Subcellular pH and predicted pH-dependent features of proteins

Area of Science:

• Proteomics
• Biophysics
• Structural Biology

Background:

• Two-dimensional proteomics gels often display bimodal isoelectric point (pI) distributions.
• Previous studies linked pI distributions to amino acid composition and protein function.
• The relationship between protein charge, subcellular environment, and stability remains incompletely understood.

Purpose of the Study:

• To investigate the relationship between protein folded state pI, pH of maximal stability, and subcellular localization.
• To determine if protein electrostatics are adapted to specific organelle pH environments.
• To explore the evolutionary pressures shaping protein charge and stability.

Main Methods:

• Electrostatics calculations were performed on protein structures with known subcellular locations.
• Predicted folded state pI values were compared to sequence-based pI values.
• The pH of maximal stability was calculated and correlated with organelle pH.

Main Results:

• Predicted folded state pI values closely matched sequence-based pI values, with adjustments for stabilizing ionizable group interactions.
• Bimodal distributions were observed for both pI and pH of maximal stability.
• Average pH of maximal stability generally correlated with organelle pH, while average pI values differed significantly from organelle pH.
• Golgi proteins showed the largest contribution from ionizable groups to stability.

Conclusions:

• Proteins are likely evolved to possess a net charge in their native subcellular environment, optimizing solubility in crowded conditions.
• The correlation between maximal stability pH and organelle pH suggests evolutionary adaptation of protein electrostatics to specific cellular compartments.
• Interactions of ionizable groups play a crucial role in protein stability, with notable contributions in Golgi proteins.