Nonrefoldability is Pervasive Across the E. coli Proteome

Area of Science:

• Biochemistry
• Proteomics
• Molecular Biology

Background:

• Protein folding is crucial for cellular function.
• Previous studies focused on small, refoldable proteins, not whole proteomes.
• Natural proteomes contain complex proteins with diverse structures.

Purpose of the Study:

• To investigate protein refolding kinetics across an entire proteome.
• To identify proteins with intrinsic refolding limitations.
• To understand factors influencing protein folding efficiency.

Main Methods:

• Developed a mass spectrometry-based proteomics approach.
• Analyzed the soluble E. coli proteome during log-phase growth.
• Assessed protein refolding kinetics on physiological timescales.

Main Results:

• One-third of the E. coli proteome is not intrinsically refoldable within physiological timescales.
• Proteins with slow refolding kinetics are enriched in specific fold-types and domain organizations.
• Identified biophysical features correlated with slow protein refolding.

Conclusions:

• A significant portion of the proteome relies on external factors for proper folding.
• Chaperones and cotranslational folding are likely essential for many proteins.
• Findings highlight the complexity of in vivo protein folding.