General Theory of Specific Binding: Insights from a Genetic-Mechano-Chemical Protein Model

Proteins need to selectively interact with specific targets among a multitude of similar molecules in the cell. However, despite a firm physical understanding of binding interactions, we lack a general theory of how proteins evolve high specificity. Here, we present such a model that combines chemistry, mechanics, and genetics and explains how their interplay governs the evolution of specific protein-ligand interactions. The model shows that there are many routes to achieving molecular discrimination-by varying degrees of flexibility and shape/chemistry complementarity-but the key ingredient is precision. Harder discrimination tasks require more collective and precise coaction of structure, forces, and movements. Proteins can achieve this through correlated mutations extending far from a binding site, which fine-tune the localized interaction with the ligand. Thus, the solution of more complicated tasks is enabled by increasing the protein size, and proteins become more evolvable and robust when they are larger than the bare minimum required for discrimination. The model makes testable, specific predictions about the role of flexibility and shape mismatch in discrimination, and how evolution can independently tune affinity and specificity. Thus, the proposed theory of specific binding addresses the natural question of why are proteins so big?. A possible answer is that molecular discrimination is often a hard task best performed by adding more layers to the protein.

Automated summary

In this study, a model combining chemistry, mechanics, and genetics is presented to explain how these factors interact in the evolution of protein-ligand interactions. The model demonstrates that precision is the key to achieving molecular discrimination, and harder discrimination tasks require more coaction of structure, forces, and movements. The model also suggests that increasing protein size enables the solution of more complicated tasks and makes proteins more evolvable and robust.