Biotin and Related Studies

In vivo-compatible spatial multi-omics via hydrogen peroxide-independent APEX2 labeling

This paper introduces Hi-APEX, a H2O2-independent APEX2 variant for in vivo spatial multi-omics, showing improved performance in capturing redox-sensitive processes and enabling in vivo applications.

A nanoscale map of the human cell surface proteome reveals spatial and functional organization

This study maps the human cell surface proteome at nanoscale resolution, identifying functional modules and spatial organization patterns in T-lymphocytes and B-lymphoblasts.

Sequence-Independent In Situ Imaging of GlycoRNA in Living Cells and Tissues based on COMPASS

The paper introduces COMPASS, a method for sequence-independent imaging of glycoRNAs in living cells and tissues, revealing their distribution in cancer and neurogenesis.

Expanding the HIF-2α proteomic interactome with TurboID proximity labeling.

This study expands the HIF-2α proteomic interactome using TurboID proximity labeling, identifying 329 novel interactors and linking some to poor patient survival in breast cancer.

Biotin-operated ligand trapping enables dynamic spatial redistribution of protein and organelle in living cells

This paper introduces BOLT, a tool for inducible trapping, controlled release, and visualization of proteins in living cells, demonstrating its use in tracking protein and organelle dynamics.

Programmable sequence-resolved in situ profiling of glycoRNA-protein interactomes by GlycoRNA-Map

This paper introduces GlycoRNA-Map, a method to profile glycoRNA-protein interactomes, revealing that glycoRNA sequences and cellular context shape their protein environments.

Computational design of a versatile, zero-radius proximity labeling enzyme

This paper designs a new proximity labeling enzyme, FlexID, using computational methods to improve spatial precision and versatility for mapping protein interactions and proteomes.

aaRSID, an engineered pyrrolysyl-tRNA synthetase platform for multi-probe proximity proteomics

The paper introduces aaRSID, an engineered pyrrolysyl-tRNA synthetase for proximity labeling, improving upon existing tools by reducing background and enabling multiplexed proteomics.

A TurboID-based proximity labelling method for detecting extracellular protein interactions in plants

This paper validates a TurboID-based proximity labeling method for detecting extracellular protein interactions in the apoplast of plants using INF1 and REL.

RBProximity-CLIP Enables Subcellular Mapping of RNA-Binding Protein Interactions at Nucleotide Resolution

RBProximity-CLIP maps RBP-RNA interactions at subcellular resolution, revealing compartment-specific targets for AGO2, YBX1, and ELAVL1.

Method to Identify Liver-to-Brain Region-Specific Crosstalk Using TurboID

The paper develops a method to identify liver-to-brain crosstalk by using ER-TurboID to recover liver-secreted proteins from specific brain regions.

Stoichiometry-dependent specificity in biotin enrichment: a benchmarking framework for proximity labeling proteomics

The paper benchmarks biotin enrichment in proximity labeling proteomics, showing that higher biotinylation improves specificity while lower levels increase background noise.

Virus-Driven Proximity Proteomics Identifies p400 as a Restriction Factor Poised on Incoming Viral Genomes

The paper uses virus-driven proximity proteomics to identify p400 as a host restriction factor targeting incoming viral genomes during the immediate-early phase of infection.

Photoproximity labeling of c-Myc reveals SLK as a cancer specific co-regulator

The paper identifies SLK as a cancer-specific co-regulator of c-Myc using photoproximity labeling, showing it stabilizes c-Myc and drives tumorigenesis through splicing changes.

μMap-uAA: Photocatalytic proximity labeling targeted with single-residue precision

The paper introduces Map-uAA, a method for mapping protein microenvironments with residue-level precision using photocatalytic proximity labeling.

The cytoplasmic C-terminal domain of the MmpL11 lipid transporter is required for interaction with its co-cistronic partner MSMEG_0240 in Mycobacterium smegmatis

This study identifies the C-terminal domain of MmpL11 as required for its interaction with MSMEG_0240 using biotin proximity labeling assays in Mycobacterium smegmatis.

A de novo designed enzyme for photo-proximity labeling of E3 ligase neighborhoods in live cells

This paper introduces EYClamp, a de novo designed enzyme for photo-proximity labeling of E3 ligase neighborhoods in live cells, identifying over 1,500 candidate neighbors for four E3 ligases.

Proximity Labelling Reveals Spatial Organisation of Mitochondrial Protein Import Complexes

The paper uses proximity labeling to identify proteins interacting with mitochondrial import complexes, revealing EXD2 as a TOM/SAM-associated factor at the mitochondrial outer membrane.

Cooperativity and Conformational Rearrangements in Protein-Protein and Protein-Ligand Interactions

The paper investigates biotin binding to streptavidin and avidin, showing two distinct energetic regimes and long-range intermolecular interactions.

Acute in vivo proximity labeling for membrane targeted proteomics in neuronal circuits

The paper develops membrane-targeted TurboID variants for in vivo proteomics in neuronal circuits, identifying subcellular proteins and their changes during acute drug exposure.

Spatial Metabolomics by Desthiobiotin Ligase (DESTNI) in Live Cells

This paper introduces DESTNI, a proximity labeling tool for spatial metabolomics, and demonstrates its application in identifying compartment-specific amino metabolite signatures in live cells.

GLproxScape reconstructs spatial chromatin occupancy landscapes from tiled genomic locus proteomics

GLproxScape reconstructs spatial chromatin occupancy landscapes from genomic locus proteomics data by modeling per-region enrichments as spatial measurements.

ASAP-ID: Proximity labelling with small tags

ASAP-ID reduces steric disruption in proximity labelling by using small tags and antibodies, identifying new lamin interactors and showing mutant-specific aggregation patterns.

High-resolution photocatalytic crosslinking of protein neighborhoods using contact-dependent antibody mapping (contactMAP)

The paper introduces contactMAP, a photocatalytic crosslinking method for high-resolution mapping of protein neighborhoods, showing it rivals or outperforms existing photo-PLP methods.

Water oxidation-driven histidine dioxidation enables probe-free proximity labeling

This paper introduces PF-Map, a probe-free proximity labeling method using water oxidation to generate radicals for spatial protein mapping, revealing a hidden vesicle trafficking subproteome.

Systematic Mapping of Protein Interactions Underlying IL-2 Secretion in Human T Cells

The paper maps protein interactions involved in IL-2 secretion in human T cells, identifying key components of the secretory pathway and their dynamic regulation.

Patterned photocatalytic proximity labelling for spatial interactomics

The paper introduces DMD-PhoxID, a method for mapping protein-proximity interactions in fixed brain tissue with subanatomical resolution using patterned photocatalytic labeling.

Cell type-specific proximity labeling of organ secretomes reveals energy balance-dependent proteomic remodeling.

A Cre-dependent ER-targeted TurboID knock-in mouse enables cell type-specific secretory proteomics, mapping adipocyte and hepatocyte responses to fasting, LPS and obesity, with B cells profiled at baseline.

An engineered streptavidin condensate platform for chemically inducible control of endogenous proteins in mammalian cells

This paper introduces a streptavidin condensate platform to inducibly control endogenous proteins in mammalian cells, demonstrating its application in regulating diverse targets and enabling dual-inducible release.

Mapping the interactome of human tRNA methyltransferase TRMT1 using dual proximity labeling

This study maps TRMT1's interactome using APEX2-based proximity labeling and DIA mass spectrometry, identifying proteins involved in RNA processing and redox biology.