Keywords

Phosphorylation, Awesome, IDP, Charge-Hydrophobicity, Proteins Journal

Reference

DOI: 10.1002/1097-0134(20001115)41:3<415::aid-prot130>3.0.co;2-7

Abstract

“Natively unfolded” proteins occupy a unique niche within the protein kingdom in that they lack ordered structure under neutral pH in vitro.
By analyzing amino acid sequences based on normalized net charge and mean hydrophobicity, the study shows that natively unfolded proteins localize in a unique region of charge-hydrophobicity phase space.
They demonstrate that a combination of low overall hydrophobicity and large net charge represents a defining feature of these proteins’ inability to fold under physiological conditions.

Notes

1. General Summary

  • The study aims to predict whether a protein will be folded or natively unfolded based solely on its amino acid sequence.
  • Introduces charge-hydrophobicity phase space as a predictive framework for protein structural state.
  • Establishes a simple empirical formula to distinguish between folded and unfolded proteins.

2. Key Features of Natively Unfolded Proteins

  • High net charge: Many uncompensated charged groups (especially negative), leading to extreme isoelectric points (pI) near neutral pH.
  • Low hydrophobicity: Fewer hydrophobic residues, reducing the driving force for folding.
  • Highly flexible and dynamic, preventing stable ordered structures under physiological conditions.

3. Main Findings

  • Analysis of 91 natively unfolded proteins:
    • Wide variability in sequence length (~50–1827 residues), net charges (+59 to −117), and pI (range pH 3–13, peaks around 4 and 10.5).
  • Hydrophobicity is a key discriminator:
    • Mean hydrophobicity of unfolded proteins ~0.39 vs. folded proteins ~0.48.
  • Combined charge and hydrophobicity analysis improves classification over using either property alone.
  • Empirical boundary formula:
    • ⟨R⟩ = 2.785⟨H⟩ − 1.151
    • Where ⟨R⟩ = mean net charge, ⟨H⟩ = mean hydrophobicity.
  • Proteins with high net charge and low hydrophobicity are predicted to be natively unfolded.
  • Exceptions (e.g., α-synuclein, NEF, helix destabilizing protein) suggest special regional interplay of charge and hydrophobicity preventing folding.

4. Functional and Structural Implications

  • Flexibility and disorder enable functional interactions with ligands (DNA, RNA, metals).
  • Disorder-to-order transitions upon ligand binding — a regulatory mechanism critical in processes like transcription and cell cycle control.
  • Many natively unfolded proteins exhibit low sequence complexity and high flexibility, suggesting that thousands of human proteins may contain disordered segments.
  • Coiled-coil proteins (e.g., collagen) can be unstructured in monomeric states but ordered in complexes.

5. Methodological Notes

  • The charge-hydrophobicity phase space is a powerful yet simple framework to categorize proteins.
  • Focus on global sequence features rather than localized motifs.
  • Suggests binding-induced folding as a common strategy for function — consistent with other models of IDP (intrinsically disordered protein) behavior.

6. RD’s Thoughts and Learnings

  • RD finds this paper foundational in understanding the intrinsic disorder landscape.
  • The empirical formula is elegant and practical, potentially useful in RD’s own work on disordered regions.
  • Highlights the importance of combining charge and hydrophobicity rather than treating them as separate factors.
  • Interesting perspective: flexibility not as a flaw but a functional feature, enabling regulation and diverse interactions.
  • RD particularly notes the idea that ligand binding shifts charge-hydrophobicity toward folded-state characteristics, supporting context-dependent folding.

Take-home Messages

  • Natively unfolded proteins are characterized by low hydrophobicity and high net charge, preventing folding under physiological conditions.
  • A simple charge-hydrophobicity formula (⟨R⟩ = 2.785⟨H⟩ − 1.151) effectively distinguishes folded from unfolded proteins.
  • These proteins play critical roles in cellular processes due to their flexibility and ability to undergo disorder-to-order transitions upon binding.
  • Intrinsic disorder is a functional feature, not a defect — enabling adaptive and regulated molecular interactions.
  • The framework offers new directions for predicting disorder and understanding protein-ligand interactions in signaling and regulation.