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Updated: Dec 15, 2025

Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames
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Dark Proteome Database: Studies on Disorder.

Nelson Perdigão1, Pedro M C Pina1, Cátia Rocha1

  • 1Instituto de Sistemas e Robótica, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal.

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|July 8, 2020
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Summary
This summary is machine-generated.

Intrinsic protein disorder is often mistakenly equated with darkness. This study confirms that protein disorder and darkness are largely unrelated, using Swiss-Prot and Dark Proteome data.

Keywords:
intrinsic disorderpredictionproteins

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Area of Science:

  • Biochemistry
  • Proteomics
  • Bioinformatics

Background:

  • Proteins can exhibit intrinsic disorder, lacking a stable three-dimensional structure.
  • The concept of 'dark proteins' refers to proteins with uncharacterized functions.
  • A common misconception links protein disorder with being 'dark' or uncharacterized.

Purpose of the Study:

  • To investigate the relationship between intrinsic protein disorder and the 'dark proteome'.
  • To clarify whether disordered proteins are predominantly uncharacterized.
  • To analyze protein disorder across established proteomic databases.

Main Methods:

  • Utilized the Swiss-Prot protein sequence database.
  • Employed the Dark Proteome database for comparison.
  • Applied three distinct computational predictors to assess protein disorder.
  • Visualized and analyzed the disorder predictions.

Main Results:

  • Calculated intrinsic disorder levels for a significant portion of Swiss-Prot proteins.
  • Compared disorder predictions with protein characterization status from the Dark Proteome.
  • Analysis consistently showed that protein disorder is largely independent of darkness.

Conclusions:

  • Intrinsic protein disorder is not synonymous with being a 'dark protein'.
  • The study refutes the misconception linking disorder and lack of characterization.
  • Disordered proteins can be well-characterized, and vice versa.