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Related Concept Videos

Protein Dynamics in Living Cells01:19

Protein Dynamics in Living Cells

Different fluorescence-based techniques are used to study the protein dynamics in living cells. These techniques include FRAP, FRET, and PET.
Fluorescent recovery after photobleaching (FRAP) is a fluorescent-protein-based detection technique used to quantify protein movement rates within the cell. This method exposes a small portion of the cell to an intense laser beam. The laser beam causes permanent photobleaching of the fluorophore-tagged proteins in the exposed region. As the bleached...
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Related Experiment Video

Updated: May 11, 2026

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
09:10

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Published on: May 22, 2018

Tools for protein posttranslational modifications analysis: FAK, a case study.

Catarina Fonseca1, Paula Voabil, Ana Sofia Carvalho

  • 1Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal.

Methods in Molecular Biology (Clifton, N.J.)
|May 14, 2013
PubMed
Summary
This summary is machine-generated.

Mass spectrometry advances reveal numerous protein modifications, but analyzing their complex interplay requires new tools. VISUALPROT visualizes all protein features, aiding the study of posttranslational modifications (PTMs) like those in focal adhesion kinase (FAK).

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Area of Science:

  • Proteomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Mass spectrometry has led to a vast increase in annotated posttranslational modifications (PTMs), with nearly 90,000 reported in Swiss-Prot.
  • Proteins undergo dynamic modifications for functional regulation, and a single protein can exhibit numerous PTMs, creating complex regulatory networks.
  • PTM crosstalk, where one modification influences another, is common, necessitating holistic analysis approaches rather than single-PTM studies.

Purpose of the Study:

  • To address the complexity of analyzing numerous PTMs and their crosstalk.
  • To introduce VISUALPROT, a novel tool for visualizing all annotated protein features in a single image.
  • To demonstrate the utility of VISUALPROT using the focal adhesion kinase (FAK) as an example.

Main Methods:

  • Development and application of the VISUALPROT software.
  • Integration of diverse protein data, including amino acid content, domains, PTM sites, and single amino acid polymorphisms.
  • Case study utilizing VISUALPROT for the focal adhesion kinase (FAK).

Main Results:

  • VISUALPROT successfully visualizes multiple annotated protein features, including PTMs, domains, and polymorphisms, in a unified graphical representation.
  • The tool facilitates a more comprehensive understanding of protein architecture and modification patterns.
  • Application to FAK highlights its complex phosphorylation landscape and domain structure.

Conclusions:

  • VISUALPROT is a valuable tool for archiving, analyzing, and visualizing complex protein modification data.
  • Visualizing multiple protein features simultaneously aids in understanding PTM crosstalk and regulation.
  • The tool enhances the study of proteins like FAK, crucial in cell signaling pathways.