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Related Concept Videos

Proteomics01:33

Proteomics

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A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...
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DNA probes are fragments of DNA labeled with a reporter tag to enable their detection or purification. The resulting labeled DNA probes can then hybridize to target nucleic acid sequences through complementary base-pairing, and may be used to recover or identify these regions.
Radioisotopes, fluorophores, or small molecule binding partners like biotin or digoxigenin, are the most widely used reporter tags for labeling DNA probes. These labels can be attached to the probe DNA molecule via...
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Related Experiment Video

Updated: Sep 16, 2025

In Vivo Proximity Biotinylation for Protein Interaction Studies in Paramecium tetraurelia
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Cross-Species Proximity-Dependent Protein Biotinylation: A Standardized Approach for Mapping Proxeomes.

Petra Van Damme1

  • 1iRIP Unit, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium. petra.vandamme@ugent.be.

Methods in Molecular Biology (Clifton, N.J.)
|July 10, 2025
PubMed
Summary

This study presents a universal protocol for preparing diverse biological samples for proximity-dependent biotinylation (BioID) analysis. The method standardizes sample preparation for reliable protein-protein interaction studies across various species and sample types.

Keywords:
InteractomicsProtein interactionsProxeomeProximity-dependent protein biotinylationUniversal BioID Protocol

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Area of Science:

  • Molecular Biology
  • Biochemistry
  • Proteomics

Background:

  • Proximity-dependent biotinylation, using tools like BioID, is crucial for studying protein-protein interactions in situ.
  • Existing methods often require extensive optimization for different biological sample types.

Purpose of the Study:

  • To develop a universally applicable protocol for preparing diverse biological samples for BioID analysis.
  • To standardize sample preparation for enhanced reliability and comparability of BioID studies.

Main Methods:

  • The protocol details sample isolation, mechanical lysis (sonication, freeze-thaw), protein concentration normalization, and biotin removal via desalting.
  • It is designed for readiness prior to liquid chromatography-mass spectrometry (LC-MS) analysis.

Main Results:

  • The protocol is adaptable for various sample types including plant tissues, bacterial cultures, and eukaryotic cells/tissues.
  • Minimal adjustments are needed across diverse biological origins.

Conclusions:

  • This standardized protocol enhances the reliability and comparability of BioID analyses.
  • It facilitates the study of protein-protein interactions across a broad range of biological systems.