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Negatively Charged Disordered Regions are Prevalent and Functionally Important Across Proteomes.

Lavi S Bigman1, Junji Iwahara2, Yaakov Levy3

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Intrinsically disordered regions (IDRs) in proteins vary in charge. Negatively charged IDRs are longer and contain longer repeat sequences, especially in nucleic acid-binding proteins.

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Area of Science:

  • Biochemistry
  • Bioinformatics
  • Proteomics

Background:

  • Intrinsically disordered regions (IDRs) are protein segments lacking stable 3D structures.
  • IDRs often contain a high proportion of charged amino acids, influencing protein function.
  • The relationship between IDR charge characteristics and protein function is not fully understood.

Purpose of the Study:

  • To investigate the sequence-function relationship in intrinsically disordered regions (IDRs).
  • To perform a comprehensive bioinformatic analysis of charge properties in human, mouse, and yeast proteomes.
  • To understand how charge composition and organization in IDRs contribute to protein function.

Main Methods:

  • Bioinformatic analysis of protein sequences from human, mouse, and yeast proteomes.
  • Characterization of intrinsically disordered regions (IDRs) based on charge properties.
  • Comparative analysis of positively and negatively charged IDRs, including repeat unit characteristics.

Main Results:

  • Approximately 50% of proteins contain at least one charged IDR.
  • Highly negatively charged IDRs are longer and have a higher net charge per residue than positively charged IDRs.
  • Aspartate/Glutamate (D/E) repeats are significantly longer than Lysine/Arginine (K/R) repeats and are more common in nucleic acid-related proteins, increasing with genome size in eukaryotes.

Conclusions:

  • Charge composition and organization in IDRs encode functional information.
  • Distinct characteristics of negatively charged D/E repeats compared to K/R repeats suggest specialized roles.
  • The prevalence of D/E repeats in nucleic acid-binding proteins highlights their importance in these functional contexts.