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Structured Random Binding: a minimal model of protein-protein interactions.

¹Department of Chemistry, The Pennsylvania State University University Park, PA 16801. USA.

|April 8, 2025

Summary

Structured Random Binding (SRB) models protein interactions, revealing a phase transition in nonspecific binding. Weak interactions can evolve into specific binding under certain conditions, mimicking real protein structures.

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Area of Science:

Statistical physics
Protein-protein interactions
Disordered systems

Background:

Nonspecific binding is a fundamental aspect of protein interactions.
Understanding the transition from transient to stable protein complexes is crucial.

Purpose of the Study:

To introduce Structured Random Binding (SRB), a minimal model for protein-protein interactions.
To investigate the phase transition in nonspecific binding driven by temperature.
To explore the evolution of weakly-bound complexes into specific ones.

Main Methods:

Utilizing statistical physics principles of disordered systems.
Developing a minimal computational model for protein interactions.
Simulating the behavior of random proteins and their complexes at varying temperatures.

Main Results:

SRB exhibits a phase transition from transient, non-specific complexes at high temperatures to frozen, specific interfaces at low temperatures.
Weakly-bound nonspecific complexes can evolve into tightly-bound, specific complexes if the peptide backbone's structural correlation length is short.
Evolved tightly-bound homodimers favor interface structures prevalent in natural protein homodimers.

Conclusions:

SRB provides a framework for understanding the physical basis of protein-protein binding specificity.
The model highlights the role of temperature and structural constraints in driving binding evolution.
SRB's findings align with observed interface structures in real protein homodimers.