Structural ontogeny of protein-protein interactions

Area of Science:

• Protein engineering
• Structural biology
• Evolutionary biology

Background:

• Targeting protein-protein interactions is crucial for drug discovery, especially for
• undruggable
• targets.

Purpose of the Study:

• To investigate the evolutionary dynamics of protein binding site formation using synthetic coevolution.
• To compare the energy landscapes and binding geometries of synthetically evolved complexes with naturally occurring ones.

Main Methods:

• Engineered novel protein-protein interactions between naïve surfaces via synthetic coevolution.
• Isolated and characterized seven distinct structural families of engineered protein Z-domain complexes.
• Utilized epistasis analysis and machine learning to estimate the fitness landscape and identify key early-stage interactions.

Main Results:

• Synthetically evolved complexes explored multiple shallow energy wells via ratchet-like docking.
• Naturally evolved complexes converged into a deep energy well with fixed geometry.
• Identified
• seed
• contacts crucial for the initial stages of complex formation.

Conclusions:

• Silent
• protein surfaces exhibit shallower energy landscapes compared to natural binding sites.
• This shallower landscape disfavors tight binding, likely due to evolutionary counterselection.
• Synthetic coevolution provides insights into the de novo formation and evolutionary principles of protein complexes.