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Volume 22 Issue 1, January 2026

Rotor-based protein microenvironment mapping

Microenvironmental changes in protein substructures are closely related to their functions and interactions. Yang, Jin, Zhang et al. report a method for real-time monitoring of these changes in target proteins in living cells through site-specific integration of AnapTh. AnapTh is an environment-sensitive noncanonical amino acid featuring a rotor-based fluorophore. The cover depicts the ‘off’ and ‘on’ states of AnapTh incorporated at specific sites within target proteins, enabling visualization of their interactions during aggregation and clustering.

See Yang et al.

Image: Mengxi Zhang, Rice University, Department of Chemistry. Cover design: Alex Wing

Q&A

  • Machine learning-based tools have revolutionized how scientists study protein structure. Here, Nature Chemical Biology speaks to Cecilia Clementi, Bruno Correia and Peilong Lu about progress in developing computational tools for predicting protein structure and properties, how these programs can be used for protein design, and the developments they would like to see in the field.

    • Russell Johnson
    Q&A

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Research Highlights

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News & Views

  • How biogenic crystals form within cells despite their building blocks being water insoluble is a conundrum. Now, it has been shown that zebrafish control the crystallization process by modulating organellar pH: first to accumulate guanine, and then to crystallize it.

    • Florent Figon
    News & Views
  • Small proteins are challenging targets for structure determination by cryo-electron microscopy. A new mass-enhancement strategy relies on rigid dimerization of a nanobody into a ‘di-gembody’ that increases protein mass by expanding the symmetry of small protein targets.

    • Morgan S. A. Gilman
    • Meredith A. Skiba
    News & Views
  • Approaches to study lipid composition with leaflet-specific resolution in living cells have been lacking. A new method — fluorogen-activating coincidence encounter sensing (FACES) — combines biorthogonal metabolic labeling with organelle-targeted fluorogen-activating proteins to selectively visualize lipids on leaflets of interest in any organelle.

    • Wyatt Beyers
    • Chi-Lun Chang
    News & Views
  • A recent study developed a refined photocatalytic labeling-based method to capture and sequence physically interacting cells in situ and discovered how tumors induce pro-tumor neutrophils via cell contact.

    • Anfei Huang
    • Wolfgang Kastenmüller
    News & Views
  • mRNA has emerged as an important class of therapeutic molecules. Now, an artificial intelligence (AI)-driven framework, which can design mRNA sequences with enhanced stability and translational efficiency, has been reported. This method for designing mRNA sequences is known as ‘generative models for RNA’ (GEMORNA) and could help to design more effective mRNA-based treatments.

    • Zhengwei Liu
    • Yizhou Dong
    News & Views
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Research Briefings

  • Clostridium autoethanogenum produces ethanol from waste gases, but the biosynthetic pathway has been debated. Now, a combination of structural and biochemical data confirms that a key step in the ethanol biosynthesis pathway is acetate reduction by a tungsten-dependent aldehyde:ferredoxin oxido-reductase. This thermodynamically unfavorable reaction is counterbalanced by the coupling of ethanol synthesis with CO oxidation.

    Research Briefing
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Articles

  • Many animals display brilliant colors thanks to the precise formation of guanine crystals within specialized organelles. Here, the authors demonstrate that dynamic pH shifts orchestrate this process: an initially acidic lumen stabilizes amorphous, protonated guanine and subsequent alkalinization triggers its crystallization.

    • Zohar Eyal
    • Rachael Deis
    • Dvir Gur
    Article Open Access
  • Microbial alcohol production from waste gases could enable sustainable carbon cycling. Now, the tungsten-dependent aldehyde:ferredoxin oxidoreductase from the gas-converting bacterium Clostridium autoethanogenum has been biochemically and structurally characterized. This monomeric enzyme is responsible for acetate reduction to acetaldehyde, the key step of ethanol production in this industrial microorganism.

    • Olivier N. Lemaire
    • Mélissa Belhamri
    • Tristan Wagner
    Article Open Access
  • Using two synaptic proteins as examples, Chen et al. reveal that phase-separation-mediated formation of molecular condensates can change the biomolecular interaction specificities; the network complexity in the condensates can have a stronger impact than affinity on the subcellular localization of proteins.

    • Yan Chen
    • Chenxue Ma
    • Mingjie Zhang
    Article
  • Alkynes found in natural products are typically assembled by metal-dependent enzymes. The enzyme BesB instead forms a terminal alkyne-containing amino acid using pyridoxal phosphate as a cofactor. Here, the authors use structural and mechanistic investigations to identify the key features of BesB that allow it to carry out its fascinating chemistry.

    • Jason B. Hedges
    • Jorge A. Marchand
    • Katherine S. Ryan
    Article
  • The use of bulky protein tags and the limited positions available for probe introduction restrict current methods for studying protein microenvironments at high spatial resolution. Here the authors genetically incorporate small environment-sensitive fluorescent amino acids to visualize real-time microenvironmental changes at specific protein substructures.

    • Shudan Yang
    • Shikai Jin
    • Han Xiao
    Article
  • An ‘intracrine’ signaling mechanism is proposed whereby a G-protein-coupled receptor (free fatty acid receptor 4) senses locally released fatty acids on intracellular membranes associated with lipid droplets to efficiently regulate lipolysis in adipocytes.

    • Shannon L. O’Brien
    • Emma Tripp
    • Davide Calebiro
    Article Open Access
  • Despite the importance of indole in plant defense and communication, its biosynthesis in core eudicots remains elusive. Here the authors report the identification of TSB-like, a pseudoenzyme that hijacks an enzyme of tryptophan biosynthesis to produce indole.

    • Matilde Florean
    • Hedwig Schultz
    • Tobias G. Köllner
    Article Open Access
  • An approach combining bioorthogonal chemistry with genetically encoded fluorogen-activating proteins enables subcellular imaging of phospholipids and glycans, as well as the visualization of lipid transport between organelles and lipid asymmetry across membrane leaflets.

    • William M. Moore
    • Roberto J. Brea
    • Itay Budin
    Article
  • Structural studies of certain Tn and STn antigen-targeting antibodies reveal that their VH and VL domains recognize the glycan antigen and the adjacent peptide region, respectively, enabling a VH domain-focused and VL domain-varying phage display library to generate antibodies targeting diverse glycopeptide epitopes.

    • Ramon Hurtado-Guerrero
    • Spyridon Gatos
    • Ola Blixt
    Article
  • Legionella effector LnaB, a recently identified actin-activated AMPylase, mediates phosphoryl-AMPylation in a yet-unknown manner. Here the authors unveil a two-step catalytic process involving dual ATPase–AMPylase activity based on structural studies, providing a biochemical basis for AMPylation.

    • Tao-Tao Chen
    • Qiuhua Lu
    • Songying Ouyang
    Article
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