Keywords

pI, Isoelectric Point, Protein Localization, Proteome, Subcellular Distribution, Physicochemical Adaptation

Reference

DOI: 10.3389/fmolb.2021.775736

Abstract

Protein isoelectric point (pI) — the pH at which a protein carries no net charge — plays a fundamental role in protein solubility, stability, and cellular localization.

  • Proteome-wide pI distributions display multimodal patterns (bimodal in prokaryotes, trimodal in eukaryotes).
  • These pI distributions are tightly linked to subcellular localization, reflecting adaptations to local pH, membrane charge, and environment.
  • Acidic proteins (low pI) dominate cytoplasmic and Golgi compartments, while basic proteins (high pI) localize to mitochondria, plasma membrane, and nucleus.
  • The relationship between pI and protein function is shaped not only by sequence but by local physicochemical conditions, such as pH gradients and membrane composition.

Notes

1. Proteome-wide pI Distributions and Bimodal/Trimodal Patterns

  • Prokaryotes (bacteria, archaea):
    • Bimodal pI distribution: Peaks at ~5.0 (acidic) and ~9.0 (basic).
    • Acidic peak corresponds to cytoplasmic proteins, basic peak to membrane-associated proteins.
  • Eukaryotes:
    • Trimodal pI distribution, adding a nuclear protein peak, reflecting diverse compartmentalization.
  • Environmental factors (pH, salinity, temperature) more critical than phylogeny in shaping pI distribution.

2. Subcellular Localization and pI Relationship

  • Acidic proteins (low pI):
    • Found in cytoplasm, vacuole, Golgi apparatus.
    • May have more protein-protein interactions, possibly due to charge balance needs.
  • Basic proteins (high pI):
    • Localized in mitochondria, nucleus, plasma membrane.
    • Likely to interact favorably with negatively charged membranes.
  • Nuclear proteins show wide pI range (4.5–10.0), reflecting functional diversity.

3. Functional Insights from pI Distribution

  • Protein solubility:
    • Proteins are least soluble at their pI, leading to selective localization and reduced aggregation.
  • Charge and membrane interaction:
    • Membrane proteins have higher pI to interact with negatively charged membranes.
  • Intracellular pH correlation:
    • pI variation aligns with compartment pH, membrane surface charge, and functional needs.
  • Proteome pI as a reflection of adaptation:
    • Similar organisms can have distinct pI distributions due to environmental pressures, not just phylogenetic distance.

4. Key Findings and Concepts

  • Multimodal pI distribution reflects cellular compartmentalization and functional specialization.
  • Cytoplasmic proteins cluster around pI 5.0-6.0, membrane proteins around pI 8.5-9.0.
  • Environmental adaptation (rather than lineage) shapes proteome pI.
  • No clear link between pI and expression level, but pI affects solubility and interaction potential.
  • Acidic proteins have a tendency for more interactions, possibly linked to intracellular pH and charge balance.

5. RD’s Takeaways and Thoughts

  • pI is not just a static feature but deeply linked to cellular architecture and function.
  • The multimodal pattern (especially the addition of nuclear-specific pI modes in eukaryotes) highlights complex regulation.
  • The observation that environment trumps phylogeny in shaping pI distributions emphasizes the importance of physicochemical adaptation over evolutionary constraints.
  • This knowledge could inform protein engineering and synthetic biology, especially when designing proteins for specific compartments or functions.
  • RD notes: perhaps useful in kinase substrate pI profiling — kinase domains and substrates may adapt to cellular pH and localization via complementary pI.

Take-home Messages

  • Protein pI is a critical determinant of subcellular localization and interaction in both prokaryotic and eukaryotic cells.
  • Multimodal pI distributions mirror compartment-specific environments (e.g., pH, membrane charge).
  • Acidic proteins dominate cytoplasmic and Golgi spaces, while basic proteins are found in membranes, mitochondria, nucleus.
  • Environmental factors (pH, temperature, salinity) strongly influence proteome pI distribution—more than evolutionary history.
  • Protein function, interaction, and stability are governed by a complex interplay of pI and cellular environment, not pI alone.