Cold spots are universal in protein-protein interactions

Area of Science:

• Protein-protein interactions
• Structural biology
• Biophysics

Background:

• Protein binding interfaces vary in size and properties.
• Hot spots are crucial for binding energy, while cold spots offer mutation potential.
• Understanding cold spots is key for protein engineering.

Purpose of the Study:

• Identify cold spots in protein-protein interactions (PPIs) caused by cavities and charge interactions.
• Analyze the prevalence and location of cold spots in various PPIs.
• Investigate factors influencing cold spot distribution, such as affinity and complex type.

Main Methods:

• Utilized a small affinity database of PPIs with known structures and affinities.
• Expanded analysis to nearly 4000 homo- and heterodimers from the Protein Data Bank (PDB).
• Characterized cold spots based on structural features (cavities, charge interactions) and location within the binding interface.

Main Results:

• Cold spots due to cavities are nearly ubiquitous in PPIs, irrespective of binding affinity.
• Unfavorable charge interactions at cold spots are relatively infrequent.
• Cold spots are predominantly located at the periphery of binding interfaces, with fewer central cold spots in high-affinity complexes.
• Non-cognate interactions and homodimers exhibit more cold spots than cognate interactions and heterodimers, respectively.
• Glycine, glutamate, and arginine are the most common amino acids found at cold spot positions.

Conclusions:

• Cold spots, particularly those caused by cavities, are a significant feature of protein-protein interactions.
• The location and frequency of cold spots are influenced by binding affinity, interaction type, and complex symmetry.
• Identifying and understanding cold spots provides valuable insights for protein evolution and engineering efforts aimed at modulating binding affinity and specificity.