultivable plant endosymbiont and synthesized by non-ribosomal peptide synthetases. Here, the authors discover a cultivable bacterial FR producer and show that FrsA thioesterase domain catalyses intermolecular transesterification of the FR side chain to the depsipeptide core during biosynthesis, improving Gq inhibition properties.

    • Cornelia Hermes
    • , René Richarz
    •  & Max Crüsemann
  • Article
    | Open Access

    Thiol-disulfide exchange is an extensively used reversible reaction in dynamic combinatorial chemistry, but usually requires long time to reach equilibrium. Here, the authors employ selenocystine as a catalyst of thiol-disulfide exchange at low temperatures and basic pH, and show that it can promote disulfide bond formation during folding of a scrambled RNase A.

    • Andrea Canal-Martín
    •  & Ruth Pérez-Fernández
  • Article
    | Open Access

    Radiotherapy has the potential to induce immunogenic cell death (ICD), however radiation-induced immune responses are often limited. Here the authors design gadolinium-based nanoscale coordination polymers to amplify radiation-mediated oxidative stress, promoting ICD and anti-tumor immune responses.

    • Zhusheng Huang
    • , Yuxiang Wang
    •  & Ahu Yuan
  • Article
    | Open Access

    Short-chain primary amines (SCPAs) are industrially important compounds that are commonly produced under harsh synthetic conditions. Here, the authors report a combination of retrobiosynthesis and precursor selection step for design of biosynthetic pathways leading to production of SCPAs, using valine decarboxylase-expressing Escherichia coli strains.

    • Dong In Kim
    • , Tong Un Chae
    •  & Sang Yup Lee
  • Article
    | Open Access

    Artificial enzymes with reprogrammed and augmented catalytic activity and substrate selectivity have emerged to tackle limitations of noble metals or transition metal oxides. Here, the authors report Au25 clusterzymes which are endowed with high catalytic activity and selectivity in a range of enzyme-mimicking reactions.

    • Haile Liu
    • , Yonghui Li
    •  & Xiao-Dong Zhang
  • Article
    | Open Access

    Citrullination of arginine is crucial for several physiological processes. Here the authors report the site-specific incorporation of citrulline into proteins in mammalian cells using an engineered tRNA synthetase/tRNA pair and a photocaged-citrulline.

    • Santanu Mondal
    • , Shu Wang
    •  & Paul R. Thompson
  • Article
    | Open Access

    Mitochondrial oxidation-induced cell death is an important physiological process activated by cancer therapeutics, but its investigation is challenging. Here, the authors report a multifunctional iridium(III) photosensitiser, Ir-OA, able to induce mitochondrial oxidative stress and monitor the corresponding changes in mitochondrial properties.

    • Chaiheon Lee
    • , Jung Seung Nam
    •  & Tae-Hyuk Kwon
  • Article
    | Open Access

    In Bacteroidetes, SusCD complexes mediate uptake of large nutrients across the outer membrane. SusCD structures in the apo state and in complex with β2,6 fructo-oligosaccharides reveal several substrate molecules in the binding cavity and suggest details of the pedal bin mechanism employed in glycan import.

    • Declan A. Gray
    • , Joshua B. R. White
    •  & Bert van den Berg